diff options
Diffstat (limited to 'sci-biology')
801 files changed, 30735 insertions, 0 deletions
diff --git a/sci-biology/ApE/ApE-2.0.7-r1.ebuild b/sci-biology/ApE/ApE-2.0.7-r1.ebuild new file mode 100644 index 000000000000..c76b28f8893a --- /dev/null +++ b/sci-biology/ApE/ApE-2.0.7-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="A Plasmid Editor" +HOMEPAGE="http://www.biology.utah.edu/jorgensen/wayned/ape/" +SRC_URI="http://www.biology.utah.edu/jorgensen/wayned/ape/Download/Linux/ApE_linux_current.zip -> ${P}.zip" + +LICENSE="ApE" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="app-arch/unzip" +RDEPEND=" + dev-lang/tcl:0 + dev-lang/tk:0" + +RESTRICT="mirror" + +S="${WORKDIR}/ApE Linux/" + +src_compile() { :; } + +src_install() { + cat >> "${T}/ApE" <<- "EOF" + #!/bin/bash + cmdArgs="" + + # AppMain.tcl searches files relative to the directory where it resides. + # Add absolute path to file here, if necessary. + for rfpath in "$@"; do + afpath="$PWD/${rfpath}" + if test -r "${afpath}"; then + cmdArgs="${cmdArgs} \"${afpath}\""; + else + cmdArgs="${cmdArgs} \"${rfpath}\""; + fi + done + + eval exec tclsh "\"/usr/share/ApE-2.0.7/AppMain.tcl\"" "${cmdArgs}" + EOF + + dobin "${T}/ApE" + insinto "/usr/share/${P}" + doins -r "${WORKDIR}"/ApE\ Linux/* + make_desktop_entry ${PN} ${PN} \ + "/usr/share/${P}/Accessory Files/Icons and images/monkey_icon.gif" \ + "Science" +} diff --git a/sci-biology/ApE/Manifest b/sci-biology/ApE/Manifest new file mode 100644 index 000000000000..c8bc584062a7 --- /dev/null +++ b/sci-biology/ApE/Manifest @@ -0,0 +1 @@ +DIST ApE-2.0.7.zip 318454 SHA256 9d718562ef250b68dfad1de7d4179540fc04c001b0fdc5e9bd70f3605561bc32 SHA512 073e3f96badf4888c10a7c7eb453a3775d5bb9136b0bd836d37d1be784847f887e0c68b37325f430eebfb90c2d94021f10d4e8ede92de89b1ab1ddc1ffdbc254 WHIRLPOOL d13e8a997c36f8e7ac951a17c195a714a243292f9a99f524758b09b1fdc9f436b11cf1124ac1a3527ff70aa8cc6dc9ac516a910246f9f6e4f8376c78e8b44013 diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml new file mode 100644 index 000000000000..4252fbfae02e --- /dev/null +++ b/sci-biology/ApE/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> + </longdescription> +</pkgmetadata> diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild new file mode 100644 index 000000000000..a3c0228b819d --- /dev/null +++ b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MODULE_AUTHOR=LDS +inherit perl-module webapp + +DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser" +HOMEPAGE="http://gmod.org/wiki/GBrowse" +KEYWORDS="~amd64 ~x86" +IUSE="-minimal mysql postgres +sqlite" + +SLOT="0" +WEBAPP_MANUAL_SLOT="yes" + +CDEPEND="!<sci-biology/GBrowse-2.44-r1 + >=sci-biology/bioperl-1.6.9 + >=dev-perl/Bio-Graphics-2.09 + >=dev-perl/GD-2.07 + >=dev-perl/CGI-Session-4.02 + dev-perl/IO-String + dev-perl/JSON + dev-perl/libwww-perl + dev-perl/Statistics-Descriptive + !minimal? ( + dev-perl/Bio-Das + >=dev-perl/Bio-SamTools-1.20 + dev-perl/Crypt-SSLeay + dev-perl/DB_File-Lock + dev-perl/DBI + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg ) + sqlite? ( dev-perl/DBD-SQLite ) + dev-perl/FCGI + dev-perl/File-NFSLock + dev-perl/GD-SVG + dev-perl/Net-OpenID-Consumer + dev-perl/Net-SMTP-SSL + )" +# >=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile +DEPEND="dev-perl/Module-Build + dev-perl/Capture-Tiny + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch ) + +src_configure() { + webapp_src_preinst + +# myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse" + myconf="--conf=/etc/gbrowse2" + myconf="${myconf} --htdocs=${MY_HTDOCSDIR}" + myconf="${myconf} --cgibin=${MY_CGIBINDIR}" + myconf="${myconf} --tmp=/var/tmp/gbrowse2" + myconf="${myconf} --persistent=/var/db/gbrowse2" + myconf="${myconf} --databases=/var/db/gbrowse2/databases" + myconf="${myconf} --installconf=no" + myconf="${myconf} --installetc=no" + perl-module_src_configure +} + +src_install() { + dodir /var/tmp/gbrowse2 + dodir /var/db/gbrowse2/sessions + dodir /var/db/gbrowse2/userdata + webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2 + perl-module_src_install + webapp_src_install +} diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest new file mode 100644 index 000000000000..204fe59d5aa7 --- /dev/null +++ b/sci-biology/GBrowse/Manifest @@ -0,0 +1 @@ +DIST GBrowse-2.48.tar.gz 11958127 SHA256 02772c5a7a31ed87733e21278efec2edd3bd6ee8a4bec9b002233e57f6dc9681 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db WHIRLPOOL 5a3ec31de1582c4c551c76908ca8e8024c8d3311404f0c94f7b75a391c340da0ededd80df34be3f10f581902ba1408d84e3e65218f46322546623e15a1020135 diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch new file mode 100644 index 000000000000..5aa0be9df918 --- /dev/null +++ b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch @@ -0,0 +1,72 @@ +diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm +--- GBrowse-2.39-orig/install_util/GBrowseInstall.pm 2011-07-19 20:14:52.434608020 +0000 ++++ GBrowse-2.39/install_util/GBrowseInstall.pm 2011-07-19 21:02:13.685107753 +0000 +@@ -454,33 +454,33 @@ + $gid =~ /^(\d+)$/; + $gid = $1; + +- unless (chown $uid,$gid,$tmp) { +- $self->ownership_warning($tmp,$user); +- } ++# unless (chown $uid,$gid,$tmp) { ++# $self->ownership_warning($tmp,$user); ++# } + + my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); + my $images = File::Spec->catfile($tmp,'images'); + my $htdocs = $self->install_path->{htdocs}; +- chown $uid,-1,$htdocs; ++# chown $uid,-1,$htdocs; + { + local $> = $uid; +- symlink($images,$htdocs_i); # so symlinkifowner match works! ++# symlink($images,$htdocs_i); # so symlinkifowner match works! + } +- chown $>,-1,$self->install_path->{htdocs}; ++# chown $>,-1,$self->install_path->{htdocs}; + + my $persistent = $self->install_path->{'persistent'}; + my $sessions = File::Spec->catfile($persistent,'sessions'); + my $userdata = File::Spec->catfile($persistent,'userdata'); +- mkpath([$sessions,$userdata],0711); ++# mkpath([$sessions,$userdata],0711); + + my $databases = $self->install_path->{'databases'}; + +- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { +- $self->ownership_warning($databases,$user); +- } ++# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { ++# $self->ownership_warning($databases,$user); ++# } + +- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); +- $self->fix_selinux; ++ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); ++ # $self->fix_selinux; + + my $base = basename($self->install_path->{htdocs}); + +@@ -489,14 +489,14 @@ + my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); + my $perl = $self->perl; + my @inc = map{"-I$_"} split ':',$self->added_to_INC; +- system $perl,@inc,$metadb_script; +- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; ++# system $perl,@inc,$metadb_script; ++# system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; + +- if (Module::Build->y_n( +- "It is recommended that you restart Apache. Shall I try this for you?",'y' +- )) { +- system "sudo /etc/init.d/apache2 restart"; +- } ++# if (Module::Build->y_n( ++# "It is recommended that you restart Apache. Shall I try this for you?",'y' ++# )) { ++# system "sudo /etc/init.d/apache2 restart"; ++# } + + print STDERR "\n***INSTALLATION COMPLETE***\n"; + print STDERR "Load http://localhost/$base for demo and documentation.\n"; +Only in GBrowse-2.39/install_util: GBrowseInstall.pm~ diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml new file mode 100644 index 000000000000..32b15c723f9d --- /dev/null +++ b/sci-biology/GBrowse/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-biology</herd> +<upstream> + <remote-id type="cpan">GBrowse</remote-id> +</upstream> +</pkgmetadata> diff --git a/sci-biology/aaindex/Manifest b/sci-biology/aaindex/Manifest new file mode 100644 index 000000000000..7b3eeafe5263 --- /dev/null +++ b/sci-biology/aaindex/Manifest @@ -0,0 +1 @@ +DIST aaindex-9.1.tar.bz2 133780 RMD160 6f5bd699de3c84bd366f9747f57712ba8aecf513 SHA1 7215e3dae85cd61919854ba5dd5abff29be91852 SHA256 ae2e5aec2fc47835f26c8d8b5776966464bc08a5fca422c130d8312880382caa diff --git a/sci-biology/aaindex/aaindex-9.1.ebuild b/sci-biology/aaindex/aaindex-9.1.ebuild new file mode 100644 index 000000000000..6c45282be145 --- /dev/null +++ b/sci-biology/aaindex/aaindex-9.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Amino acid indices and similarity matrices" +LICENSE="public-domain" +HOMEPAGE="http://www.genome.ad.jp/aaindex" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="emboss? ( sci-biology/emboss )" + +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir AAINDEX + echo + einfo "Indexing AAindex for usage with EMBOSS." + EMBOSS_DATA="." aaindexextract -auto -infile ${PN}1 || die \ + "Indexing AAindex failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins ${PN}{1,2,3} || die "Failed to install raw database." + fi + dodoc ${PN}.doc || die "Failed to install documentation." + if use emboss; then + insinto /usr/share/EMBOSS/data/AAINDEX + doins AAINDEX/* || die "Failed to install EMBOSS data files." + fi +} diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml new file mode 100644 index 000000000000..ccb567e64e02 --- /dev/null +++ b/sci-biology/aaindex/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + Amino acid indices and similarity matrices maintained at Kyoto + University. An amino acid index is a set of 20 numerical values + representing any of the different physicochemical and biological + properties of amino acids. The AAindex1 section of the Amino Acid + Index Database is a collection of published indices together with the + result of cluster analysis using the correlation coefficient as the + distance between two indices. This section currently contains 494 + indices. Another important feature of amino acids that can be + represented numerically is the similarity between amino acids. Thus, a + similarity matrix, also called a mutation matrix, is a set of 210 + numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used + for sequence alignments and similarity searches. The AAindex2 section + of the Amino Acid Index Database is a collection of published amino + acid mutation matrices together with the result of cluster analysis. + This section currently contains 83 matrices. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest new file mode 100644 index 000000000000..77dfde1ec9c8 --- /dev/null +++ b/sci-biology/abyss/Manifest @@ -0,0 +1,3 @@ +DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914 +DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01 +DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07 diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild b/sci-biology/abyss/abyss-1.3.3.ebuild new file mode 100644 index 000000000000..08a82e2f692a --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.3.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit autotools eutils toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="amd64 x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +src_prepare() { + tc-export AR + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-ac_prog_ar.patch + + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + econf \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(use_enable openmp) +} diff --git a/sci-biology/abyss/abyss-1.3.4.ebuild b/sci-biology/abyss/abyss-1.3.4.ebuild new file mode 100644 index 000000000000..e230da8847ff --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.4.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch + ) + +src_prepare() { + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild b/sci-biology/abyss/abyss-1.3.6.ebuild new file mode 100644 index 000000000000..04dcc7ce6a25 --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.6.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + dev-libs/boost + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-ac_prog_ar.patch + ) + +src_prepare() { + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch new file mode 100644 index 000000000000..300868f52b76 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 5c6cb92..b99bedd 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + + # Checks for header files. + AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch new file mode 100644 index 000000000000..42066f7f2152 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 506ea0c..a0a403c 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -15,6 +15,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch new file mode 100644 index 000000000000..c2cc35c31d98 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 1a169cf..36cc05b 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -16,6 +16,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch new file mode 100644 index 000000000000..158e9b1262e4 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 9d4bb66..aa94364 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + AC_CHECK_TOOL(GHC, ghc) + AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) + diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch new file mode 100644 index 000000000000..c2cc35c31d98 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 1a169cf..36cc05b 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -16,6 +16,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/abyss/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest new file mode 100644 index 000000000000..8209935b6d9e --- /dev/null +++ b/sci-biology/allpathslg/Manifest @@ -0,0 +1,3 @@ +DIST allpathslg-42337.tar.gz 2739498 SHA256 a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512 7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c WHIRLPOOL 79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9 +DIST allpathslg-47093.tar.gz 3057279 SHA256 493e21ae727250ea632b73b61545c32de2d8fb31e6a92605393ebb4af251f828 SHA512 499d23de52cad666fac663eb4a7d770b2129c4f9622f6c808ce30283429b6f67fb343f8712b07c7cb062c429117a0855da960ffc1d2ffb4e7ec2f544ba5a6314 WHIRLPOOL a3bc58dc140be3cddbd44c7035e628c4425bf86bc38592004df21d4dc91958ced9f08d667b43c15c214e53e3098805f368a856e66e5c2049b0e03d043b098ebc +DIST allpathslg-52415.tar.gz 3129266 SHA256 3c62024a0eacdc223bc727be4718da644fb302f785c7c7347a09ff422ce96362 SHA512 afe25b07d2e07dee3ced2283ffe858f24acfb35d53e9c11fcbcc47373594453d798c344d5604eb24d5c8d3685a185a3b8807bb3547d8066cbaab8d8cf927d1d6 WHIRLPOOL de15dfeddeca2f64fd8780839c45096c28cb47ec219d781f6754f9cf65ad6dfc39b8a48aaa2c36f777282fb08ac78ef8cd04c2e1d79f4f797710d3bb38792785 diff --git a/sci-biology/allpathslg/allpathslg-42337.ebuild b/sci-biology/allpathslg/allpathslg-42337.ebuild new file mode 100644 index 000000000000..9fb44dfcc905 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-42337.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="amd64 -x86" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +src_prepare() { + sed -i 's/-ggdb3//' configure.ac || die + eautoreconf +} + +src_install() { + einstall || die + # Provided by sci-biology/vaal + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + rm "${D}/usr/bin/$i" || die + done +} diff --git a/sci-biology/allpathslg/allpathslg-47093.ebuild b/sci-biology/allpathslg/allpathslg-47093.ebuild new file mode 100644 index 000000000000..ab971ec46c89 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-47093.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools eutils flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 -x86" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc4.9.patch + sed -i 's/-ggdb//' configure.ac || die + eautoreconf +} + +src_install() { + default + # Provided by sci-biology/vaal + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + rm "${ED}/usr/bin/$i" || die + done +} diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild new file mode 100644 index 000000000000..29de20e37670 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-52415.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12 +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="openmp" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +pkg_pretend() { + # as of release 44849, GCC 4.7.0 (or higher) is required + # seems pre gcc-4.7 users must stay with: + # ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz + if [[ ${MERGE_TYPE} != binary ]]; then + [[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \ + die "You need to use gcc >4.7" + fi +} + +src_prepare() { + local i + sed \ + -e 's/-ggdb//' \ + -e 's:CEHCK:CHECK:g' \ + -i configure.ac || die + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + sed -e "/bin_PROGRAMS/s: ${i} : :g" -i src/Makefile.am || die + done + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch new file mode 100644 index 000000000000..46e5493d28ce --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch @@ -0,0 +1,16 @@ + src/paths/long/VariantCallTools.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/paths/long/VariantCallTools.cc b/src/paths/long/VariantCallTools.cc +index dfe2787..725878b 100644 +--- a/src/paths/long/VariantCallTools.cc ++++ b/src/paths/long/VariantCallTools.cc +@@ -1674,7 +1674,7 @@ void EdgesOnRef::FindAllPathsNoLoop(const GraphT& dg, int entrace_edge, int exit + int n1 = to_right2[entrace_edge]; + int n2 = to_left2[exit_edge]; + +- PartialPath start = {{n1},{}}; ++ PartialPath start{{n1},vec<int>{}}; + stack<PartialPath> visited; + visited.push(start); + while (! visited.empty()) { diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/allpathslg/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest new file mode 100644 index 000000000000..35e082de93b9 --- /dev/null +++ b/sci-biology/amap/Manifest @@ -0,0 +1 @@ +DIST amap.2.2.tar.gz 102861 RMD160 6b47b66ab5095e35bcb14a599a25687fef8e799c SHA1 618e498581302e140270a0e029ab87d378c450ef SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4 diff --git a/sci-biology/amap/amap-2.2-r2.ebuild b/sci-biology/amap/amap-2.2-r2.ebuild new file mode 100644 index 000000000000..389102a8e757 --- /dev/null +++ b/sci-biology/amap/amap-2.2-r2.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils toolchain-funcs java-pkg-opt-2 java-ant-2 + +MY_P=${PN}.${PV} + +DESCRIPTION="Protein multiple-alignment-based sequence annealing" +HOMEPAGE="http://bio.math.berkeley.edu/amap/" +SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="java" + +RDEPEND="java? ( >=virtual/jre-1.5 )" +DEPEND="java? ( >=virtual/jdk-1.5 )" + +S=${WORKDIR}/${PN}-align + +src_prepare() { + epatch "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-includes.patch +} + +src_compile() { + emake -C align CXX="$(tc-getCXX)" \ + OPT_CXXFLAGS="${CXXFLAGS}" || die "make failed" + + if use java; then + pushd "${S}"/display + eant -Ddisplay all || die + popd + fi +} + +src_install() { + dobin align/${PN} || die + dodoc align/{README,PROBCONS.README} || die + insinto /usr/share/${PN}/examples + doins examples/* || die + if use java; then + java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar + java-pkg_dolauncher amapdisplay --jar amapdisplay.jar + fi +} diff --git a/sci-biology/amap/files/amap-2.2-includes.patch b/sci-biology/amap/files/amap-2.2-includes.patch new file mode 100644 index 000000000000..77c4261db5cf --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-includes.patch @@ -0,0 +1,44 @@ +Fixes build with gcc 4.3 and 4.6 + +http://bugs.gentoo.org/217921 +http://bugs.gentoo.org/360517 + +--- amap-align/align/Amap.cc ++++ amap-align/align/Amap.cc +@@ -12,6 +12,8 @@ + #include "ProbabilisticModel.h" + #include "EvolutionaryTree.h" + #include "SparseMatrix.h" ++#include <limits> ++#include <climits> + #include <string> + #include <sstream> + #include <iomanip> +@@ -23,6 +25,7 @@ + #include <cstdlib> + #include <cerrno> + #include <iomanip> ++#include <cstring> + + string parametersInputFilename = ""; + string parametersOutputFilename = "no training"; +--- amap-align/align/MultiSequenceDag.h ++++ amap-align/align/MultiSequenceDag.h +@@ -13,6 +13,7 @@ + #include <map> + #include <queue> + #include <iostream> ++#include <limits> + #include "MultiSequence.h" + #include "SparseMatrix.h" + +--- amap-align/align/SafeVector.h.org 2011-03-26 11:50:11.935069583 +0100 ++++ amap-align/align/SafeVector.h 2011-03-26 11:50:21.112553151 +0100 +@@ -9,6 +9,7 @@ + #define SAFEVECTOR_H + + #include <cassert> ++#include <cstddef> + #include <vector> + + ///////////////////////////////////////////////////////////////// diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch new file mode 100644 index 000000000000..5a9841c98255 --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-makefile.patch @@ -0,0 +1,35 @@ +Respect {CXX,LD}FLAGS + +http://bugs.gentoo.org/332009 + +--- amap-align/align/Makefile ++++ amap-align/align/Makefile +@@ -15,6 +15,8 @@ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' + + # debug mode +@@ -26,8 +28,7 @@ + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops +- ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + ################################################################################ + # 3) Dependencies + ################################################################################ + +@@ -38,7 +37,7 @@ + all : $(TARGETS) + + amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc +- $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o amap Amap.cc -lm + + .PHONY : clean + clean: diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml new file mode 100644 index 000000000000..34294c65ca04 --- /dev/null +++ b/sci-biology/amap/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest new file mode 100644 index 000000000000..27ad50ff28ed --- /dev/null +++ b/sci-biology/amos/Manifest @@ -0,0 +1 @@ +DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61 diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild new file mode 100644 index 000000000000..a4c860bdbe7f --- /dev/null +++ b/sci-biology/amos/amos-3.1.0-r1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="qt4" + +DEPEND="qt4? ( dev-qt/qtcore:4 )" +RDEPEND="${DEPEND} + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch +} + +src_install() { + default + python_replicate_script "${ED}"/usr/bin/goBambus2 +} diff --git a/sci-biology/amos/amos-3.1.0.ebuild b/sci-biology/amos/amos-3.1.0.ebuild new file mode 100644 index 000000000000..945ec9f41b4c --- /dev/null +++ b/sci-biology/amos/amos-3.1.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="qt4" + +DEPEND="qt4? ( dev-qt/qtcore:4 )" +RDEPEND="${DEPEND} + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch +} diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch new file mode 100644 index 000000000000..de2a41184c52 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch @@ -0,0 +1,15 @@ + src/Align/find-tandem.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc +index ddf1cab..a29e21e 100644 +--- a/src/Align/find-tandem.cc ++++ b/src/Align/find-tandem.cc +@@ -7,6 +7,7 @@ + #include <vector> + #include <ctime> + #include <sys/time.h> ++#include <unistd.h> + using namespace std; + + const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch new file mode 100644 index 000000000000..97a8f59d0208 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch @@ -0,0 +1,25 @@ +--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 ++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 +@@ -1,7 +1,7 @@ + #pipeline script for assembly + Bambus 2 + #contributed by Todd J Treangen + +-import string, sys, os, subprocess#, spincursor ++import sys, os, subprocess#, spincursor + + RED = "\033[0;31m" + GREEN = "\033[0;32m" +@@ -360,7 +360,7 @@ + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) + +- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) ++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) + + if xopt_dict["verbose"] == 1: + print "10) running OutputResults" +@@ -388,4 +388,3 @@ + else: + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) +-) diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml new file mode 100644 index 000000000000..a73ee9189a98 --- /dev/null +++ b/sci-biology/amos/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">amos</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest new file mode 100644 index 000000000000..7ec0fa4e73a4 --- /dev/null +++ b/sci-biology/arb/Manifest @@ -0,0 +1,7 @@ +DIST arb-5.1-glibc2.10.patch.bz2 24659 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f +DIST arb-5.1-linker.patch.bz2 4406 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43 +DIST arb-5.1.tgz 9727285 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf +DIST arb-5.2-linker.patch.bz2 4441 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677a3f2216021eed04ba76ac886c6 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903 WHIRLPOOL 95435cfc7f5a530442ad294cb8cd79a666f54cc3c99195e9c05a923e41b0211e5bad7b67cd4d8c5ee37ef30de22fba4472dc8990d95aaf3c8d3edb2d3d26c984 +DIST arb-5.2.tgz 9729004 SHA256 cd68cfae317aae378da69c4c4ec8036a2babec064896d0b9d845fac2133f6edd SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56 WHIRLPOOL ec5422b4b689a77b479231c04d7b5a2f4f0ef23cd06b024920432134132d7c2c5b24c407b2561074a41606e7945ce88970789f5db82e43cc9ef9313ea48c0583 +DIST arb-5.3-linker.patch.xz 3604 SHA256 09580d0c1ff54c4956382cef850aecb9008e62e083f3246604cac72f06d05e95 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7 WHIRLPOOL f77d767c5b5c911ba3ddc9ef5b3e482cb1975b5d56f50b76166bd4a0b55e251e73eeee46709147207b2f3553d482bab99398d8bd03aef8f0b79928a8a66d0bfe +DIST arb-5.3.tgz 9543106 SHA256 c40a3f33f39996e3e331fb41acd452e5a20b7e638b856b0b66ea8e07c977abf8 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282 WHIRLPOOL 9b4723043b4f8b9a68973f49cb7dc8c3cf3558ff646d20f7d4f20f6e4797b6c9a986fdb1dc47178f2c80251db59f61dffd1b01bbdd880f864fc749ef59e62958 diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild new file mode 100644 index 000000000000..7db2d798ec55 --- /dev/null +++ b/sci-biology/arb/arb-5.1-r1.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + mirror://gentoo/${P}-glibc2.10.patch.bz2 + http://dev.gentoo.org/~jlec/${P}-linker.patch.bz2" + +LICENSE="arb" +SLOT="0" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +RDEPEND="${DEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-glibc2.10.patch\ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/${PV}-libs.patch \ + "${FILESDIR}"/${PV}-bfr-overflow.patch + sed -i \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -e 's/--export-dynamic/-Wl,--export-dynamic/g' \ + "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links || die +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" || die +} diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild new file mode 100644 index 000000000000..97f7dc5dfbdd --- /dev/null +++ b/sci-biology/arb/arb-5.2.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2" + +SLOT="0" +LICENSE="arb" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +CDEPEND="app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +DEPEND="${CDEPEND} + sys-process/time" +RDEPEND="${CDEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/5.1-libs.patch \ + "${FILESDIR}"/5.1-bfr-overflow.patch \ + "${FILESDIR}"/${PV}-libpng15.patch \ + "${FILESDIR}"/${P}-gcc-47.patch + sed \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -e 's:-O4::g' \ + -e 's:-pipe::g' \ + -i "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" +} diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild new file mode 100644 index 000000000000..97f8b78ddca2 --- /dev/null +++ b/sci-biology/arb/arb-5.3.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis" +HOMEPAGE="http://www.arb-home.de/" +SRC_URI=" + http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz + http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz" + +SLOT="0" +LICENSE="arb" +IUSE="+opengl" +KEYWORDS="~amd64 ~x86" + +CDEPEND="app-text/sablotron + media-libs/libpng + media-libs/tiff + www-client/lynx + x11-libs/libXaw + x11-libs/libXpm + x11-libs/motif:0 + opengl? ( + media-libs/glew + media-libs/freeglut + || ( + media-libs/mesa[motif] + ( media-libs/mesa x11-libs/libGLw ) ) )" +DEPEND="${CDEPEND} + sys-process/time" +RDEPEND="${CDEPEND} + sci-visualization/gnuplot" +# Recommended: libmotif3 gv xfig xterm treetool java + +src_unpack() { + unpack ${A} + mv arbsrc* ${P} +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${P}-linker.patch \ + "${FILESDIR}"/5.1-libs.patch \ + "${FILESDIR}"/5.1-bfr-overflow.patch \ + "${FILESDIR}"/5.2-libpng15.patch \ + "${FILESDIR}"/${PN}-5.2-gcc-47.patch + sed \ + -e 's/all: checks/all:/' \ + -e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \ + -e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \ + -i "${S}/Makefile" || die + cp config.makefile.template config.makefile + sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die + use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile + use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile + emake ARBHOME="${S}" links +} + +src_compile() { + emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile + use amd64 && mv arb.tgz arb.64.gentoo.tgz + use x86 && mv arb.tgz arb.32.gentoo.tgz + ln -s arb.*.tgz arb.tgz || die +} + +src_install() { + ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die + cat <<- EOF > "${S}/99${PN}" + ARBHOME=/opt/arb + PATH=/opt/arb/bin + LD_LIBRARY_PATH=/opt/arb/lib + EOF + doenvd "${S}/99${PN}" +} diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch new file mode 100644 index 000000000000..21d21f5ac17f --- /dev/null +++ b/sci-biology/arb/files/5.1-bfr-overflow.patch @@ -0,0 +1,16 @@ + ARB_GDE/GDE_HGLfile.cxx | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx +index e353a89..f69635a 100644 +--- a/ARB_GDE/GDE_HGLfile.cxx ++++ b/ARB_GDE/GDE_HGLfile.cxx +@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type) + if(this_elem->id[0] == '\0') + strncpy(this_elem->id,uniqueID(),79); + if(this_elem->short_name[0] == '\0') +- strncpy(this_elem->short_name,this_elem->id,79); ++ strncpy(this_elem->short_name,this_elem->id,31); + if(this_elem->seqlen == 0) + this_elem->protect= + PROT_BASE_CHANGES+ diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch new file mode 100644 index 000000000000..bf0bacad3286 --- /dev/null +++ b/sci-biology/arb/files/5.1-libs.patch @@ -0,0 +1,16 @@ +diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl +index b653a66..b346c96 100644 +--- a/SOURCE_TOOLS/provide_libs.pl ++++ b/SOURCE_TOOLS/provide_libs.pl +@@ -118,11 +118,6 @@ sub provide_libs($$$) { + foreach my $lib (keys %needed_by) { + update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir); + } +- if ($opengl==1) { +- foreach my $lib (keys %needed_by_opengl) { +- update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir); +- } +- } + } + + sub main() { diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch new file mode 100644 index 000000000000..3d750e76efe3 --- /dev/null +++ b/sci-biology/arb/files/5.2-libpng15.patch @@ -0,0 +1,45 @@ +Fix building with libpng-1.5 + +https://bugs.gentoo.org/show_bug.cgi?id=378353 + +Patch written by Samuli Suominen <ssuominen@gentoo.org> +--- a/GL/glpng/glpng.c ++++ b/GL/glpng/glpng.c +@@ -285,7 +285,7 @@ + endinfo = png_create_info_struct(png); + + // DH: added following lines +- if (setjmp(png->jmpbuf)) ++ if (setjmp(png_jmpbuf(png))) + { + png_destroy_read_struct(&png, &info, &endinfo); + return 0; +@@ -390,7 +390,7 @@ + endinfo = png_create_info_struct(png); + + // DH: added following lines +- if (setjmp(png->jmpbuf)) ++ if (setjmp(png_jmpbuf(png))) + { + png_destroy_read_struct(&png, &info, &endinfo); + return 0; +@@ -569,7 +569,7 @@ + #define ALPHA *q + + switch (trans) { +- case PNG_CALLBACK: ++ case PNG_CALLBACKT: + FORSTART + ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b); + FOREND +--- a/GL/glpng/glpng.h ++++ b/GL/glpng/glpng.h +@@ -57,7 +57,7 @@ + #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS + + /* Transparency parameters */ +-#define PNG_CALLBACK -3 /* Call the callback function to generate alpha */ ++#define PNG_CALLBACKT -3 /* Call the callback function to generate alpha */ + #define PNG_ALPHA -2 /* Use alpha channel in PNG file, if there is one */ + #define PNG_SOLID -1 /* No transparency */ + #define PNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */ diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch new file mode 100644 index 000000000000..186e78e450b3 --- /dev/null +++ b/sci-biology/arb/files/arb-5.2-gcc-47.patch @@ -0,0 +1,15 @@ + AWTI/AWTI_import.cxx | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx +index 8e730ac..e3f9ff4 100644 +--- a/AWTI/AWTI_import.cxx ++++ b/AWTI/AWTI_import.cxx +@@ -12,6 +12,7 @@ + #include <GEN.hxx> + + #include <climits> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/arb/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/ariadne/Manifest b/sci-biology/ariadne/Manifest new file mode 100644 index 000000000000..a4bf86d55d3c --- /dev/null +++ b/sci-biology/ariadne/Manifest @@ -0,0 +1 @@ +DIST ariadne-1.3.tar.Z 69427 SHA256 8b6b0acb6e8d02b1303d94b20906bf2bf1dee3de4eceeb1b927cfba7a96fd00d SHA512 6c803f945bbcf36c08407e907ad716dc7cd01c7bed555777af46a5dc626b56ca3d1de7d16cab82bfa8bd5a91e06f42c590c0489594251405999459459e9c7289 WHIRLPOOL 460d8acf2bb49e097a9544ecc089ca60c3478b64ab4d903bd6ee801eccd62fc560bdccf1454c9f22632081cbf1df35de09a4f81d6c131d3f52f36753bc692927 diff --git a/sci-biology/ariadne/ariadne-1.3-r1.ebuild b/sci-biology/ariadne/ariadne-1.3-r1.ebuild new file mode 100644 index 000000000000..80a05b612ca9 --- /dev/null +++ b/sci-biology/ariadne/ariadne-1.3-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs eutils + +DESCRIPTION="Protein sequences and profiles comparison" + +HOMEPAGE="http://www.well.ox.ac.uk/ariadne/" +SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z" + +LICENSE="ARIADNE" +SLOT="0" +KEYWORDS="~amd64 x86" +IUSE="" + +DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/SRC-${PV}" + +src_unpack(){ + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-gcc4.patch + sed -e "s/CC = gcc/CC = $(tc-getCC)/" \ + -e "s/OPTIMISE = -O2/OPTIMISE = ${CFLAGS}/" \ + -i Makefile || die + sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die +} + +src_install() { + dobin Linux/{ariadne,prospero} || die + dolib Linux/libseq.a || die + insinto /usr/include/${PN} + doins Include/*.h || die + dodoc README || die +} diff --git a/sci-biology/ariadne/ariadne-1.3-r2.ebuild b/sci-biology/ariadne/ariadne-1.3-r2.ebuild new file mode 100644 index 000000000000..1fa55ce322db --- /dev/null +++ b/sci-biology/ariadne/ariadne-1.3-r2.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Protein sequences and profiles comparison" +HOMEPAGE="http://www.well.ox.ac.uk/ariadne/" +SRC_URI="http://www.well.ox.ac.uk/${PN}/${P}.tar.Z" + +LICENSE="ARIADNE" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=">=sci-biology/ncbi-tools-0.20041020-r1" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/SRC-${PV} + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc4.patch \ + "${FILESDIR}"/${P}-implicits.patch + sed -i -e "s/\$(CFLAGS)/\$(LDFLAGS) &/" Makefile || die #359045 + sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die +} + +src_compile() { + emake CC="$(tc-getCC)" OPTIMISE="${CFLAGS}" +} + +src_install() { + dobin Linux/{ariadne,prospero} + use static-libs && dolib.a Linux/libseq.a + insinto /usr/include/${PN} + doins Include/*.h || die + dodoc README || die +} diff --git a/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch new file mode 100644 index 000000000000..0192efd4db5e --- /dev/null +++ b/sci-biology/ariadne/files/ariadne-1.3-gcc4.patch @@ -0,0 +1,10 @@ +--- cl.c.old 2006-09-12 17:13:02.000000000 -0400 ++++ cl.c 2006-09-12 17:13:34.000000000 -0400 +@@ -658,6 +658,7 @@ + fclose(fp); + if ( ! stat( filename, &buf ) ) + { ++ char *ctime(), *t; + sprintf( date, "%s", ctime(&buf.st_mtime) ); + t = date; + while ( *t ) diff --git a/sci-biology/ariadne/files/ariadne-1.3-implicits.patch b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch new file mode 100644 index 000000000000..31c442b12265 --- /dev/null +++ b/sci-biology/ariadne/files/ariadne-1.3-implicits.patch @@ -0,0 +1,23 @@ +topalign.c:96:5: warning: implicit declaration of function ‘toupper’ +prospero.c:63:3: warning: implicit declaration of function ‘strcpy’ + +--- SRC-1.3/prospero.c ++++ SRC-1.3/prospero.c +@@ -26,6 +26,7 @@ + */ + + #include<stdio.h> ++#include<string.h> + #include<math.h> + #include"cl.h" + #include"seq_util.h" +--- SRC-1.3/topalign.c ++++ SRC-1.3/topalign.c +@@ -26,6 +26,7 @@ + */ + + #include<stdio.h> ++#include<ctype.h> + #include<math.h> + #include"seq_util.h" + #include"ariadne.h" diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml new file mode 100644 index 000000000000..3e55c00f9d7b --- /dev/null +++ b/sci-biology/ariadne/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + ARIADNE is a package of two programs, ariadne and prospero, that + compare protein sequences and profiles using the Smith-Waterman + algorithm, and assesses statistical significance using a new accurate + formula, described in Mott, 2000, "Accurate Formula for P-values of + gapped local sequence and profile alignments" J. Mol Biol. 300:649-659. + The sequence/profile comparison algorithms used in ARIADNE are + standard, and are probably not the fastest implementations available. + The novel part is the method for determining statistical significance, + which will give thresholds of significance that are accurate to within + 5% 95% of the time. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest new file mode 100644 index 000000000000..cdfb577937e0 --- /dev/null +++ b/sci-biology/augustus/Manifest @@ -0,0 +1 @@ +DIST augustus.2.5.5.tar.gz 70826249 SHA256 2bd97784fa651addf836e2100a7d4106b43e50fe06f13c664001d4625d0eab9a SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f WHIRLPOOL 875f56f10251767fb066b5e21b0c2361c952d5cc44daa811658be8119957ffa34fd4552fde7e17384d5bc916aee5ef91982ded3999d0077cf3834d5fc20e7f1a diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild new file mode 100644 index 000000000000..e58be6db6d6a --- /dev/null +++ b/sci-biology/augustus/augustus-2.5.5.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://augustus.gobics.de/" +SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="examples" + +S="${WORKDIR}/${PN}.${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-sane-build.patch + tc-export CC CXX +} + +src_compile() { + emake clean && emake +} + +src_install() { + dobin bin/* +# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign} + + exeinto /usr/libexec/${PN} + doexe scripts/*.p* + insinto /usr/libexec/${PN} + doins scripts/*.conf + + insinto /usr/share/${PN} + doins -r config + + echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} + + if use examples; then + insinto /usr/share/${PN}/ + doins -r docs/tutorial examples + fi +} diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch new file mode 100644 index 000000000000..39cd0762b1c1 --- /dev/null +++ b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch @@ -0,0 +1,156 @@ + Makefile | 8 +++--- + scripts/Makefile | 6 +++- + scripts/aln2wig/Makefile | 8 +++--- + scripts/compileSpliceCands/Makefile | 6 ++-- + src/Makefile | 43 ++++++++++++++++++---------------- + 5 files changed, 38 insertions(+), 33 deletions(-) + +diff --git a/Makefile b/Makefile +index e23a667..64610c8 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,9 +3,9 @@ + # + + all: +- cd src && ${MAKE} +- cd scripts && ${MAKE} ++ $(MAKE) -C src ++ $(MAKE) -C scripts + + clean: +- cd src && ${MAKE} clean +- cd scripts && ${MAKE} clean ++ $(MAKE) -C src clean ++ $(MAKE) -C scripts clean +diff --git a/scripts/Makefile b/scripts/Makefile +index 6d4dd67..ab6a885 100644 +--- a/scripts/Makefile ++++ b/scripts/Makefile +@@ -1,5 +1,7 @@ + all : +- cd aln2wig && ${MAKE} ++ $(MAKE) -C aln2wig ++ $(MAKE) -C compileSpliceCands + + clean : +- cd aln2wig && ${MAKE} clean ++ $(MAKE) -C aln2wig clean ++ $(MAKE) -C compileSpliceCands +diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile +index 64d09f5..9752980 100644 +--- a/scripts/aln2wig/Makefile ++++ b/scripts/aln2wig/Makefile +@@ -1,10 +1,10 @@ +-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb ++CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic + + psl2wig : aln2wig.o +- gcc $(CFLAGS) -o aln2wig aln2wig.o; +- cp aln2wig ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o; ++ cp aln2wig ../../bin/ + psl2wig.o : aln2wig.c +- gcc $(CFLAGS) -c aln2wig.c ++ $(CC) $(CFLAGS) -c aln2wig.c + + all : psl2wig + +diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile +index cddada5..8079791 100644 +--- a/scripts/compileSpliceCands/Makefile ++++ b/scripts/compileSpliceCands/Makefile +@@ -1,8 +1,8 @@ + compileSpliceCands : compileSpliceCands.o list.h list.o +- gcc -o compileSpliceCands compileSpliceCands.o list.o; +-# cp compileSpliceCands ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; ++ cp compileSpliceCands ../../bin/ + compileSpliceCands.o : compileSpliceCands.c +- gcc -Wall -pedantic -ansi -c compileSpliceCands.c ++ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c + + all : compileSpliceCands + +diff --git a/src/Makefile b/src/Makefile +index 71795b6..732b953 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -6,8 +6,8 @@ + # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. + # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh) + # +-CC = g++ +-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static ++CXX ?= g++ ++CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static + INCLS = -I../include -I. + LIBS = # -lcwd + OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \ +@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte + PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign + INFO = cflags + +-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info ++all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin + + .SUFFIXES: + .SUFFIXES: .cc .o .so + + .cc.o: +- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS) ++ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS) + +-augustus: augustus.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++bin: $(PROGR) ++ cp $(PROGR) ../bin/ ++ ++augustus: augustus.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp augustus ../bin/ + +-etraining: etraining.cc $(TOBJS) $(OBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++etraining: etraining.o $(TOBJS) $(OBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp etraining ../bin/ + +-evaluate: evaluate.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++evaluate: evaluate.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-consensusFinder: consensusFinder.cc consensus.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++consensusFinder: consensusFinder.o consensus.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-curve2hints: curve2hints.cc exon_seg.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++curve2hints: curve2hints.o exon_seg.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \ ++fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \ + types.o properties.o geneticcode.o pp_profile.o lldouble.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp fastBlockSearch ../bin/ + +-prepareAlign: pp_prepare_align.cc +- $(CC) $(CFLAGS) -o $@ $^ ++prepareAlign: pp_prepare_align.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ + cp prepareAlign ../bin/ + + info: +- echo "$(CFLAGS)" > $(INFO) ++ echo "$(CXXFLAGS)" > $(INFO) + + clean: +- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ++ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/* + + tidy: clean + rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO) diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/augustus/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest new file mode 100644 index 000000000000..1c1972c599d5 --- /dev/null +++ b/sci-biology/bamtools/Manifest @@ -0,0 +1,2 @@ +DIST bamtools-1.0.2.tar.gz 207523 SHA256 d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8 SHA512 1934d40d50f3fdf2b1fcacb8b59cf954a3c791d3095649ac4f1246563e9d8d4afe385e42a2c6c383f0bb519eede401d12c71203d279b33e01575222f9f84c244 WHIRLPOOL 9fb4d4feb3ff867866a96533231a1b8284fd5156ab142cad727d32f8f3c157e246cca59185c3bdc253b19bde2514404a7107a62443780b060f6e8f270622c990 +DIST bamtools-2.3.0.tar.gz 539446 SHA256 288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af SHA512 432f66384cffc04ab6bc7dc66d8f7b79c1e468d0068db4cabb5cac05f9b6bef7968eff71ffb3ee51b84e23d9bb66a11ef267024138f40116c25e7f18e7210a5c WHIRLPOOL dd888f67c3d0b0ce2f5f2875e242e5df0d54cefd13693230b5f10eb57dd780304b601027cf65f6598a54061a7166903bf06c6c9a46939f6ce6bbb246cab89993 diff --git a/sci-biology/bamtools/bamtools-1.0.2.ebuild b/sci-biology/bamtools/bamtools-1.0.2.ebuild new file mode 100644 index 000000000000..08c40d0705d3 --- /dev/null +++ b/sci-biology/bamtools/bamtools-1.0.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" +HOMEPAGE="https://github.com/pezmaster31/bamtools" +SRC_URI="mirror://github/pezmaster31/bamtools/"${P}".tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="sys-libs/zlib" +RDEPEND="${DEPEND}" + +src_install() { + for i in bin/bamtools-${PV} lib/libbamtools.so.${PV} lib/libbamtools-utils.so.${PV}; do + TMPDIR="$(pwd)" scanelf -Xr $i || die + done + + dobin bin/bamtools + dolib lib/* + insinto /usr/include/bamtools/api + doins include/api/* + insinto /usr/include/bamtools/shared + doins include/shared/* + dodoc README +} diff --git a/sci-biology/bamtools/bamtools-2.3.0.ebuild b/sci-biology/bamtools/bamtools-2.3.0.ebuild new file mode 100644 index 000000000000..cb86750cc0cf --- /dev/null +++ b/sci-biology/bamtools/bamtools-2.3.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" +HOMEPAGE="https://github.com/pezmaster31/bamtools" +SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=" + >=dev-libs/jsoncpp-0.5.0-r1 + sys-libs/zlib" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${P}-unbundle.patch ) + +src_install() { + cmake-utils_src_install + use static-libs || rm "${ED}"/usr/$(get_libdir)/*.a +} diff --git a/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch new file mode 100644 index 000000000000..318396e75c36 --- /dev/null +++ b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch @@ -0,0 +1,32 @@ + src/CMakeLists.txt | 1 - + src/api/CMakeLists.txt | 4 ++-- + src/toolkit/bamtools_filter.cpp | 2 +- + 3 files changed, 3 insertions(+), 4 deletions(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index e359695..2bd2185 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -6,7 +6,6 @@ + # ========================== + + add_subdirectory( api ) +-add_subdirectory( third_party ) + add_subdirectory( toolkit ) + add_subdirectory( utils ) + +diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt +index 66eb35f..65f4639 100644 +--- a/src/api/CMakeLists.txt ++++ b/src/api/CMakeLists.txt +@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} ) + target_link_libraries( BamTools-static ${APILibs} ) + + # set library install destinations +-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") +-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") ++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin") ++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}") + + # export API headers + include(../ExportHeader.cmake) diff --git a/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch new file mode 100644 index 000000000000..c07c59d2cddd --- /dev/null +++ b/sci-biology/bamtools/files/bamtools-2.3.0-unbundle.patch @@ -0,0 +1,23 @@ +--- bamtools-2.3.0/src/api/CMakeLists.txt.ori 2013-08-27 18:00:43.000000000 +0200 ++++ bamtools-2.3.0/src/api/CMakeLists.txt 2013-08-27 18:00:47.000000000 +0200 +@@ -54,8 +54,8 @@ + target_link_libraries( BamTools-static ${APILibs} ) + + # set library install destinations +-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") +-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") ++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin") ++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}") + + # export API headers + include(../ExportHeader.cmake) +--- bamtools-2.3.0/src/CMakeLists.txt.ori 2013-08-27 18:03:10.000000000 +0200 ++++ bamtools-2.3.0/src/CMakeLists.txt 2013-08-27 18:03:23.000000000 +0200 +@@ -6,7 +6,6 @@ + # ========================== + + add_subdirectory( api ) +-add_subdirectory( third_party ) + add_subdirectory( toolkit ) + add_subdirectory( utils ) + diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml new file mode 100644 index 000000000000..f2c00c1fdd0c --- /dev/null +++ b/sci-biology/bamtools/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <herd>proxy-maintainers</herd> + <maintainer> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> + </maintainer> + <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> + <upstream> + <remote-id type="github">pezmaster31/bamtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest new file mode 100644 index 000000000000..7fd843d7d423 --- /dev/null +++ b/sci-biology/beast-mcmc/Manifest @@ -0,0 +1,2 @@ +DIST beast-mcmc-1.5.2.tar.bz2 38834702 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 SHA512 8549db6cb49d64eb3a97fa6478bdbabfecd44ccc6236c474a1961ec5d6fc8326072fb961035df70982a9f1c08a36572529a07b88e2d33a43fa0fd5c07df3a414 WHIRLPOOL 595f606640daa32c79373c9003ddbc1f80dcbbf01e9e9c18191328b80eb50b45ac70032027dd1efb0e256d78b88bfe1742151a16f6f333938099943a7b2cd16a +DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5 diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild new file mode 100644 index 000000000000..d25ed786a751 --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/" + +WANT_ANT_TASKS="ant-junit4" +EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +#inherit java-pkg-2 java-ant-2 eutils subversion +inherit java-pkg-2 java-ant-2 eutils + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="http://code.google.com/p/beast-mcmc/" +#SRC_URI="" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS="dev-java/colt:0 + dev-java/jdom:1.0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom-1.0 + java-pkg_jar-from colt + java-pkg_jar-from itext + java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-1 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples || die + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild new file mode 100644 index 000000000000..35993562814c --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild @@ -0,0 +1,86 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/" + +WANT_ANT_TASKS="ant-junit4" +EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +#inherit java-pkg-2 java-ant-2 eutils subversion +inherit java-pkg-2 java-ant-2 eutils + +MY_P=BEASTv${PV} + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="http://code.google.com/p/beast-mcmc/" +#SRC_URI="" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS=" + dev-java/colt:0 + dev-java/jdom:1.0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/release/Linux/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die + #rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom-1.0 + java-pkg_jar-from colt + java-pkg_jar-from itext +# java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-2 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) +} diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild new file mode 100644 index 000000000000..30c1a3751011 --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/" + +WANT_ANT_TASKS="ant-junit4" +EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_ANT_ENCODING="latin1" +JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" + +inherit java-pkg-2 java-ant-2 eutils subversion + +DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" +HOMEPAGE="http://code.google.com/p/beast-mcmc/" +SRC_URI="" +#SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# TODO: sys-cluster/mpijava +COMMON_DEPS="dev-java/colt:0 + dev-java/jdom:1.0 + dev-java/itext:0 + dev-java/junit:4 + dev-java/jebl:0 + dev-java/matrix-toolkits-java + dev-java/commons-math:2 + dev-java/jdom-jaxen:1.0" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPS}" + +S="${WORKDIR}/beast_release_${PV//./_}" + +src_prepare() { + sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die + cd lib + rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die + java-pkg_jar-from jdom-1.0 + java-pkg_jar-from colt + java-pkg_jar-from itext + java-pkg_jar-from jebl + java-pkg_jar-from matrix-toolkits-java + java-pkg_jar-from commons-math-1 + java-pkg-2_src_prepare +} + +src_compile() { + eant dist_all_BEAST -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die + eant dist -f build_pathogen.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} + +src_install() { + java-pkg_dojar build/dist/*.jar dist/*.jar + + java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' +# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' + java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' + + insinto /usr/share/${PN} + doins -r examples || die + dodoc NOTIFY doc/*.pdf +} + +src_test() { + eant junit -f build_BEAST_MCMC.xml \ + -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die +} diff --git a/sci-biology/beast-mcmc/metadata.xml b/sci-biology/beast-mcmc/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/beast-mcmc/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest new file mode 100644 index 000000000000..e8ecdb88e2ea --- /dev/null +++ b/sci-biology/bedtools/Manifest @@ -0,0 +1,2 @@ +DIST BEDTools.v2.16.2.tar.gz 978293 SHA256 f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772 +DIST bedtools-2.20.1.tar.gz 4213348 SHA256 b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 SHA512 b5c27601365a2126c58492791a52a262c874073cc1626bb1e38545ccf6e3594d12d2d2116304374b3446a588611cfd410c8ff166170823071b33c444c9fd36a7 WHIRLPOOL b768a7e064444d5d0434aea5251e132d68fbeb580783034c8e327666eaace0307febc80e9d6d3eea2f0f648263ce0ac836fac7a676586a6e6a8ec4daf39e6a84 diff --git a/sci-biology/bedtools/bedtools-2.16.2.ebuild b/sci-biology/bedtools/bedtools-2.16.2.ebuild new file mode 100644 index 000000000000..7de4f347c710 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.16.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit flag-o-matic + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" +HOMEPAGE="http://code.google.com/p/bedtools/" +SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +S="${WORKDIR}/BEDTools-Version-${PV}" + +src_prepare() { + filter-ldflags -Wl,--as-needed + sed -i \ + -e '/export CXXFLAGS/ d' \ + -e '/export CXX/ d' \ + Makefile || die +} + +src_install() { + dobin bin/* + dodoc README* RELEASE_HISTORY + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild b/sci-biology/bedtools/bedtools-2.20.1.ebuild new file mode 100644 index 000000000000..cdba954f6d27 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.20.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit flag-o-matic + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats" +HOMEPAGE="http://code.google.com/p/bedtools/" +SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +S="${WORKDIR}/bedtools2-${PV}" + +src_prepare() { + filter-ldflags -Wl,--as-needed + sed -i \ + -e '/export CXXFLAGS/ d' \ + -e '/export CXX/ d' \ + Makefile || die +} + +src_install() { + dobin bin/* + dodoc README* RELEASE_HISTORY + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml new file mode 100644 index 000000000000..6edffa4a6dc3 --- /dev/null +++ b/sci-biology/bedtools/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <herd>proxy-maintainers</herd> + <maintainer> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> + </maintainer> + <longdescription> + BEDTools: a flexible suite of utilities for comparing genomic features. + </longdescription> + <upstream> + <remote-id type="google-code">bedtools</remote-id> + <remote-id type="github">arq5x/bedtools2</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest new file mode 100644 index 000000000000..532e6e077652 --- /dev/null +++ b/sci-biology/bfast/Manifest @@ -0,0 +1 @@ +DIST bfast-0.7.0a.tar.gz 2456617 SHA256 ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836 WHIRLPOOL f9098c00a2f328fd5116447aae86f0aed078f6c2e6a49a4459e09f0c2a2023e0d60be1893fc2337b85444c24efb2636953517eda2ced336d1bc6dc8d94706e6b diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild new file mode 100644 index 000000000000..908334354033 --- /dev/null +++ b/sci-biology/bfast/bfast-0.7.0a.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Blat-like Fast Accurate Search Tool" +HOMEPAGE="https://sourceforge.net/projects/bfast/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="test" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="dev-perl/XML-Simple" + +src_prepare() { + sed \ + -e 's/-m64//' \ + -e 's/CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"/CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"/' \ + -e 's:-g -O2::g' \ + -i configure.ac || die + sed \ + -e 's:. test.definitions.sh:. ./test.definitions.sh:g' \ + -i tests/*sh || die + + sed \ + -e '/docdir/d' \ + -i Makefile.am || die + + use test && AUTOTOOLS_IN_SOURCE_BUILD=1 + + autotools-utils_src_prepare +} diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml new file mode 100644 index 000000000000..45107864e217 --- /dev/null +++ b/sci-biology/bfast/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">bfast</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/biogrep/Manifest b/sci-biology/biogrep/Manifest new file mode 100644 index 000000000000..0bd1b4ccfa7a --- /dev/null +++ b/sci-biology/biogrep/Manifest @@ -0,0 +1 @@ +DIST biogrep-1.0.tar.gz 71867 RMD160 8f22aaa432febbf7d433402ca5da1afe7a98a217 SHA1 b4c24777e94d9f04dfda0d2d6a4599e3bc470a4f SHA256 15421d79f6f16d6bf9bef132a97f7f9ede1bd42d3fb90572df04a1e1abd8cfd8 diff --git a/sci-biology/biogrep/biogrep-1.0-r1.ebuild b/sci-biology/biogrep/biogrep-1.0-r1.ebuild new file mode 100644 index 000000000000..f4af74c73bff --- /dev/null +++ b/sci-biology/biogrep/biogrep-1.0-r1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit toolchain-funcs + +DESCRIPTION="Multithreading application for matching large sets of patternsagainst biosequence dbs" +HOMEPAGE="http://web.mit.edu/bamel/biogrep.shtml" +SRC_URI="http://web.mit.edu/bamel/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +src_prepare() { + tc-export CC +} + +src_install() { + emake prefix="${D}"/usr install || die "install failed" + dodoc AUTHORS ChangeLog NEWS README || die "dodoc failed" +} diff --git a/sci-biology/biogrep/biogrep-1.0.ebuild b/sci-biology/biogrep/biogrep-1.0.ebuild new file mode 100644 index 000000000000..b2161dcaae5b --- /dev/null +++ b/sci-biology/biogrep/biogrep-1.0.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Multithreading application for matching large sets of patterns +against biosequence dbs." +HOMEPAGE="http://web.mit.edu/bamel/biogrep.shtml" +SRC_URI="http://web.mit.edu/bamel/${P}.tar.gz" +LICENSE="GPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +src_install() { + emake prefix="${D}"/usr install || die "install failed" + dodoc AUTHORS ChangeLog NEWS README || die "dodoc failed" +} diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml new file mode 100644 index 000000000000..173e3b48f53e --- /dev/null +++ b/sci-biology/biogrep/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +<maintainer> + <email>jlec@gentoo.org</email> +</maintainer> +</pkgmetadata> + diff --git a/sci-biology/biojava/Manifest b/sci-biology/biojava/Manifest new file mode 100644 index 000000000000..3a20f1c431f2 --- /dev/null +++ b/sci-biology/biojava/Manifest @@ -0,0 +1,2 @@ +DIST biojava-1.6-all.jar 24571007 SHA256 2d10334fe6022d1b64219505ba4d2a32027ab7218d775878506d3e7c00f6ce7e SHA512 300bd6e02fe052c810c52cb2cc4255628bee704af187ad746b97e57941778dc3a1996b3917db021d74db8c716f94c90c94c5a5e2d4bc212c06259381045f3034 WHIRLPOOL e5a52aaa6e9a9d6780d5f55b6d164db07388e9c595296d4e4a11dc241aa0745fa726279d19a0c97d1966b0a14c06af2b9b588873ad522aeeff881534f0871f10 +DIST biojava-1.7-all.jar 28062592 SHA256 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f SHA512 867862b45f014bcd1afd37691e91b948ede05e96f84c7051953d32dad49908781235aad80301e22a15fa8b4145e80c78cf3935d6e581a2e60b56c9308f8adaa8 WHIRLPOOL 5669293ce362e82562454c5902d523e69f64d90e117e75b5de844e0ef5866d250507b86f78245ac82f19932ad9aa196ad17d96a3f703187a3ab2daf00893af9b diff --git a/sci-biology/biojava/biojava-1.6.ebuild b/sci-biology/biojava/biojava-1.6.ebuild new file mode 100644 index 000000000000..edfadace1dcc --- /dev/null +++ b/sci-biology/biojava/biojava-1.6.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +# TODO: +# -Fix javadoc generation OutOfMemoryError +# -Add launchers for 2 apps in biojava-apps.jar +# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag) + +EAPI=2 + +#JAVA_PKG_IUSE="doc source test" +JAVA_PKG_IUSE="source test" + +inherit eutils java-pkg-2 java-ant-2 + +DESCRIPTION="A Java framework for processing biological data" +HOMEPAGE="http://biojava.org" +SRC_URI="http://www.biojava.org/download/bj16/all/${P}-all.jar" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +COMMON_DEPEND="dev-java/jgrapht:0 + dev-java/commons-cli:1 + dev-java/commons-dbcp:0 + dev-java/commons-pool:0 + dev-java/bytecode:0" + +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPEND}" +DEPEND=">=virtual/jdk-1.5 + app-arch/unzip + ${COMMON_DEPEND} + test? + ( + dev-java/junit:4 + dev-java/ant-junit4 + )" + +S="${WORKDIR}/biojava-live_${PV}" + +JAVA_ANT_IGNORE_SYSTEM_CLASSES="true" + +src_prepare() { + einfo "Removing budled jars." + find . -name "*.jar" -print -delete + rm -r doc/* + java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar + java-pkg_jar-from commons-cli-1 + java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar + java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar + java-pkg_jar-from bytecode +} + +src_compile() { + #ANT_OPTS="${ANT_OPTS} -Xmx512m" + eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all) +} + +src_install() { + java-pkg_newjar ant-build/biojava.jar ${PN}.jar + java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar + java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar + #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos} + use source && java-pkg_dosrc {src,apps,demos}/org +} + +src_test() { + java-pkg_jar-from junit-4 junit.jar junit-4.4.jar + ANT_TASKS="ant-junit4" eant runtests +} diff --git a/sci-biology/biojava/biojava-1.7.ebuild b/sci-biology/biojava/biojava-1.7.ebuild new file mode 100644 index 000000000000..77ff74c2d159 --- /dev/null +++ b/sci-biology/biojava/biojava-1.7.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +# TODO: +# -Fix javadoc generation OutOfMemoryError +# -Add launchers for 2 apps in biojava-apps.jar +# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag) + +EAPI=2 + +#JAVA_PKG_IUSE="doc source test" +JAVA_PKG_IUSE="source test" + +inherit eutils java-pkg-2 java-ant-2 + +DESCRIPTION="A Java framework for processing biological data" +HOMEPAGE="http://biojava.org" +SRC_URI="http://www.biojava.org/download/bj17/all/${P}-all.jar" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +COMMON_DEPEND="dev-java/jgrapht:0 + dev-java/commons-cli:1 + dev-java/commons-dbcp:0 + dev-java/commons-pool:0 + dev-java/commons-collections:0 + dev-java/bytecode:0" + +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEPEND}" +DEPEND=">=virtual/jdk-1.5 + app-arch/unzip + ${COMMON_DEPEND} + test? + ( + dev-java/junit:4 + dev-java/ant-junit4 + )" + +S="${WORKDIR}/biojava-${PV}" + +JAVA_ANT_IGNORE_SYSTEM_CLASSES="true" + +src_prepare() { + einfo "Removing bundled jars..." + find . -name "*.jar" -print -delete + java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar + java-pkg_jar-from commons-cli-1 + java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar + java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar + java-pkg_jar-from bytecode +} + +src_compile() { + #ANT_OPTS="${ANT_OPTS} -Xmx512m" + eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all) +} + +src_install() { + java-pkg_newjar ant-build/biojava.jar ${PN}.jar + java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar + java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar + #use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos} + use source && java-pkg_dosrc {src,apps,demos}/org +} + +src_test() { + java-pkg_jar-from junit-4 junit.jar junit-4.4.jar + ANT_TASKS="ant-junit4" eant runtests +} diff --git a/sci-biology/biojava/metadata.xml b/sci-biology/biojava/metadata.xml new file mode 100644 index 000000000000..0a18364544e8 --- /dev/null +++ b/sci-biology/biojava/metadata.xml @@ -0,0 +1,6 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <herd>java</herd> +</pkgmetadata> diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest new file mode 100644 index 000000000000..b189a8ae405f --- /dev/null +++ b/sci-biology/bioperl-db/Manifest @@ -0,0 +1 @@ +DIST BioPerl-DB-1.006900.tar.gz 492799 SHA256 50df2447b7f3e26aebcf02ed7344d3ef562c3f5393c1584a8ae086185c8c9139 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 WHIRLPOOL b484ce9f464a7189e5b2fffd6facdd426e8b9009ffca5e1661986490bc45dc0269faec5e9eeebdb23ec5c706f62a670fbb6bfc5a60b11c268c7e6f34bf1f03f2 diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild new file mode 100644 index 000000000000..b78237d1e434 --- /dev/null +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-DB +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="test" +SRC_TEST="do" + +CDEPEND=" + >=sci-biology/bioperl-${PV} + dev-perl/DBD-mysql + dev-perl/DBI + sci-biology/biosql" +DEPEND="${CDEPEND} + dev-perl/Module-Build" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild new file mode 100644 index 000000000000..aad5b6e4abe5 --- /dev/null +++ b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/bioperl/${PN}.git + https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +CDEPEND=">=sci-biology/bioperl-${PV} + dev-perl/DBI + sci-biology/biosql" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-db-${PV}" + +src_configure() { + # This disables tests. TODO: Enable tests + sed -i -e '/biosql_conf();/d' \ + -e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml new file mode 100644 index 000000000000..642468c809b7 --- /dev/null +++ b/sci-biology/bioperl-db/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="cpan">BioPerl-DB</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl-network/Manifest b/sci-biology/bioperl-network/Manifest new file mode 100644 index 000000000000..54877a23bece --- /dev/null +++ b/sci-biology/bioperl-network/Manifest @@ -0,0 +1 @@ +DIST BioPerl-Network-1.006900.tar.gz 2198089 SHA256 5b31ab7d048ee8e7bd6ba933f96b904d7ee06b46ab29c00276eca3513a77c32a SHA512 d0a95af17cb024cbc615c784f1dbcddd7bfc5b54524163ab127f1077ded18df222fe067c085f3dd17dd416d6417b8f726526be164e1e33144991393f6b6d5842 WHIRLPOOL 65ff9e2509c0136232b7cff1aa5e8ad55f26241f51e70e6d34f9383c0af4bfdb0c5358b1a69075d480e9e1fdfa19342058fbe33ea4d4a633220ef3a80d6ed984 diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild new file mode 100644 index 000000000000..285db499bff4 --- /dev/null +++ b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-Network +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="test" +SRC_TEST="do" + +CDEPEND=">=sci-biology/bioperl-${PV} + >=dev-perl/Graph-0.86" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS" + perl-module_src_install +} diff --git a/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild new file mode 100644 index 000000000000..5b93a4ddbeed --- /dev/null +++ b/sci-biology/bioperl-network/bioperl-network-9999-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/bioperl/${PN}.git + https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="test" +SRC_TEST="do" + +CDEPEND=">=sci-biology/bioperl-${PV} + >=dev-perl/Graph-0.86" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-network-${PV}" + +src_install() { + mydoc="AUTHORS BUGS" + perl-module_src_install +} diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml new file mode 100644 index 000000000000..045af7cc6148 --- /dev/null +++ b/sci-biology/bioperl-network/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="cpan">BioPerl-Network</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest new file mode 100644 index 000000000000..bd1970f7c390 --- /dev/null +++ b/sci-biology/bioperl-run/Manifest @@ -0,0 +1 @@ +DIST BioPerl-Run-1.006900.tar.gz 14546677 SHA256 6eddca8aae38a139caaa0b28505e2ff3e919e8ed39b7539a662b0145f1f08d96 SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c WHIRLPOOL a671180b3680d94683e771ba661e0f86430814200efcd8df1552dbc3c30228d90ea8be1b47cc36603cbfc6eadacb276414ae6d79e30ec80495fd836eb1732cca diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild new file mode 100644 index 000000000000..d633fe3be7a1 --- /dev/null +++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +BIOPERL_RELEASE=1.6.9 + +MY_PN=BioPerl-Run +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.006900 +inherit perl-module + +DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications" +HOMEPAGE="http://www.bioperl.org/" + +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="-minimal test" +#SRC_TEST="do" + +RESTRICT="test" + +CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE} + !minimal? ( + dev-perl/Algorithm-Diff + dev-perl/XML-Twig + dev-perl/IO-String + dev-perl/IPC-Run + dev-perl/File-Sort + )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install + # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) + # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D + #find "${D}" -name '*ConfigData*' -print -delete +} diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild new file mode 100644 index 000000000000..13c3ca1477da --- /dev/null +++ b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/bioperl/${PN}.git + https://github.com/bioperl/${PN}.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="-minimal test" +#SRC_TEST="do" + +RESTRICT="test" + +CDEPEND=">=sci-biology/bioperl-${PV} + !minimal? ( + dev-perl/Algorithm-Diff + dev-perl/XML-Twig + dev-perl/IO-String + dev-perl/IPC-Run + )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/BioPerl-run-${PV}" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install + # TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file) + # with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D + find "${D}" -name '*ConfigData*' -print -delete +} diff --git a/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff new file mode 100644 index 000000000000..5683347a6b52 --- /dev/null +++ b/sci-biology/bioperl-run/files/bioperl-run-Pise-test-patch.diff @@ -0,0 +1,22 @@ +--- Makefile.PL.original 2003-09-28 23:33:16.000000000 -0400 ++++ Makefile.PL 2003-09-28 23:33:50.000000000 -0400 +@@ -73,19 +73,6 @@ + my $DISTNAME = "bioperl-run"; + my $VERSION = "1.2.2"; + +-my $proceed = prompt("Do you want to run the Pise tests (requires a network connection) y/n",'n'); +-if( $proceed =~ /^[yY]/) { +- my $address = prompt("Enter your email address (no default)",''); +- +- if (open T,">t/pise-email.test") { +-print T "$address\n"; +-close T; +- } else { warn("Cannot open file t/pise-email.test for writing - no Pise tests will be run"); } +-} else { +- if( -e "t/pise-email.test" ) { +-unlink "t/pise-email.test"; +- } +-} + #$do_autoload_finesse = 0; + #$NAME = 'Bio'; + #$DISTNAME = "GFD"; diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml new file mode 100644 index 000000000000..f8c7078a2813 --- /dev/null +++ b/sci-biology/bioperl-run/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="cpan">BioPerl-Run</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest new file mode 100644 index 000000000000..756ab900c480 --- /dev/null +++ b/sci-biology/bioperl/Manifest @@ -0,0 +1 @@ +DIST BioPerl-1.6.901.tar.gz 12284856 SHA256 8c74bde900222ce3926491ee103997c841c8755148c8dcaf0be1abfd61c5ac01 SHA512 227387437c940da1435ed83fad6ec2168ca12a729c90dc557e84750c6474213874c23a8f23e50db4027909469627baee581faa11be6208c8e0a5453a01c7eca4 WHIRLPOOL feb1f93a617e0135ab84b0eeb36ac986e817ce76ada0f40518090f6a480fbb1047339b33fcd11ccff444f89c4a06c41b5abaab66b662a50f17ae34f9b22d66fd diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild new file mode 100644 index 000000000000..afaa8236b5a2 --- /dev/null +++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +MY_PN=BioPerl +MODULE_AUTHOR=CJFIELDS +MODULE_VERSION=1.6.901 +inherit perl-module + +SUBPROJECTS="+db +network +run" +MIN_PV=$PV + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" + +REQUIRED_USE="minimal? ( !graphviz )" + +CDEPEND=" + dev-perl/libwww-perl + !minimal? ( + dev-perl/Algorithm-Munkres + dev-perl/Array-Compare + dev-perl/yaml + dev-perl/Bio-ASN1-EntrezGene + dev-perl/Clone + dev-perl/Convert-Binary-C + dev-perl/Data-Stag + dev-perl/GD + dev-perl/Graph + >=dev-perl/HTML-Parser-3.60 + dev-perl/List-MoreUtils + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/set-scalar + dev-perl/SOAP-Lite + dev-perl/Sort-Naturally + dev-perl/Spreadsheet-ParseExcel + >=virtual/perl-Storable-2.05 + >=dev-perl/SVG-2.26 + >=dev-perl/SVG-Graph-0.01 + dev-perl/URI + >=dev-perl/XML-DOM-XPath-0.13 + dev-perl/XML-Parser + >=dev-perl/XML-SAX-0.15 + dev-perl/XML-Simple + dev-perl/XML-Twig + >=dev-perl/XML-Writer-0.4 + dev-perl/XML-DOM + dev-perl/XML-XPath + ) + graphviz? ( dev-perl/GraphViz ) + sqlite? ( dev-perl/DBD-SQLite )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" +PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} ) + network? ( >=sci-biology/bioperl-network-${MIN_PV} ) + run? ( >=sci-biology/bioperl-run-${MIN_PV} )" + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild new file mode 100644 index 000000000000..1cf70db6b533 --- /dev/null +++ b/sci-biology/bioperl/bioperl-9999-r1.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module git-2 + +SUBPROJECTS="+db +network +run" + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/" +SRC_URI="" +EGIT_REPO_URI="git://github.com/${PN}/${PN}-live.git + https://github.com/${PN}/${PN}-live.git" + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="-minimal graphviz ${SUBPROJECTS}" + +CDEPEND=" + dev-perl/Data-Stag + dev-perl/libwww-perl + !minimal? ( + dev-perl/Ace + dev-perl/Bio-ASN1-EntrezGene + dev-perl/Spreadsheet-ParseExcel + dev-perl/Spreadsheet-WriteExcel + >=dev-perl/XML-SAX-0.15 + dev-perl/Graph + dev-perl/SOAP-Lite + dev-perl/Array-Compare + dev-perl/SVG + dev-perl/XML-Simple + dev-perl/XML-Parser + dev-perl/XML-Twig + >=dev-perl/HTML-Parser-3.60 + >=dev-perl/XML-Writer-0.4 + dev-perl/Clone + dev-perl/XML-DOM + dev-perl/set-scalar + dev-perl/XML-XPath + dev-perl/XML-DOM-XPath + dev-perl/Algorithm-Munkres + dev-perl/Data-Stag + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/Convert-Binary-C + dev-perl/SVG-Graph + ) + graphviz? ( dev-perl/GraphViz )" +DEPEND="dev-perl/Module-Build + ${CDEPEND}" +RDEPEND="${CDEPEND}" +PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) + db? ( >=sci-biology/bioperl-db-${PV} ) + network? ( >=sci-biology/bioperl-network-${PV} ) + run? ( >=sci-biology/bioperl-run-${PV} )" + +S="${WORKDIR}/BioPerl-${PV}" + +src_configure() { + sed -i -e '/add_post_install_script.*symlink_script.pl/d' \ + -e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" \ + -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" \ + || die + if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml new file mode 100644 index 000000000000..210ba364d45f --- /dev/null +++ b/sci-biology/bioperl/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="run">Install sci-biology/bioperl-run</flag> + <flag name="network">Install sci-biology/bioperl-run</flag> + <flag name="db">Install sci-biology/bioperl-run</flag> + </use> + <upstream> + <remote-id type="cpan">BioPerl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest new file mode 100644 index 000000000000..e835e2490342 --- /dev/null +++ b/sci-biology/biopython/Manifest @@ -0,0 +1 @@ +DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2 diff --git a/sci-biology/biopython/biopython-1.65.ebuild b/sci-biology/biopython/biopython-1.65.ebuild new file mode 100644 index 000000000000..9c23f0bd0635 --- /dev/null +++ b/sci-biology/biopython/biopython-1.65.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} pypy ) + +inherit distutils-r1 eutils + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/" +SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/matplotlib[$(python_gen_usedep 'python*')] + dev-python/networkx[$(python_gen_usedep 'python*')] + dev-python/numpy[$(python_gen_usedep 'python*')] + dev-python/rdflib[$(python_gen_usedep 'python*')] + dev-python/pygraphviz[$(python_gen_usedep 'python2*')] + dev-python/reportlab[$(python_gen_usedep 'python*')] + media-gfx/pydot[$(python_gen_usedep 'python2*')] + " +DEPEND="${RDEPEND} + sys-devel/flex" + +DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) + +PATCHES=( "${FILESDIR}"/${P}-test-fix-backport.patch ) + +python_test() { + [[ ${EPYTHON} == pypy ]] && return + cd Tests || die + ${PYTHON} run_tests.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + dodir /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die +} + +pkg_postinst() { + elog "For database support you need to install:" + optfeature "MySQL" dev-python/mysql-python + optfeature "PostGreSQL" dev-python/psycopg + echo + elog "Some applications need extra packages:" + optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss +} diff --git a/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch new file mode 100644 index 000000000000..2efdef97d799 --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.65-test-fix-backport.patch @@ -0,0 +1,40 @@ +From 08c72f8778a87701586a03dffcce33c7589bc6d7 Mon Sep 17 00:00:00 2001 +From: Peter Cock <p.j.a.cock@googlemail.com> +Date: Sun, 18 Jan 2015 02:07:54 +0000 +Subject: [PATCH] Clearer error message; update failing test. + +One of the orchid examples now returns different enough +results that the test was failing. The new error message +makes it much easier to pick another positive example to +add to the the white-list. +--- + Tests/test_NCBI_qblast.py | 9 +++++---- + 1 file changed, 5 insertions(+), 4 deletions(-) + +diff --git a/Tests/test_NCBI_qblast.py b/Tests/test_NCBI_qblast.py +index 88bfe61..19f7b35 100644 +--- a/Tests/test_NCBI_qblast.py ++++ b/Tests/test_NCBI_qblast.py +@@ -66,7 +66,7 @@ def test_orchid_est(self): + AGCCATGGATTTCTCAGAAGAAAATGATTATACTTCTTAATCAGGCAACTGATATTATCAATTTATGGCA + GCAGAGTGGTGGCTCCTTGTCCCAGCAGCAGTAATTACTTTTTTTTCTCTTTTTGTTTCCAAATTAAGAA + ACATTAGTATCATATGGCTATTTGCTCAATTGCAGATTTCTTTCTTTTGTGAATG""", +- 0.0000001, None, ["21554275", "18409071", "296087288"]) ++ 0.0000001, None, ["21554275", "18409071", "296087288", "566183510"]) + + def run_qblast(self, program, database, query, e_value, entrez_filter, expected_hits): + try: +@@ -120,9 +120,10 @@ def run_qblast(self, program, database, query, e_value, entrez_filter, expected_ + print("Update this test to have some redundancy...") + for alignment in record.alignments: + print(alignment.hit_id) +- assert found_result, "Missing all of %s in alignments" \ +- % ", ".join(expected_hits) +- self.assertTrue(found_result) ++ self.assertTrue(found_result, ++ "Missing all expected hits (%s), instead have: %s" ++ % (", ".join(expected_hits), ++ ", ".join(a.hit_id for a in record.alignments))) + + # Check the expected result(s) are found in the descriptions + if expected_hits is None: diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/biopython/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/bioruby/Manifest b/sci-biology/bioruby/Manifest new file mode 100644 index 000000000000..9c1f1499ea6f --- /dev/null +++ b/sci-biology/bioruby/Manifest @@ -0,0 +1 @@ +DIST bioruby-1.4.3.0001.tar.gz 1500656 SHA256 20d6548e1c5977464afd74019693dde9e45a030d48d974db08a7b85c4214fb35 SHA512 77ad96388e1e8b1dccab582a3bc309b99b36cac1803f79b42707fc4dbf439de31ed491ce5e1c2e59f695643756ae0df2e275bbcd9ad6827f251b52edd677d821 WHIRLPOOL ccb952d4cd3b8700acbf356a0965842b068aa2fb861dfab58e7442e5570ab79604a8be1fb86a9d80d6bc9a8f9dc886daf98cb84fe7298b4f334e0e6be198f9e7 diff --git a/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild new file mode 100644 index 000000000000..b50f3fa137fb --- /dev/null +++ b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +USE_RUBY="ruby19 ruby20" + +inherit ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://www.bioruby.org/" +SRC_URI="http://www.${PN}.org/archive/${P}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="amd64 ~ppc x86" + +ruby_add_rdepend "dev-ruby/libxml" + +PATCHES=( "${FILESDIR}"/${P}-fix-tests.patch ) + +each_ruby_configure() { + ${RUBY} setup.rb config || die +} + +each_ruby_compile() { + ${RUBY} setup.rb setup || die +} + +each_ruby_install() { + ${RUBY} setup.rb install --prefix="${D}" || die +} + +each_ruby_test() { + ${RUBY} -rubygems test/runner.rb || die +} diff --git a/sci-biology/bioruby/bioruby-9999.ebuild b/sci-biology/bioruby/bioruby-9999.ebuild new file mode 100644 index 000000000000..838f8430c972 --- /dev/null +++ b/sci-biology/bioruby/bioruby-9999.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +USE_RUBY="ruby19 ruby20" +EGIT_REPO_URI="git://github.com/bioruby/bioruby.git + https://github.com/bioruby/bioruby.git" + +inherit git-2 ruby-fakegem + +DESCRIPTION="An integrated environment for bioinformatics using the Ruby language" +LICENSE="Ruby" +HOMEPAGE="http://www.bioruby.org/" +SRC_URI="" +SLOT="0" +IUSE="" +KEYWORDS="" + +ruby_add_rdepend "dev-ruby/libxml" + +all_ruby_unpack() { + git-2_src_unpack +} + +each_ruby_configure() { + ${RUBY} setup.rb config || die +} + +each_ruby_compile() { + ${RUBY} setup.rb setup || die +} + +each_ruby_install() { + ${RUBY} setup.rb install --prefix="${D}" || die +} + +each_ruby_test() { + ${RUBY} -rubygems test/runner.rb || die +} diff --git a/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch new file mode 100644 index 000000000000..71c4ca27104a --- /dev/null +++ b/sci-biology/bioruby/files/bioruby-1.4.3.0001-fix-tests.patch @@ -0,0 +1,29 @@ +From edda65b8fb32c2eee6b0652074981c31aa68b0eb Mon Sep 17 00:00:00 2001 +From: Naohisa Goto <ng@bioruby.org> +Date: Fri, 23 Aug 2013 23:51:59 +0900 +Subject: [PATCH] Test bug fix: Read test file with binary mode to avoid + encoding error + + * Test bug fix: Read test file with binary mode to avoid string encoding + error. Thanks to nieder (github.com/nieder) who reports the bug. + (https://github.com/bioruby/bioruby/issues/84) +--- + test/unit/bio/db/test_phyloxml.rb | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/unit/bio/db/test_phyloxml.rb b/test/unit/bio/db/test_phyloxml.rb +index 0744c64..c24278d 100644 +--- a/test/unit/bio/db/test_phyloxml.rb ++++ b/test/unit/bio/db/test_phyloxml.rb +@@ -100,7 +100,7 @@ def test_open_with_block + end + + def test_new +- str = File.read(TestPhyloXMLData.example_xml) ++ str = File.open(TestPhyloXMLData.example_xml, "rb") { |f| f.read } + assert_instance_of(Bio::PhyloXML::Parser, + phyloxml = Bio::PhyloXML::Parser.new(str)) + common_test_next_tree(phyloxml) +-- +1.8.4 + diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml new file mode 100644 index 000000000000..d4648212cbad --- /dev/null +++ b/sci-biology/bioruby/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/biosql/Manifest b/sci-biology/biosql/Manifest new file mode 100644 index 000000000000..cd5198309e65 --- /dev/null +++ b/sci-biology/biosql/Manifest @@ -0,0 +1 @@ +DIST biosql-1.0.1.tar.bz2 253516 SHA256 3604ceaf6f3e42a11613b49577b7c68f04d9e094cca4e5d932359c815fc9ad01 diff --git a/sci-biology/biosql/biosql-1.0.1.ebuild b/sci-biology/biosql/biosql-1.0.1.ebuild new file mode 100644 index 000000000000..ed77d3770701 --- /dev/null +++ b/sci-biology/biosql/biosql-1.0.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A generic bioinformatics relational database model" +HOMEPAGE="http://www.biosql.org/" +SRC_URI="http://biosql.org/DIST/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0" +IUSE="mysql postgres" +KEYWORDS="amd64 x86" + +# WARNING: bioperl-db is claimed to be incompatible with >=postgresql-8.3 (see INSTALL) + +DEPEND="mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg )" +RDEPEND="${DEPEND}" + +src_install() { + insinto /usr/share/${PN} + doins -r sql scripts/* || die + insinto /usr/share/doc/${P} + doins -r doc/* + dodoc Changes INSTALL README Release.txt +} + +pkg_postinst() { + echo + elog "Please read the BioSQL schema installation instructions in" + elog "/usr/share/doc/${P} to begin using the schema." + echo +} diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/biosql/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest new file mode 100644 index 000000000000..c1b249e1a095 --- /dev/null +++ b/sci-biology/blat/Manifest @@ -0,0 +1 @@ +DIST blatSrc34.zip 2142975 SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild new file mode 100644 index 000000000000..c61327420f26 --- /dev/null +++ b/sci-biology/blat/blat-34-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_PN="${PN}Src" + +DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" +HOMEPAGE="http://www.cse.ucsc.edu/~kent/" +SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" + +SLOT="0" +LICENSE="blat" +KEYWORDS="~amd64 ~x86 ~x64-macos" +IUSE="" + +S="${WORKDIR}/${MY_PN}" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + sed \ + -e "1i\CFLAGS=${CFLAGS}" \ + -e "1i\LDFLAGS=${LDFLAGS}" \ + -i inc/common.mk || die + tc-export CC +} + +src_compile() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + mkdir -p "${S}/bin/${MACHTYPE}" + emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + dobin "${S}/bin/${MACHTYPE}/"* +} diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild new file mode 100644 index 000000000000..41d48bf26bd3 --- /dev/null +++ b/sci-biology/blat/blat-34.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs + +DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" +LICENSE="blat" +HOMEPAGE="http://www.cse.ucsc.edu/~kent/" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +MY_PN="${PN}Src" +SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" +S="${WORKDIR}/${MY_PN}" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_compile() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk" + sed -i 's/\(${STRIP} \)/#\1/' "${S}"/{*/makefile,utils/*/makefile,*/*.mk} + mkdir -p "${S}/bin/${MACHTYPE}" + emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed" +} + +src_install() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + dobin "${S}/bin/${MACHTYPE}/"* +} diff --git a/sci-biology/blat/files/34-gentoo.patch b/sci-biology/blat/files/34-gentoo.patch new file mode 100644 index 000000000000..8bdd05bff68d --- /dev/null +++ b/sci-biology/blat/files/34-gentoo.patch @@ -0,0 +1,226 @@ + blat/makefile | 2 +- + gfClient/makefile | 2 +- + gfServer/makefile | 2 +- + hg/pslPretty/makefile | 2 +- + hg/pslReps/makefile | 2 +- + hg/pslSort/makefile | 2 +- + inc/common.mk | 11 +++-------- + makefile | 28 ++++++++++++++-------------- + utils/faToNib/makefile | 2 +- + utils/faToTwoBit/makefile | 2 +- + utils/nibFrag/makefile | 2 +- + utils/twoBitInfo/makefile | 2 +- + utils/twoBitToFa/makefile | 2 +- + 13 files changed, 28 insertions(+), 33 deletions(-) + +diff --git a/blat/makefile b/blat/makefile +index b889c7b..739503a 100644 +--- a/blat/makefile ++++ b/blat/makefile +@@ -7,7 +7,7 @@ MYLIBS = $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a + O = blat.o + + blat: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/blat${EXE} + + all: +diff --git a/gfClient/makefile b/gfClient/makefile +index c3288de..36e957e 100644 +--- a/gfClient/makefile ++++ b/gfClient/makefile +@@ -8,5 +8,5 @@ O = gfClient.o + X = gfClient + + gfClient: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} +diff --git a/gfServer/makefile b/gfServer/makefile +index c06b3a5..f042d22 100644 +--- a/gfServer/makefile ++++ b/gfServer/makefile +@@ -8,7 +8,7 @@ O = gfServer.o + X = gfServer + + gfServer: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} + + test: +diff --git a/hg/pslPretty/makefile b/hg/pslPretty/makefile +index c780b96..cbbcd0d 100644 +--- a/hg/pslPretty/makefile ++++ b/hg/pslPretty/makefile +@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = pslPretty.o + + pslPretty: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L + + test:: testRna testDnax + +diff --git a/hg/pslReps/makefile b/hg/pslReps/makefile +index 6e8f6d7..2b73b60 100644 +--- a/hg/pslReps/makefile ++++ b/hg/pslReps/makefile +@@ -9,7 +9,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = pslReps.o + + pslReps: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L + + lib: + cd ../../lib && ${MAKE} +diff --git a/hg/pslSort/makefile b/hg/pslSort/makefile +index 81fe083..eb63257 100644 +--- a/hg/pslSort/makefile ++++ b/hg/pslSort/makefile +@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = pslSort.o + + pslSort: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L + + + lib: +diff --git a/inc/common.mk b/inc/common.mk +index 1823163..3a04e2b 100644 +--- a/inc/common.mk ++++ b/inc/common.mk +@@ -1,20 +1,15 @@ +-CC=gcc +-ifeq (${COPT},) +- COPT=-O +-endif +-CFLAGS= + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} + HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type + HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc + + # Stronger warning checks, and warnings-->errors, for libraries and CGIs: + ifeq (darwin,$(findstring darwin,${OSTYPE})) +- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable ++ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable + else + ifeq (solaris,$(findstring solaris,${OSTYPE})) + HG_WARN_ERR = -DJK_WARN -Wall + else +- HG_WARN_ERR = -DJK_WARN -Wall -Werror ++ HG_WARN_ERR = -DJK_WARN -Wall + endif + endif + # Apply the stronger checks to all code on our development machine: +@@ -37,7 +32,7 @@ ifeq (${BINDIR},) + endif + MKDIR=mkdir -p + ifeq (${STRIP},) +- STRIP=strip ++ STRIP=true + endif + CVS=cvs + +diff --git a/makefile b/makefile +index 6f9fddf..dded1cd 100644 +--- a/makefile ++++ b/makefile +@@ -1,18 +1,18 @@ + all: +- cd lib && ${MAKE} +- cd jkOwnLib && ${MAKE} +- cd blat && $(MAKE) +- cd gfClient && $(MAKE) +- cd gfServer && $(MAKE) +- cd hg/pslPretty && $(MAKE) +- cd hg/pslReps && $(MAKE) +- cd hg/pslSort && $(MAKE) +- cd utils/nibFrag && $(MAKE) +- cd utils/faToNib && $(MAKE) +- cd utils/faToTwoBit && $(MAKE) +- cd utils/twoBitToFa && $(MAKE) +- cd utils/twoBitInfo && $(MAKE) +- cd webBlat && $(MAKE) ++ $(MAKE) -C lib ++ $(MAKE) -C jkOwnLib ++ $(MAKE) -C blat ++ $(MAKE) -C gfClient ++ $(MAKE) -C gfServer ++ $(MAKE) -C hg/pslPretty ++ $(MAKE) -C hg/pslReps ++ $(MAKE) -C hg/pslSort ++ $(MAKE) -C utils/nibFrag ++ $(MAKE) -C utils/faToNib ++ $(MAKE) -C utils/faToTwoBit ++ $(MAKE) -C utils/twoBitToFa ++ $(MAKE) -C utils/twoBitInfo ++ $(MAKE) -C webBlat + + clean: + rm -f */*.o */*/*.o +diff --git a/utils/faToNib/makefile b/utils/faToNib/makefile +index fd0e3eb..63a1593 100644 +--- a/utils/faToNib/makefile ++++ b/utils/faToNib/makefile +@@ -8,4 +8,4 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = faToNib.o + + faToNib: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L +diff --git a/utils/faToTwoBit/makefile b/utils/faToTwoBit/makefile +index b1b44a9..1e8c1c8 100644 +--- a/utils/faToTwoBit/makefile ++++ b/utils/faToTwoBit/makefile +@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + O = faToTwoBit.o + + faToTwoBit: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/faToTwoBit${EXE} + + clean: +diff --git a/utils/nibFrag/makefile b/utils/nibFrag/makefile +index 260a6f3..e37b9ab 100755 +--- a/utils/nibFrag/makefile ++++ b/utils/nibFrag/makefile +@@ -4,7 +4,7 @@ include ../../inc/common.mk + O = nibFrag.o + + nibFrag: $(O) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a + + + +diff --git a/utils/twoBitInfo/makefile b/utils/twoBitInfo/makefile +index 649784f..9434d1c 100644 +--- a/utils/twoBitInfo/makefile ++++ b/utils/twoBitInfo/makefile +@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + O = twoBitInfo.o + + twoBitInfo: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/twoBitInfo${EXE} + + clean: +diff --git a/utils/twoBitToFa/makefile b/utils/twoBitToFa/makefile +index cf979f2..081f3b8 100644 +--- a/utils/twoBitToFa/makefile ++++ b/utils/twoBitToFa/makefile +@@ -8,7 +8,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + O = twoBitToFa.o + + twoBitToFa: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L + #${STRIP} ${BINDIR}/twoBitToFa${EXE} + + clean: diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/blat/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest new file mode 100644 index 000000000000..96859ca6bf5f --- /dev/null +++ b/sci-biology/blossoc/Manifest @@ -0,0 +1 @@ +DIST blossoc-1.4.0.tar.gz 194885 SHA256 b23f51349f72f31263b8aca162c7590a5f52b72fd5e0d91b4a2591098ff5bdbe diff --git a/sci-biology/blossoc/blossoc-1.4.0.ebuild b/sci-biology/blossoc/blossoc-1.4.0.ebuild new file mode 100644 index 000000000000..7e5b6694d395 --- /dev/null +++ b/sci-biology/blossoc/blossoc-1.4.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit autotools eutils + +DESCRIPTION="A linkage disequilibrium association mapping tool" +HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/" +SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="sci-libs/gsl + dev-libs/boost + sci-biology/snpfile" +RDEPEND="${DEPEND}" + +src_prepare() { + sed -i '/TESTS += first_test.sh/ d' "${S}/Makefile.am" || die + epatch "${FILESDIR}"/${P}-gcc43.patch + eautoreconf +} + +src_install() { + emake install DESTDIR="${D}" || die "emake install failed" +} diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch new file mode 100644 index 000000000000..d8e354c1745f --- /dev/null +++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch @@ -0,0 +1,15 @@ +Fixes build with >=GCC-4.3 + +http://bugs.gentoo.org/show_bug.cgi?id=292949 + +Patch written by Sebastian Luther <SebastianLuther@gmx.de> +--- pph.cc ++++ pph.cc +@@ -23,6 +23,7 @@ + */ + + #include "pph.hh" ++#include <cstdio> + #include <cmath> + #include <snpfile/matrix.hh> + using namespace BiRC::SNPFile; diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/blossoc/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest new file mode 100644 index 000000000000..1345a9e07e4e --- /dev/null +++ b/sci-biology/bowtie/Manifest @@ -0,0 +1,2 @@ +DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800 +DIST bowtie-1.0.0-src.zip 7710572 SHA256 51e434a78e053301f82ae56f4e94f71f97b19f7175324777a7305c8f88c5bac5 SHA512 d867a61c9d4caa2fbe8161b93acc9ccf04294055796a82ccf8d6456019e97299d90d9f16492f873606ae394bbc735108fc97ddf4e5d576a7376f3f9744118831 WHIRLPOOL a70d6516db8ee0c8838795e3b1df0ae1986342cee5dcafd80a39b06cb07ece79d7ebfc6e88b36625d9b33f4f42f559364f42dd4d881fd729c27eac9e673951a1 diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild new file mode 100644 index 000000000000..c26c986ed194 --- /dev/null +++ b/sci-biology/bowtie/bowtie-0.12.8.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="An ultrafast memory-efficient short read aligner" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86 ~x64-macos" + +DEPEND="app-arch/unzip" +RDEPEND="" + +# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de) +# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc-47.patch +} + +src_compile() { + unset CFLAGS + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="" +} + +src_install() { + dobin bowtie bowtie-* + exeinto /usr/share/${PN}/scripts + doexe scripts/* + newman MANUAL bowtie.1 + dodoc AUTHORS NEWS TUTORIAL +} diff --git a/sci-biology/bowtie/bowtie-1.0.0.ebuild b/sci-biology/bowtie/bowtie-1.0.0.ebuild new file mode 100644 index 000000000000..b8181190243c --- /dev/null +++ b/sci-biology/bowtie/bowtie-1.0.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="An ultrafast memory-efficient short read aligner" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~x64-macos" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_compile() { + unset CFLAGS + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" +} + +src_install() { + dobin bowtie bowtie-* + exeinto /usr/share/${PN}/scripts + doexe scripts/* + + insinto /usr/share/${PN} + doins -r genomes indexes + + newman MANUAL bowtie.1 + dodoc AUTHORS NEWS TUTORIAL doc/README + dohtml doc/{manual.html,style.css} +} diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch new file mode 100644 index 000000000000..3c8a1e1d9ca4 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch @@ -0,0 +1,45 @@ + alphabet.h | 24 ++++++++++++------------ + 1 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/alphabet.h b/alphabet.h +index b464ddf..08d0281 100644 +--- a/alphabet.h ++++ b/alphabet.h +@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) { + return s_rc; + } + ++/// Reverse a string in-place ++template <typename TStr> ++static inline void reverseInPlace(TStr& s) { ++ typedef typename Value<TStr>::Type TVal; ++ size_t len = length(s); ++ for(size_t i = 0; i < (len>>1); i++) { ++ TVal tmp = s[i]; ++ s[i] = s[len-i-1]; ++ s[len-i-1] = tmp; ++ } ++} ++ + /** + * Reverse-complement s in-place. Ns go to Ns. + */ +@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) { + } + } + +-/// Reverse a string in-place +-template <typename TStr> +-static inline void reverseInPlace(TStr& s) { +- typedef typename Value<TStr>::Type TVal; +- size_t len = length(s); +- for(size_t i = 0; i < (len>>1); i++) { +- TVal tmp = s[i]; +- s[i] = s[len-i-1]; +- s[len-i-1] = tmp; +- } +-} +- + /** + * Return the reverse-complement of s. + */ diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml new file mode 100644 index 000000000000..e493417070fb --- /dev/null +++ b/sci-biology/bowtie/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">bowtie-bio</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest new file mode 100644 index 000000000000..9c0d995bfb1f --- /dev/null +++ b/sci-biology/bwa/Manifest @@ -0,0 +1 @@ +DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0 diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild new file mode 100644 index 000000000000..76ed0cca912b --- /dev/null +++ b/sci-biology/bwa/bwa-0.7.12.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" +HOMEPAGE="http://bio-bwa.sourceforge.net/" +SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86 ~x64-macos" + +PATCHES=( "${FILESDIR}"/${P}-Makefile.patch ) + +src_prepare() { + epatch ${PATCHES[@]} + tc-export CC AR +} + +src_install() { + dobin bwa + + doman bwa.1 + + exeinto /usr/libexec/${PN} + doexe qualfa2fq.pl xa2multi.pl + + dodoc NEWS.md README-alt.md README.md +} diff --git a/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch new file mode 100644 index 000000000000..406e9b052376 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.12-Makefile.patch @@ -0,0 +1,27 @@ +--- Makefile ++++ Makefile +@@ -1,8 +1,8 @@ +-CC= gcc ++CC?= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS?= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar ++AR?= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o + AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -26,10 +26,10 @@ + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml new file mode 100644 index 000000000000..97a33fbf5c42 --- /dev/null +++ b/sci-biology/bwa/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest new file mode 100644 index 000000000000..c3cf3842c604 --- /dev/null +++ b/sci-biology/cd-hit/Manifest @@ -0,0 +1,3 @@ +DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 RMD160 118a37f44795db666cb9c6b53a5d29f4e72b73cb SHA1 5cd6e51390a7cee860fe97a51480d28f49bdcf61 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281 +DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 RMD160 00fca8d2527a4a6b1eda861f8f750e10ee565ae7 SHA1 743c4b6ec79b9d5acd1e1171587e96c03e3e3003 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a +DIST cd-hit-v4.6-2012-04-25.tgz 652228 RMD160 318239a9416fd3cd57754546c8fcc0a4cea7f5d8 SHA1 e47c662c0a284ae99e47205d6a4eaea805a76cae SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9 diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild new file mode 100644 index 000000000000..d47948f0d821 --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2011-01-31" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Clustering Database at High Identity with Tolerance" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="openmp" + +S="${WORKDIR}"/${RELEASE} + +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + +src_prepare() { + tc-export CXX + use openmp || append-flags -DNO_OPENMP + epatch "${FILESDIR}"/${PV}-gentoo.patch +} + +src_compile() { + local myconf= + use openmp && myconf="openmp=yes" + emake ${myconf} || die +} + +src_install() { + dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die + dodoc ChangeLog cdhit-user-guide.pdf || die +} diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild new file mode 100644 index 000000000000..bafa3301d724 --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2011-03-07" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Clustering Database at High Identity with Tolerance" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="openmp" + +S="${WORKDIR}"/${RELEASE} + +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + +src_prepare() { + tc-export CXX + use openmp || append-flags -DNO_OPENMP + epatch "${FILESDIR}"/${PV}-gentoo.patch +} + +src_compile() { + local myconf= + use openmp && myconf="openmp=yes" + emake ${myconf} +} + +src_install() { + dodir /usr/bin + emake PREFIX="${ED}/usr/bin" install + dodoc ChangeLog cdhit-user-guide.pdf +} diff --git a/sci-biology/cd-hit/cd-hit-4.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.ebuild new file mode 100644 index 000000000000..d7dd15559c5c --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.6.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2012-04-25" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Clustering Database at High Identity with Tolerance" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="doc openmp" + +S="${WORKDIR}"/${RELEASE} + +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + +src_prepare() { + tc-export CXX + use openmp || append-flags -DNO_OPENMP + epatch "${FILESDIR}"/${PV}-gentoo.patch +} + +src_compile() { + local myconf= + use openmp && myconf="openmp=yes" + emake ${myconf} +} + +src_install() { + dodir /usr/bin + emake PREFIX="${ED}/usr/bin" install + dodoc ChangeLog + use doc && dodoc doc/* +} diff --git a/sci-biology/cd-hit/files/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch new file mode 100644 index 000000000000..c3eaf79cc8f2 --- /dev/null +++ b/sci-biology/cd-hit/files/4.5.1-gentoo.patch @@ -0,0 +1,85 @@ +diff --git a/Makefile b/Makefile +index f1eaa26..92d3130 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -O2 -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,16 +18,16 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += -ggdb + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -37,39 +37,39 @@ clean: + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c + diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch new file mode 100644 index 000000000000..5aa9b79e02ae --- /dev/null +++ b/sci-biology/cd-hit/files/4.5.4-gentoo.patch @@ -0,0 +1,98 @@ + Makefile | 36 ++++++++++++++++++------------------ + 1 files changed, 18 insertions(+), 18 deletions(-) + +diff --git a/Makefile b/Makefile +index e8bac1d..bd31093 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -O2 -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,16 +18,16 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += -ggdb + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -37,47 +37,47 @@ clean: + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div + + cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o +- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 ++ $(CXX) $(CXXFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c + + cdhit-454.o: cdhit-454.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-454.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c + + PREFIX ?= /usr/local/bin + diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch new file mode 100644 index 000000000000..7a376eb8e73c --- /dev/null +++ b/sci-biology/cd-hit/files/4.6-gentoo.patch @@ -0,0 +1,117 @@ + Makefile | 47 ++++++++++++++++++++++------------------------- + 1 files changed, 22 insertions(+), 25 deletions(-) + +diff --git a/Makefile b/Makefile +index e9796a1..97dd72b 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,16 +1,13 @@ +- +-CC = g++ -Wall -ggdb +-CC = g++ -pg +-CC = g++ ++CXX ?= g++ + + # without OpenMP +-CCFLAGS = -DNO_OPENMP ++#CXXFLAGS = -DNO_OPENMP + + # with OpenMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,22 +15,22 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += + else +-CCFLAGS += -O2 ++CXXFLAGS += + endif + + ifdef MAX_SEQ +-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ) ++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ) + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++#LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -43,47 +40,47 @@ clean: + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div + + cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o +- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454 + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c + + cdhit-454.o: cdhit-454.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-454.c++ -c ++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c + + PREFIX ?= /usr/local/bin + diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml new file mode 100644 index 000000000000..bd5607ab16b5 --- /dev/null +++ b/sci-biology/cd-hit/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> +CD-HIT is a very widely used program for clustering and comparing large sets +of protein or nucleotide sequences. CD-HIT is very fast and can handle +extremely large databases. CD-HIT helps to significantly reduce the +computational and manual efforts in many sequence analysis tasks and aids in +understanding the data structure and correct the bias within a dataset. +The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, +CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT +(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a +user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 +datasets and identifies the sequences in db2 that are similar to db1 above +a threshold. CD-HIT-454 is a program to identify natural and artificial +duplicates from pyrosequencing reads. The usage of other programs and +scripts can be found in CD-HIT user's guide. +</longdescription> + <upstream> + <remote-id type="google-code">cdhit</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest new file mode 100644 index 000000000000..2394b3a452f6 --- /dev/null +++ b/sci-biology/clustal-omega/Manifest @@ -0,0 +1,2 @@ +DIST clustal-omega-1.2.0.tar.gz 1156741 SHA256 cbf5ad4e1ce88641cca307be1edfe95d3882997d71c11b43c8e1fcd6e388c61d SHA512 d207699e1158178e2d7122620026b199251ab86bcc3f72a08d58f23e2dd5c2961340e872a13c34f1d6832c5eef5ff8ab09c43f0cb51a81d6c4ef554f936434e2 WHIRLPOOL 41505b42829d440fd312f1538ef78fb7d0f668008cd00bcc52022139eb2ff21d05d89519af2a18e5a2f845e24a5d374a81eb4163c2720a32f71ead7ce40e4eac +DIST clustal-omega-1.2.1.tar.gz 1164492 SHA256 0ef32727aa25c6ecf732083e668a0f45bc17085c28a5c7b4459f4750419f2b0a SHA512 1aa69e319f999f7cd746e2d2ffcafeafc0eb15ed4777abb5b32df63a39a23fa2091977efccfcf9428468103b8e48c4ab0a3ce3967b9c55daaadf3a6a3b57e8de WHIRLPOOL b079dcd659839a85e7772b717ef5dce25b816f2c96eb0f6eea5a4a53f2abd25fb4435291f2a7b739d72d94c06fdbd9c85300ff4cbb03b2861d31d1ad3d196577 diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild new file mode 100644 index 000000000000..ccded19116cd --- /dev/null +++ b/sci-biology/clustal-omega/clustal-omega-1.2.0.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Scalable multiple alignment of protein sequences" +HOMEPAGE="http://www.clustal.org/omega/" +SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND="dev-libs/argtable" +RDEPEND="${DEPEND}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_prepare() { + sed \ + -e "s:-O3::g" \ + -i configure.ac || die + autotools-utils_src_prepare +} + +src_install() { + autotools-utils_src_install + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + rm -fr "${ED}"/usr/$(get_libdir)/pkgconfig || die + fi +} diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild new file mode 100644 index 000000000000..e56766f9416e --- /dev/null +++ b/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Scalable multiple alignment of protein sequences" +HOMEPAGE="http://www.clustal.org/omega/" +SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND="dev-libs/argtable" +RDEPEND="${DEPEND}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_prepare() { + sed \ + -e "s:-O3::g" \ + -i configure.ac || die + autotools-utils_src_prepare +} + +src_install() { + autotools-utils_src_install + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + rm -fr "${ED}"/usr/$(get_libdir)/pkgconfig || die + fi +} diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/clustal-omega/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest new file mode 100644 index 000000000000..b1f7bb630cd0 --- /dev/null +++ b/sci-biology/clustalw-mpi/Manifest @@ -0,0 +1 @@ +DIST clustalw-mpi-0.13.tar.gz 154911 RMD160 9da3e418efcb0cfd0c5df2705ee217b9dacc3917 SHA1 ae5026e8b4ba58bb0caa5643ea90434d9589df5a SHA256 2fcb0dc0001b034f2931153654fc66d67db360f0bf3fbcde19dc389bbe145845 diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild new file mode 100644 index 000000000000..11f1e57e2731 --- /dev/null +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm" +HOMEPAGE="http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php" +SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="public-domain" +IUSE="mpi_njtree static_pairalign" + +DEPEND="virtual/mpi" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + if use mpi_njtree; then + sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ + die "Failed to configure MPI code for NJ trees." + fi + if use static_pairalign; then + sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ + die "Failed to configure static scheduling for pair alignments." + fi +} + +src_install() { + dobin ${PN} + newdoc README.${PN} README +} diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch new file mode 100644 index 000000000000..6e36061cbb39 --- /dev/null +++ b/sci-biology/clustalw-mpi/files/0.13-gentoo.patch @@ -0,0 +1,23 @@ + Makefile | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index f2107ce..835232b 100644 +--- a/Makefile ++++ b/Makefile +@@ -25,12 +25,12 @@ TREES_FLAG = -DSERIAL_NJTREE + PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN + #PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN + +-CFLAGS = -c -O3 ++CFLAGS += -c + #CFLAGS = -c -O3 -funroll-all-loops +-LFLAGS = -lm ++LIBS = -lm + + clustalw-mpi: $(OBJECTS) +- $(CC) -o $@ $(OBJECTS) $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml new file mode 100644 index 000000000000..905eba1a07b8 --- /dev/null +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-biology</herd> +<use> + <flag name='mpi_njtree'>Use MPI (as opposed to serial) code for computing + neighbor-joining trees</flag> + <flag name='static_pairalign'>Use static (as opposed to dynamic) scheduling + for pair alignments</flag> +</use> +</pkgmetadata> diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest new file mode 100644 index 000000000000..7d1b7dca8a7f --- /dev/null +++ b/sci-biology/clustalw/Manifest @@ -0,0 +1,2 @@ +DIST clustalw-2.1.tar.gz 350761 SHA256 e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921 WHIRLPOOL 93158f400cbdf11ecddcac15b5b4cee9af61d9b933f7100ad18d01d346de54c6bad5a9a12fe5a70a265c92581d3ee9cfbc41b17ee2c2ff80ff2a6658efba5f40 +DIST clustalw1.83.UNIX.tar.gz 166863 SHA256 8b757e02ae95ac0a0dd37db640497aa90f7a13a11784ce2a17f41b64e3059c60 SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a WHIRLPOOL 5a075579737d8a9ba5f62d6f90feb53a275bd31a8131d1b7d21395cf46cfefbdf4e48563b55734c995b9e3d8f9c37c78ea77f4e48920d64781190645ea36112b diff --git a/sci-biology/clustalw/clustalw-1.83-r3.ebuild b/sci-biology/clustalw/clustalw-1.83-r3.ebuild new file mode 100644 index 000000000000..6047a08ed466 --- /dev/null +++ b/sci-biology/clustalw/clustalw-1.83-r3.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="General purpose multiple alignment program for DNA and proteins" +HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz" + +LICENSE="clustalw" +SLOT="1" +KEYWORDS="alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="" + +S="${WORKDIR}"/${PN}${PV} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-as-needed.patch + + sed \ + -e "/^CC/s:cc:$(tc-getCC):g" \ + -i makefile || die + sed \ + -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \ + -i clustalw.c || die +} + +src_install() { + dobin clustalw + dodoc README clustalv.doc clustalw.doc clustalw.ms + insinto /usr/share/doc/${PF} + doins clustalw_help +} diff --git a/sci-biology/clustalw/clustalw-2.1.ebuild b/sci-biology/clustalw/clustalw-2.1.ebuild new file mode 100644 index 000000000000..8664ee3108ec --- /dev/null +++ b/sci-biology/clustalw/clustalw-2.1.ebuild @@ -0,0 +1,14 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +DESCRIPTION="General purpose multiple alignment program for DNA and proteins" +HOMEPAGE="http://www.clustal.org/" +SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" + +LICENSE="GPL-3 LGPL-3" +SLOT="2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="" diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch new file mode 100644 index 000000000000..62b4654cddea --- /dev/null +++ b/sci-biology/clustalw/files/1.83-as-needed.patch @@ -0,0 +1,17 @@ +--- makefile 2003-01-29 09:53:45.000000000 +0100 ++++ makefile.new 2009-08-17 08:33:16.000000000 +0200 +@@ -11,11 +11,11 @@ + HEADERS = general.h clustalw.h + + CC = cc +-CFLAGS = -c -O +-LFLAGS = -O -lm ++CFLAGS += -c ++LIBS = -lm + + clustalw : $(OBJECTS) amenu.o clustalw.o +- $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) + + interface.o : interface.c $(HEADERS) param.h + $(CC) $(CFLAGS) $*.c diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/clustalw/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest new file mode 100644 index 000000000000..acbf2db29963 --- /dev/null +++ b/sci-biology/clustalx/Manifest @@ -0,0 +1 @@ +DIST clustalx-2.1.tar.gz 341649 SHA256 e10adb728c320598a165ca529f1aa3d2560061de0236e0a0926eaca9554afa05 SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026 WHIRLPOOL 6cbe8dcf2be3a535e8ac0ef0b9b476d4429a80bd94b394c0194f46ed039f9ac2b97b0ec2ed680838a0973b3187b2dbc90285733657975e03288b9840ba3d6b15 diff --git a/sci-biology/clustalx/clustalx-2.1-r1.ebuild b/sci-biology/clustalx/clustalx-2.1-r1.ebuild new file mode 100644 index 000000000000..9aa885eaa5bb --- /dev/null +++ b/sci-biology/clustalx/clustalx-2.1-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils qt4-r2 + +DESCRIPTION="Graphical interface for the ClustalW multiple alignment program" +HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/" +SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND=" + dev-qt/qtcore:4 + dev-qt/qtgui:4" +RDEPEND="${DEPEND} + >=sci-biology/clustalw-${PV}" + +src_prepare() { + sed \ + -e "s|colprot.xml|${EPREFIX}/usr/share/${PN}/colprot.xml|" \ + -e "s|coldna.xml|${EPREFIX}/usr/share/${PN}/coldna.xml|" \ + -e "s|colprint.xml|${EPREFIX}/usr/share/${PN}/colprint.xml|" \ + -i ClustalQtParams.h || \ + die "Failed to patch shared files location." + sed \ + -e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \ + -i HelpDisplayWidget.cpp || \ + die "Failed to patch help file location." + rm -rf usr || die +} + +src_install() { + dobin clustalx + insinto /usr/share/${PN} + doins colprot.xml coldna.xml colprint.xml clustalx.hlp + make_desktop_entry ${PN} ClustalX +} diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/clustalx/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest new file mode 100644 index 000000000000..e9cd6b128266 --- /dev/null +++ b/sci-biology/consed/Manifest @@ -0,0 +1,4 @@ +DIST consed-19-linux.tar.gz 29835559 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089 +DIST consed-19-sources.tar.gz 6867357 SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3 +DIST consed-27-linux.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21 +DIST consed-27-sources.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21 diff --git a/sci-biology/consed/consed-19-r2.ebuild b/sci-biology/consed/consed-19-r2.ebuild new file mode 100644 index 000000000000..3ce704e8792f --- /dev/null +++ b/sci-biology/consed/consed-19-r2.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit toolchain-funcs + +DESCRIPTION="A genome sequence finishing program" +HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" +SRC_URI="${P}-sources.tar.gz + ${P}-linux.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=x11-libs/motif-2.3:0" +RDEPEND="${DEPEND} + >=sci-biology/phred-000925 + >=sci-biology/phrap-1.080721" + +S="${WORKDIR}" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" + einfo "and place it in ${DISTDIR}," + einfo "obtain the file" + einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die + sed -i \ + -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \ + -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ + -e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die + sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die + sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${PN}/examples + doins -r standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer || die + echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed" + doenvd "${S}/99consed" || die + dodoc README.txt *_announcement.txt || die +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild new file mode 100644 index 000000000000..0bf33a7278cf --- /dev/null +++ b/sci-biology/consed/consed-27.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="A genome sequence finishing program" +HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" +SRC_URI=" + ${P}-sources.tar.gz + ${P}-linux.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=x11-libs/motif-2.3:0" +RDEPEND="${DEPEND} + sci-biology/samtools + >=sci-biology/phred-000925 + >=sci-biology/phrap-1.080721 + dev-lang/perl" + +S="${WORKDIR}" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" + einfo "and place it in ${DISTDIR}," + einfo "obtain the file" + einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die + sed -i \ + -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ + -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ + -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ + -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die + sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die + sed \ + -e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \ + -i "${S}"/scripts/* || die +} + +src_compile() { + emake + emake -C misc/mktrace + emake -C misc/phd2fasta + (cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} + dobin scripts/* contributions/* + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} + insinto /usr/share/${PN}/examples + doins -r \ + standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer + echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die + echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die + mkdir -p "${ED}"/etc/consedrc || die + touch "${ED}"/etc/consedrc || die + doenvd "${S}/99consed" || die + sed \ + -e "s#/usr/local/genome#${EPREFIX}/usr#" \ + -i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die + sed \ + -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \ + -i "${ED}"/usr/bin/phredPhrap || die + sed \ + -e 's#/wt1/gordon/genome#/usr/bin#' \ + -i "${ED}"/usr/bin/fastq2Phrap.perl || die + dodoc README.txt *_announcement.txt || die +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/consed/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/cufflinks/Manifest b/sci-biology/cufflinks/Manifest new file mode 100644 index 000000000000..017836ee07ad --- /dev/null +++ b/sci-biology/cufflinks/Manifest @@ -0,0 +1,2 @@ +DIST cufflinks-1.3.0.tar.gz 676660 SHA256 c1e194e30e6ba2e1cbbd35e5f92be59f9fdef95a12079b3141790efbbdbdfd86 SHA512 b493c06b00093958aa3bf4aefa6435b89aa3fa8f90b9adea955b38aaa0301fafe3f028321573855d2af9515f9792a8a9c3851bd9352846131658e54b5a6ac68a WHIRLPOOL 649ed7638bdc655cc38d9c0ec6c81bc464e648e6e684e31af955a424510ee4702e2cec8e3dbfa2d97859ed27e04ff45fe2e07cb0a548c87674337bb94f5352ce +DIST cufflinks-2.2.1.tar.gz 766280 SHA256 e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae SHA512 4da7f3a6090ea8cf469a85208c91073abdcd8b0e71c51b0f7052ce8001c368055b9d9cb7726d463196f5b3ab0b4a49bf5241d321ac3fe061225ecc47b4ca209b WHIRLPOOL bd40e6612f3c16466cf14efe706e38663c61d01661f901d9fdb140d0419e47e2ff10515dc7a0ff81da081e87af6d5d393d88cc4d036e8b921491fb5a790ae224 diff --git a/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild new file mode 100644 index 000000000000..36322f463de6 --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-1.3.0-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/" +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Artistic" +IUSE="debug" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=sci-biology/samtools-0.1.18 + <sci-biology/samtools-1 + <dev-libs/boost-1.56:=" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-boost.patch + "${FILESDIR}"/${P}-gcc-4.7.patch + ) + +src_configure() { + local myeconfargs=( + --disable-optim + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" + --with-bam="${EPREFIX}/usr/" + $(use_enable debug) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild new file mode 100644 index 000000000000..66298cbc1972 --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-2.2.1-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils flag-o-matic toolchain-funcs + +DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/" +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Artistic" +IUSE="debug" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + || ( + ( + >=sci-biology/samtools-0.1.18 + sci-libs/htslib + ) + <sci-biology/samtools-1 + ) + >=dev-libs/boost-1.47.0:= + <dev-libs/boost-1.56.0:= + dev-cpp/eigen:3 +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-hts.patch + "${FILESDIR}"/${P}-flags.patch + ) + +src_prepare() { + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" + --with-bam="${EPREFIX}/usr/" + $(use_enable debug) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/cufflinks/cufflinks-2.2.1.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild new file mode 100644 index 000000000000..5e7f763389f9 --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-2.2.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools-utils flag-o-matic toolchain-funcs + +DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/" +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Artistic" +IUSE="debug" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=sci-biology/samtools-0.1.18 + <sci-biology/samtools-1 + >=dev-libs/boost-1.47.0:= + <dev-libs/boost-1.56.0:= + dev-cpp/eigen:3 +" +RDEPEND="${DEPEND}" + +src_prepare() { + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" + --with-bam="${EPREFIX}/usr/" + $(use_enable debug) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch new file mode 100644 index 000000000000..73e52b4343a0 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-autotools.patch @@ -0,0 +1,38 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -27,6 +27,7 @@ AC_PROG_AWK + AC_PROG_CXX + AC_PROG_CC + AC_PROG_MAKE_SET ++AM_PROG_AR + AC_PROG_RANLIB + AC_PROG_INSTALL + AM_PATH_PYTHON([2.4]) +@@ -54,7 +55,7 @@ AC_CANONICAL_HOST + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized" + ext_CFLAGS="" + debug_CFLAGS="" + #echo "${host_cpu}-${host_os}" +@@ -99,15 +100,15 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with + [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" +-CXXFLAGS="$CFLAGS" ++CXXFLAGS="$CXXFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" +-LDFLAGS="$ext_LDFLAGS" ++LDFLAGS="$LDFLAGS $ext_LDFLAGS" + + # Checks for structures/functions that can be used to determine system memory + AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include <sys/sysinfo.h>]) + AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include <sys/sysctl.h>]) + +-AM_INIT_AUTOMAKE([-Wall -Werror tar-pax foreign]) ++AM_INIT_AUTOMAKE([-Wall tar-pax foreign subdir-objects]) + + AC_CONFIG_FILES([Makefile + src/Makefile]) diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch new file mode 100644 index 000000000000..d45391bf4f3a --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-boost.patch @@ -0,0 +1,1320 @@ + ax_boost_thread.m4 | 6 +++--- + src/abundances.cpp | 56 +++++++++++++++++++++++++------------------------- + src/biascorrection.cpp | 2 +- + src/bundles.cpp | 10 ++++----- + src/bundles.h | 10 ++++----- + src/common.h | 4 ++-- + src/compress_gtf.cpp | 12 +++++------ + src/cuffdiff.cpp | 30 +++++++++++++-------------- + src/cufflinks.cpp | 34 +++++++++++++++--------------- + src/differential.cpp | 38 +++++++++++++++++----------------- + src/filters.cpp | 8 ++++---- + src/genes.h | 6 +++--- + src/gtf_to_sam.cpp | 8 ++++---- + src/hits.cpp | 4 ++-- + src/replicates.cpp | 6 +++--- + src/replicates.h | 18 ++++++++-------- + src/scaffolds.cpp | 28 ++++++++++++------------- + src/scaffolds.h | 2 +- + 18 files changed, 141 insertions(+), 141 deletions(-) + +diff --git a/ax_boost_thread.m4 b/ax_boost_thread.m4 +index d1d42f6..6f99f1b 100644 +--- a/ax_boost_thread.m4 ++++ b/ax_boost_thread.m4 +@@ -105,20 +105,20 @@ AC_DEFUN([AX_BOOST_THREAD], + for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + if test "x$link_thread" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/boost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], ++ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [link_thread="no"]) + done + fi + + else +- BOOST_THREAD_LIB="$ax_boost_user_thread_lib"; ++ BOOST_THREAD_LIB="$ax_boost_user_thread_lib -lboost_system"; + AC_SUBST(BOOST_THREAD_LIB) + link_thread="yes"; + +diff --git a/src/abundances.cpp b/src/abundances.cpp +index d8f81d0..6e717dc 100644 +--- a/src/abundances.cpp ++++ b/src/abundances.cpp +@@ -140,7 +140,7 @@ AbundanceStatus AbundanceGroup::status() const + { + bool has_lowdata_member = false; + bool has_ok_member = false; +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + if (ab->status() == NUMERIC_FAIL) + { +@@ -205,7 +205,7 @@ void TranscriptAbundance::FPKM_variance(double v) + + bool AbundanceGroup::has_member_with_status(AbundanceStatus member_status) + { +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + if (ab->status() == member_status) + { +@@ -219,7 +219,7 @@ double AbundanceGroup::num_fragments() const + { + double num_f = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + num_f += ab->num_fragments(); + } +@@ -231,7 +231,7 @@ double AbundanceGroup::mass_fraction() const + { + double mass = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + mass += ab->mass_fraction(); + } +@@ -242,7 +242,7 @@ double AbundanceGroup::mass_variance() const + { + double mass_var = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + mass_var += ab->mass_variance(); + } +@@ -253,7 +253,7 @@ double AbundanceGroup::FPKM() const + { + double fpkm = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + fpkm += ab->FPKM(); + } +@@ -265,7 +265,7 @@ double AbundanceGroup::gamma() const + { + double gamma = 0; + +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + gamma += ab->gamma(); + } +@@ -281,7 +281,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep, + assert (to_keep.size() == _abundances.size()); + + size_t num_kept = 0; +- foreach(bool keeper, to_keep) ++ for_each(bool keeper, to_keep) + { + num_kept += keeper; + } +@@ -331,7 +331,7 @@ void AbundanceGroup::filter_group(const vector<bool>& to_keep, + void AbundanceGroup::get_transfrags(vector<shared_ptr<Abundance> >& transfrags) const + { + transfrags.clear(); +- foreach(shared_ptr<Abundance> pA, _abundances) ++ for_each(shared_ptr<Abundance> pA, _abundances) + { + shared_ptr<Scaffold> pS = pA->transfrag(); + if (pS) +@@ -345,7 +345,7 @@ set<string> AbundanceGroup::gene_id() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->gene_id(); + s.insert(sub.begin(), sub.end()); +@@ -358,7 +358,7 @@ set<string> AbundanceGroup::gene_name() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->gene_name(); + s.insert(sub.begin(), sub.end()); +@@ -372,7 +372,7 @@ set<string> AbundanceGroup::tss_id() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->tss_id(); + s.insert(sub.begin(), sub.end()); +@@ -385,7 +385,7 @@ set<string> AbundanceGroup::protein_id() const + { + set<string> s; + +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + set<string> sub = pA->protein_id(); + s.insert(sub.begin(), sub.end()); +@@ -398,7 +398,7 @@ const string& AbundanceGroup::locus_tag() const + { + static string default_locus_tag = "-"; + const string* pLast = NULL; +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (pLast) + { +@@ -422,7 +422,7 @@ const string& AbundanceGroup::reference_tag() const + { + static string default_reference_tag = "-"; + const string* pLast = NULL; +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (pLast) + { +@@ -448,7 +448,7 @@ double AbundanceGroup::effective_length() const + double group_fpkm = FPKM(); + if (group_fpkm == 0) + return 0; +- foreach (shared_ptr<Abundance> ab, _abundances) ++ for_each (shared_ptr<Abundance> ab, _abundances) + { + eff_len += (ab->effective_length() * (ab->FPKM() / group_fpkm)); + } +@@ -1216,7 +1216,7 @@ void AbundanceGroup::estimate_count_covariance() + { + // if the entire group is unstable, then set LOWDATA on all members of + // it to reduce false positives in differential expression analysis. +- foreach(shared_ptr<Abundance> ab, _abundances) ++ for_each(shared_ptr<Abundance> ab, _abundances) + { + ab->status(NUMERIC_LOW_DATA); + } +@@ -1468,7 +1468,7 @@ void AbundanceGroup::calculate_conf_intervals() + double sum_transfrag_FPKM_hi = 0; + double max_fpkm = 0.0; + //double min_fpkm = 1e100; +- foreach(shared_ptr<Abundance> pA, _abundances) ++ for_each(shared_ptr<Abundance> pA, _abundances) + { + double FPKM_hi; + double FPKM_lo; +@@ -1586,7 +1586,7 @@ void AbundanceGroup::calculate_conf_intervals() + // double sum_transfrag_FPKM_hi = 0; + // double max_fpkm = 0.0; + // //double min_fpkm = 1e100; +-// foreach(shared_ptr<Abundance> pA, _abundances) ++// for_each(shared_ptr<Abundance> pA, _abundances) + // { + // double FPKM_hi; + // double FPKM_lo; +@@ -1732,7 +1732,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments, + if (mapped_transcripts.empty()) + { + //gammas = vector<double>(transfrags.size(), 0.0); +- foreach (shared_ptr<Abundance> ab, _abundances) ++ for_each (shared_ptr<Abundance> ab, _abundances) + { + ab->gamma(0); + } +@@ -1783,7 +1783,7 @@ bool AbundanceGroup::calculate_gammas(const vector<MateHit>& nr_alignments, + if (filtered_transcripts.empty()) + { + //gammas = vector<double>(transfrags.size(), 0.0); +- foreach (shared_ptr<Abundance> ab, _abundances) ++ for_each (shared_ptr<Abundance> ab, _abundances) + { + ab->gamma(0); + } +@@ -2117,7 +2117,7 @@ void AbundanceGroup::calculate_kappas() + double S_FPKM = 0.0; + double Z_kappa = 0.0; + double X_S = 0.0; +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (pA->effective_length() > 0) + { +@@ -2128,7 +2128,7 @@ void AbundanceGroup::calculate_kappas() + } + + //fprintf (stderr, "*********\n"); +- foreach (shared_ptr<Abundance> pA, _abundances) ++ for_each (shared_ptr<Abundance> pA, _abundances) + { + if (S_FPKM > 0) + { +@@ -2201,7 +2201,7 @@ void get_alignments_from_scaffolds(const vector<shared_ptr<Abundance> >& abundan + { + set<const MateHit*> hits_in_gene_set; + +- foreach(shared_ptr<Abundance> pA, abundances) ++ for_each(shared_ptr<Abundance> pA, abundances) + { + shared_ptr<Scaffold> pS = pA->transfrag(); + assert (pS); +@@ -2787,7 +2787,7 @@ AbundanceStatus empirical_mean_replicate_gamma_mle(const vector<shared_ptr<Abund + gamma_covariance = ublas::zero_matrix<double>(N,N); + ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N); + // +- foreach(ublas::vector<double>& mle, mle_gammas) ++ for_each(ublas::vector<double>& mle, mle_gammas) + { + expected_mle_gamma += mle; + } +@@ -3122,7 +3122,7 @@ AbundanceStatus bootstrap_gamma_mle(const vector<shared_ptr<Abundance> >& transc + gamma_covariance = ublas::zero_matrix<double>(N,N); + ublas::vector<double> expected_mle_gamma = ublas::zero_vector<double>(N); + +- foreach(ublas::vector<double>& mle, mle_gammas) ++ for_each(ublas::vector<double>& mle, mle_gammas) + { + //cerr << "MLE # "<< MLENUM++ << endl; + //cerr << mle << endl; +@@ -3586,7 +3586,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts, + + double round_err = 0.0; + double num_good = 0; +- foreach (double& g, gammas) ++ for_each (double& g, gammas) + { + if (g < min_isoform_fraction) + { +@@ -3598,7 +3598,7 @@ AbundanceStatus gamma_mle(const vector<shared_ptr<Abundance> >& transcripts, + num_good += 1; + } + } +- foreach (double& g, gammas) ++ for_each (double& g, gammas) + { + if (g != 0) + { +diff --git a/src/biascorrection.cpp b/src/biascorrection.cpp +index 0d49851..55884f4 100644 +--- a/src/biascorrection.cpp ++++ b/src/biascorrection.cpp +@@ -207,7 +207,7 @@ void BiasLearner::preProcessTranscript(const Scaffold& transcript) + vector<double> startHist(transcript.length()+1, 0.0); // +1 catches overhangs + vector<double> endHist(transcript.length()+1, 0.0); + +- foreach (const MateHit* hit_p, transcript.mate_hits()) ++ for_each (const MateHit* hit_p, transcript.mate_hits()) + { + const MateHit& hit = *hit_p; + if (!hit.left_alignment() && !hit.right_alignment()) +diff --git a/src/bundles.cpp b/src/bundles.cpp +index ead07f2..a392514 100644 +--- a/src/bundles.cpp ++++ b/src/bundles.cpp +@@ -228,7 +228,7 @@ void load_ref_rnas(FILE* ref_mRNA_file, + } + } + +- foreach (shared_ptr<Scaffold> s, ref_mRNAs) ++ for_each (shared_ptr<Scaffold> s, ref_mRNAs) + { + assert (s); + } +@@ -418,7 +418,7 @@ void HitBundle::finalize_open_mates() + + for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr) + { +- foreach (MateHit& hit, itr->second) ++ for_each (MateHit& hit, itr->second) + { + delete hit.left_alignment(); + delete hit.right_alignment(); +@@ -438,7 +438,7 @@ void HitBundle::remove_hitless_scaffolds() + void HitBundle::remove_unmapped_hits() + { + +- foreach (MateHit& hit, _hits) ++ for_each (MateHit& hit, _hits) + { + if (unmapped_hit(hit)) + { +@@ -586,7 +586,7 @@ void HitBundle::finalize(bool is_combined) + } + else + { +- foreach (MateHit& hit, _hits) ++ for_each (MateHit& hit, _hits) + { + hit.incr_collapse_mass(hit.common_scale_mass()); + } +@@ -1316,7 +1316,7 @@ void identify_bad_splices(const HitBundle& bundle, + ins_itr = bad_splice_ops.insert(make_pair(ref_id, vector<AugmentedCuffOp>())); + vector<AugmentedCuffOp>& bad_introns = ins_itr.first->second; + +- foreach (const MateHit& hit, bundle.hits()) ++ for_each (const MateHit& hit, bundle.hits()) + { + if (hit.left_alignment()) + { +diff --git a/src/bundles.h b/src/bundles.h +index 15f51ee..aec725e 100644 +--- a/src/bundles.h ++++ b/src/bundles.h +@@ -57,7 +57,7 @@ public: + ~HitBundle() + { + vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds(); +- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) ++ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) + { + // This bundle and the factory that actually owns the ref_mRNAs + // are the only objects that should have access to these scaffolds +@@ -73,7 +73,7 @@ public: + } + } + +- foreach (MateHit& hit, _hits) ++ for_each (MateHit& hit, _hits) + { + delete hit.left_alignment(); + delete hit.right_alignment(); +@@ -81,7 +81,7 @@ public: + + for(OpenMates::iterator itr = _open_mates.begin(); itr != _open_mates.end(); ++itr) + { +- foreach (MateHit& hit, itr->second) ++ for_each (MateHit& hit, itr->second) + { + delete hit.left_alignment(); + delete hit.right_alignment(); +@@ -113,7 +113,7 @@ public: + _hits.clear(); + _non_redundant.clear(); + vector<shared_ptr<Scaffold> >& bundle_ref_scaffs = ref_scaffolds(); +- foreach(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) ++ for_each(shared_ptr<Scaffold>& ref_scaff, bundle_ref_scaffs) + { + if (ref_scaff.use_count() <= 3) + { +@@ -250,7 +250,7 @@ public: + next_ref_scaff = ref_mRNAs.begin(); + next_mask_scaff = mask_gtf_recs.begin(); + +- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) ++ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) + { + ref_scaff->clear_hits(); + } +diff --git a/src/common.h b/src/common.h +index b715e9c..1ed7d77 100644 +--- a/src/common.h ++++ b/src/common.h +@@ -22,8 +22,8 @@ + using boost::math::normal; + + #include <boost/foreach.hpp> +-#define foreach BOOST_FOREACH +-#define reverse_foreach BOOST_REVERSE_FOREACH ++#define for_each BOOST_FOREACH ++#define reverse_for_each BOOST_REVERSE_FOREACH + + #include <boost/thread.hpp> + #include <boost/shared_ptr.hpp> +diff --git a/src/compress_gtf.cpp b/src/compress_gtf.cpp +index a2cd10a..a3796fd 100644 +--- a/src/compress_gtf.cpp ++++ b/src/compress_gtf.cpp +@@ -159,7 +159,7 @@ void compress_genes(FILE* ftranscripts, + vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i]; + vector<Scaffold> gene_scaffs; + string gene_id; +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + if (gene_id == "") + gene_id = s->annotated_gene_id(); +@@ -175,7 +175,7 @@ void compress_genes(FILE* ftranscripts, + Scaffold smashed_gene; + if (!proj_intersection && !proj_union) + { +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + /* + *transfrag, +@@ -224,7 +224,7 @@ void compress_genes(FILE* ftranscripts, + int gmax = -1; + int gmin = numeric_limits<int>::max(); + +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + //iso_ops.push_back(s->augmented_ops()); + //sort (iso_ops.back().begin(), iso_ops.back().end()); +@@ -234,7 +234,7 @@ void compress_genes(FILE* ftranscripts, + gmax = s->right(); + } + +- foreach (shared_ptr<Scaffold> s, gene) ++ for_each (shared_ptr<Scaffold> s, gene) + { + if (s->left() > gmin) + { +@@ -347,7 +347,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* gtf_out) + vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table; + vector<pair<string, vector<double> > > sample_count_table; + +- foreach (FILE* ref_gtf, ref_gtf_files) ++ for_each (FILE* ref_gtf, ref_gtf_files) + { + vector<shared_ptr<Scaffold> > ref_mRNAs; + ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true); +@@ -393,7 +393,7 @@ int main(int argc, char** argv) + + vector<FILE*> ref_gtf_files; + +- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames) ++ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames) + { + FILE* ref_gtf = NULL; + if (ref_gtf_in_filename != "") +diff --git a/src/cuffdiff.cpp b/src/cuffdiff.cpp +index 575b064..7725910 100644 +--- a/src/cuffdiff.cpp ++++ b/src/cuffdiff.cpp +@@ -490,7 +490,7 @@ void print_FPKM_tracking(FILE* fout, + const vector<FPKMContext>& fpkms = track.fpkm_series; + + AbundanceStatus status = NUMERIC_OK; +- foreach (const FPKMContext& c, fpkms) ++ for_each (const FPKMContext& c, fpkms) + { + if (c.status == NUMERIC_FAIL) + status = NUMERIC_FAIL; +@@ -811,7 +811,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + ::load_ref_rnas(mask_gtf, rt, mask_rnas, false, false); + } + +- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) + { + fac->set_ref_rnas(ref_mRNAs); + if (mask_gtf) +@@ -826,7 +826,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + int tmp_max_frag_len = 0; + + ProgressBar p_bar("Inspecting maps and determining fragment length distributions.",0); +- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) + { + #if ENABLE_THREADS + while(1) +@@ -877,7 +877,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + { + long double total_mass = 0.0; + long double total_norm_mass = 0.0; +- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups) + { + total_mass += rg->total_map_mass(); + total_norm_mass += rg->normalized_map_mass(); +@@ -886,7 +886,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + if (total_mass > 0) + { + double scaling_factor = total_mass / total_norm_mass; +- foreach (shared_ptr<ReadGroupProperties> rg, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg, all_read_groups) + { + double scaled_mass = scaling_factor * rg->normalized_map_mass(); + +@@ -916,7 +916,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + + if (most_reps != 1 && poisson_dispersion == false) + { +- foreach (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> fac, bundle_factories) + { + if (fac->num_replicates() == 1) + { +@@ -990,7 +990,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + shared_ptr<MassDispersionModel const> disperser; + disperser = fit_dispersion_model("pooled", scale_factors, sample_count_table); + +- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) + { + rg_props->mass_dispersion_model(disperser); + } +@@ -999,7 +999,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + + long double total_norm_mass = 0.0; + long double total_mass = 0.0; +- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) + { + total_norm_mass += rg_props->normalized_map_mass(); + total_mass += rg_props->total_map_mass(); +@@ -1007,7 +1007,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + + // scale the normalized masses so that both quantile total count normalization + // are roughly on the same numerical scale +- foreach (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) ++ for_each (shared_ptr<ReadGroupProperties> rg_props, all_read_groups) + { + long double new_norm = rg_props->normalized_map_mass() * (total_mass / total_norm_mass); + rg_props->normalized_map_mass(new_norm); +@@ -1039,7 +1039,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >()); + quantitate_next_locus(rt, bundle_factories, test_launcher); + bool more_loci_remain = false; +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + if (rep_fac->bundles_remain()) + { +@@ -1071,7 +1071,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + } + } + +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + rep_fac->reset(); + } +@@ -1081,9 +1081,9 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + if (corr_bias) + { + p_bar = ProgressBar("Learning bias parameters.", 0); +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { +- foreach (shared_ptr<BundleFactory> fac, rep_fac->factories()) ++ for_each (shared_ptr<BundleFactory> fac, rep_fac->factories()) + { + #if ENABLE_THREADS + while(1) +@@ -1124,7 +1124,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + boost::this_thread::sleep(boost::posix_time::milliseconds(5)); + } + #endif +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + rep_fac->reset(); + } +@@ -1167,7 +1167,7 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, vector<string>& sam_hit_filename_list + //shared_ptr<vector<shared_ptr<SampleAbundances> > > abundances(new vector<shared_ptr<SampleAbundances> >()); + quantitate_next_locus(rt, bundle_factories, test_launcher); + bool more_loci_remain = false; +- foreach (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) ++ for_each (shared_ptr<ReplicatedBundleFactory> rep_fac, bundle_factories) + { + if (rep_fac->bundles_remain()) + { +diff --git a/src/cufflinks.cpp b/src/cufflinks.cpp +index 796af98..1030ae8 100644 +--- a/src/cufflinks.cpp ++++ b/src/cufflinks.cpp +@@ -471,7 +471,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs, + { + for(size_t l = 0; l < lhs.size(); ++l) + { +- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) ++ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) + { + // if we're past all the overlaps, just stop + if (ref_scaff->left() >= lhs[l].right() + overhang_3) +@@ -504,7 +504,7 @@ void combine_strand_assemblies(vector<Scaffold>& lhs, + } + for(size_t r = 0; r < rhs.size(); ++r) + { +- foreach(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) ++ for_each(shared_ptr<Scaffold> ref_scaff, *ref_scaffs) + { + if (ref_scaff->left() >= rhs[r].right() + overhang_3) + { +@@ -665,7 +665,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle, + if (ref_guided && enable_faux_reads && !hits.empty()) + { + vector<Scaffold> pseudohits; +- foreach(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) ++ for_each(shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) + { + ref_scaff->tile_with_scaffs(pseudohits, tile_len, tile_off); + } +@@ -842,7 +842,7 @@ bool scaffolds_for_bundle(const HitBundle& bundle, + } + if (assembled_successfully) + { +- foreach(Scaffold& scaff, tmp_scaffs) ++ for_each(Scaffold& scaff, tmp_scaffs) + { + scaffolds.push_back(shared_ptr<Scaffold>(new Scaffold(scaff))); + } +@@ -886,7 +886,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + + // need the avg read length for depth of coverage calculation + double avg_read_length = 0; +- foreach (MateHit& hit, hits_in_cluster) ++ for_each (MateHit& hit, hits_in_cluster) + { + if (hit.left_alignment()) + avg_read_length += hit.left_alignment()->read_len(); +@@ -905,7 +905,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + } + else + { +- foreach(shared_ptr<Abundance> ab, transfrag_cluster.abundances()) ++ for_each(shared_ptr<Abundance> ab, transfrag_cluster.abundances()) + { + ab->status(NUMERIC_HI_DATA); + } +@@ -939,7 +939,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + { + shared_ptr<Abundance> ab_i = abundances[i]; + bool found = false; +- foreach (shared_ptr<Abundance> ab_j, filtered_transcripts) ++ for_each (shared_ptr<Abundance> ab_j, filtered_transcripts) + { + if (ab_i == ab_j) + { +@@ -961,7 +961,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + transfrags_by_strand); + + +- foreach (const AbundanceGroup& strand_group, transfrags_by_strand) ++ for_each (const AbundanceGroup& strand_group, transfrags_by_strand) + { + vector<AbundanceGroup> transfrags_by_gene; + +@@ -974,7 +974,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + cluster_transcripts<ConnectByExonOverlap>(strand_group, transfrags_by_gene); + } + +- foreach(const AbundanceGroup& gene, transfrags_by_gene) ++ for_each(const AbundanceGroup& gene, transfrags_by_gene) + { + const vector<shared_ptr<Abundance> >& iso_abundances = gene.abundances(); + vector<Isoform> isoforms; +@@ -985,7 +985,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + string ref_gene_id = ""; + + double major_isoform_FPKM = 0; +- foreach (shared_ptr<Abundance> iso_ab, iso_abundances) ++ for_each (shared_ptr<Abundance> iso_ab, iso_abundances) + { + if (iso_ab->transfrag()->is_ref()) + { +@@ -1002,7 +1002,7 @@ void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster, + major_isoform_FPKM = max(iso_ab->FPKM(), major_isoform_FPKM); + } + +- foreach (shared_ptr<Abundance> iso_ab, iso_abundances) ++ for_each (shared_ptr<Abundance> iso_ab, iso_abundances) + { + // Calculate transcript depth of coverage and FMI from FPKM + double FPKM = iso_ab->FPKM(); +@@ -1067,7 +1067,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds, + { + vector<Scaffold> c; + scaffolds[i]->get_complete_subscaffolds(c); +- foreach (Scaffold& s, c) ++ for_each (Scaffold& s, c) + { + split_partials.push_back(shared_ptr<Scaffold>(new Scaffold(s))); + } +@@ -1076,7 +1076,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds, + scaffolds = split_partials; + + vector<shared_ptr<Abundance> > abundances; +- foreach(shared_ptr<Scaffold> s, scaffolds) ++ for_each(shared_ptr<Scaffold> s, scaffolds) + { + TranscriptAbundance* pT = new TranscriptAbundance; + pT->transfrag(s); +@@ -1091,7 +1091,7 @@ void quantitate_transcript_clusters(vector<shared_ptr<Scaffold> >& scaffolds, + cluster_transcripts<ConnectByExonOverlap>(transfrags, + transfrags_by_cluster); + +- foreach(AbundanceGroup& cluster, transfrags_by_cluster) ++ for_each(AbundanceGroup& cluster, transfrags_by_cluster) + { + quantitate_transcript_cluster(cluster, total_map_mass, genes, bundle_too_large); + } +@@ -1233,10 +1233,10 @@ void assemble_bundle(const RefSequenceTable& rt, + if (init_bundle_mode == REF_GUIDED) + { + hit_introns = new set<AugmentedCuffOp>(); +- foreach(const MateHit& h, bundle.non_redundant_hits()) ++ for_each(const MateHit& h, bundle.non_redundant_hits()) + { + Scaffold s(h); +- foreach (AugmentedCuffOp a, s.augmented_ops()) ++ for_each (AugmentedCuffOp a, s.augmented_ops()) + { + if (a.opcode == CUFF_INTRON) + { +@@ -1567,7 +1567,7 @@ void driver(const string& hit_file_name, FILE* ref_gtf, FILE* mask_gtf) + verbose_msg("%d ReadHits still live\n", num_deleted); + verbose_msg("Found %lu reference contigs\n", rt.size()); + +- foreach(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) ++ for_each(shared_ptr<Scaffold> ref_scaff, ref_mRNAs) + { + ref_scaff->clear_hits(); + } +diff --git a/src/differential.cpp b/src/differential.cpp +index 3e5cff0..6b108cb 100644 +--- a/src/differential.cpp ++++ b/src/differential.cpp +@@ -84,7 +84,7 @@ void TestLauncher::abundance_avail(const string& locus_id, + // acquire the lock itself. + bool TestLauncher::all_samples_reported_in(vector<shared_ptr<SampleAbundances> >& abundances) + { +- foreach (shared_ptr<SampleAbundances> ab, abundances) ++ for_each (shared_ptr<SampleAbundances> ab, abundances) + { + if (!ab) + { +@@ -436,7 +436,7 @@ pair<int, SampleDiffs::iterator> get_de_tests(const string& description, + // ublas::vector<double> null_kappa_mean; + // null_kappa_mean = ublas::zero_vector<double>(curr_kappa_cov.size1()); + // +-// foreach(ublas::vector<double>& sample, samples) ++// for_each(ublas::vector<double>& sample, samples) + // { + // null_kappa_mean += sample; + // } +@@ -1056,7 +1056,7 @@ void sample_abundance_worker(const string& locus_tag, + { + vector<shared_ptr<Abundance> > abundances; + +- foreach(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds()) ++ for_each(shared_ptr<Scaffold> s, sample_bundle->ref_scaffolds()) + { + TranscriptAbundance* pT = new TranscriptAbundance; + pT->transfrag(s); +@@ -1082,7 +1082,7 @@ void sample_abundance_worker(const string& locus_tag, + } + else + { +- foreach(shared_ptr<Abundance> ab, abundances) ++ for_each(shared_ptr<Abundance> ab, abundances) + { + ab->status(NUMERIC_HI_DATA); + } +@@ -1093,7 +1093,7 @@ void sample_abundance_worker(const string& locus_tag, + cluster_transcripts<ConnectByAnnotatedGeneId>(sample.transcripts, + transcripts_by_gene_id); + +- foreach(AbundanceGroup& ab_group, transcripts_by_gene_id) ++ for_each(AbundanceGroup& ab_group, transcripts_by_gene_id) + { + ab_group.locus_tag(locus_tag); + set<string> gene_ids = ab_group.gene_id(); +@@ -1119,7 +1119,7 @@ void sample_abundance_worker(const string& locus_tag, + &cds_count_cov, + &cds_fpkm_cov, + &cds_gamma_boot_cov); +- foreach(AbundanceGroup& ab_group, transcripts_by_cds) ++ for_each(AbundanceGroup& ab_group, transcripts_by_cds) + { + ab_group.locus_tag(locus_tag); + set<string> protein_ids = ab_group.protein_id(); +@@ -1135,7 +1135,7 @@ void sample_abundance_worker(const string& locus_tag, + vector<shared_ptr<Abundance> > cds_abundances; + double max_cds_mass_variance = 0.0; + set<shared_ptr<ReadGroupProperties const> > rg_props; +- foreach (AbundanceGroup& ab_group, sample.cds) ++ for_each (AbundanceGroup& ab_group, sample.cds) + { + cds_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group))); + max_cds_mass_variance = max(ab_group.max_mass_variance(), max_cds_mass_variance); +@@ -1155,7 +1155,7 @@ void sample_abundance_worker(const string& locus_tag, + cluster_transcripts<ConnectByAnnotatedGeneId>(cds, + cds_by_gene); + +- foreach(AbundanceGroup& ab_group, cds_by_gene) ++ for_each(AbundanceGroup& ab_group, cds_by_gene) + { + ab_group.locus_tag(locus_tag); + set<string> gene_ids = ab_group.gene_id(); +@@ -1185,7 +1185,7 @@ void sample_abundance_worker(const string& locus_tag, + &tss_gamma_boot_cov); + + +- foreach(AbundanceGroup& ab_group, transcripts_by_tss) ++ for_each(AbundanceGroup& ab_group, transcripts_by_tss) + { + ab_group.locus_tag(locus_tag); + set<string> tss_ids = ab_group.tss_id(); +@@ -1202,7 +1202,7 @@ void sample_abundance_worker(const string& locus_tag, + // Group TSS clusters by gene + vector<shared_ptr<Abundance> > primary_transcript_abundances; + set<shared_ptr<ReadGroupProperties const> > rg_props; +- foreach (AbundanceGroup& ab_group, sample.primary_transcripts) ++ for_each (AbundanceGroup& ab_group, sample.primary_transcripts) + { + primary_transcript_abundances.push_back(shared_ptr<Abundance>(new AbundanceGroup(ab_group))); + max_tss_mass_variance = max(max_tss_mass_variance, ab_group.max_mass_variance()); +@@ -1223,13 +1223,13 @@ void sample_abundance_worker(const string& locus_tag, + cluster_transcripts<ConnectByAnnotatedGeneId>(primary_transcripts, + primary_transcripts_by_gene); + +- foreach(AbundanceGroup& ab_group, primary_transcripts_by_gene) ++ for_each(AbundanceGroup& ab_group, primary_transcripts_by_gene) + { + ab_group.locus_tag(locus_tag); + set<string> gene_ids = ab_group.gene_id(); + // if (gene_ids.size() > 1) + // { +-// foreach (string st, gene_ids) ++// for_each (string st, gene_ids) + // { + // fprintf(stderr, "%s\n", st.c_str()); + // } +@@ -1314,7 +1314,7 @@ void sample_worker(const RefSequenceTable& rt, + bool perform_cds_analysis = final_est_run; + bool perform_tss_analysis = final_est_run; + +- foreach(shared_ptr<Scaffold> s, bundle.ref_scaffolds()) ++ for_each(shared_ptr<Scaffold> s, bundle.ref_scaffolds()) + { + if (s->annotated_tss_id() == "") + { +@@ -1439,7 +1439,7 @@ void sample_worker(const RefSequenceTable& rt, + /////////////////////////////////////////////// + + +- foreach(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds()) ++ for_each(shared_ptr<Scaffold> ref_scaff, bundle.ref_scaffolds()) + { + ref_scaff->clear_hits(); + } +@@ -1465,7 +1465,7 @@ void dump_locus_variance_info(const string& filename) + + fprintf(fdump, + "condition\tdescription\tlocus_counts\tempir_var\tlocus_fit_var\tsum_iso_fit_var\tcross_replicate_js\tnum_transcripts\tbayes_gamma_trace\tempir_gamma_trace\tcount_mean\tgamma_var\tgamma_bootstrap_var\tlocus_salient_frags\tlocus_total_frags\tcount_sharing\n"); +- foreach (LocusVarianceInfo& L, locus_variance_info_table) ++ for_each (LocusVarianceInfo& L, locus_variance_info_table) + { + for (size_t i = 0; i < L.gamma.size(); ++i) + { +@@ -1503,22 +1503,22 @@ void test_differential(const string& locus_tag, + for (size_t i = 0; i < samples.size(); ++i) + { + const AbundanceGroup& ab_group = samples[i]->transcripts; +- foreach (shared_ptr<Abundance> ab, ab_group.abundances()) ++ for_each (shared_ptr<Abundance> ab, ab_group.abundances()) + { + add_to_tracking_table(i, *ab, tracking.isoform_fpkm_tracking); + } + +- foreach (AbundanceGroup& ab, samples[i]->cds) ++ for_each (AbundanceGroup& ab, samples[i]->cds) + { + add_to_tracking_table(i, ab, tracking.cds_fpkm_tracking); + } + +- foreach (AbundanceGroup& ab, samples[i]->primary_transcripts) ++ for_each (AbundanceGroup& ab, samples[i]->primary_transcripts) + { + add_to_tracking_table(i, ab, tracking.tss_group_fpkm_tracking); + } + +- foreach (AbundanceGroup& ab, samples[i]->genes) ++ for_each (AbundanceGroup& ab, samples[i]->genes) + { + add_to_tracking_table(i, ab, tracking.gene_fpkm_tracking); + } +diff --git a/src/filters.cpp b/src/filters.cpp +index 0a10b50..5ab31e0 100644 +--- a/src/filters.cpp ++++ b/src/filters.cpp +@@ -752,7 +752,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + + if (library_type != "transfrags") + { +- foreach (Scaffold& scaff, scaffolds) ++ for_each (Scaffold& scaff, scaffolds) + { + if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV)) + continue; +@@ -761,7 +761,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + vector<double> coverage(scaff_len, 0.0); + + double total = 0; +- foreach(const MateHit* hit, scaff.mate_hits()) ++ for_each(const MateHit* hit, scaff.mate_hits()) + { + int start, end, frag_len; + if (!scaff.map_frag(*hit, start, end, frag_len)) continue; +@@ -906,7 +906,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + } + else + { +- foreach (Scaffold& scaff, scaffolds) ++ for_each (Scaffold& scaff, scaffolds) + { + if (!(scaff.strand() == CUFF_FWD || scaff.strand() == CUFF_REV)) + continue; +@@ -915,7 +915,7 @@ void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds) + vector<double> coverage(scaff_len, 0.0); + + double total = 0; +- foreach(const MateHit* hit, scaff.mate_hits()) ++ for_each(const MateHit* hit, scaff.mate_hits()) + { + int start, end, frag_len; + if (!scaff.map_frag(*hit, start, end, frag_len)) continue; +diff --git a/src/genes.h b/src/genes.h +index 4dfa996..eb48a14 100644 +--- a/src/genes.h ++++ b/src/genes.h +@@ -169,7 +169,7 @@ public: + + bool has_ref_trans() const + { +- foreach (const Isoform& iso, _isoforms) ++ for_each (const Isoform& iso, _isoforms) + { + if (iso.is_ref_trans()) + return true; +@@ -180,7 +180,7 @@ public: + double estimated_count() const + { + double est = 0.0; +- foreach (const Isoform& iso, _isoforms) ++ for_each (const Isoform& iso, _isoforms) + { + est += iso.estimated_count(); + } +@@ -191,7 +191,7 @@ public: + { + double eff = 0.0; + double total_fpkm = 0; +- foreach (const Isoform& iso, _isoforms) ++ for_each (const Isoform& iso, _isoforms) + { + eff += iso.FPKM() * iso.effective_length(); + total_fpkm += iso.FPKM(); +diff --git a/src/gtf_to_sam.cpp b/src/gtf_to_sam.cpp +index 12f70c1..f52d40a 100644 +--- a/src/gtf_to_sam.cpp ++++ b/src/gtf_to_sam.cpp +@@ -241,13 +241,13 @@ void set_relative_fpkms(vector<shared_ptr<Scaffold> >& ref_mRNAs) + vector<shared_ptr<Scaffold> >& gene = grouped_scaffolds[i]; + + double total_fpkm = 0.0; +- foreach(shared_ptr<Scaffold> scaff, gene) ++ for_each(shared_ptr<Scaffold> scaff, gene) + { + total_fpkm += scaff->fpkm(); + } + if (total_fpkm > 0) + { +- foreach (shared_ptr<Scaffold> scaff, gene) ++ for_each (shared_ptr<Scaffold> scaff, gene) + { + scaff->fpkm(scaff->fpkm() / total_fpkm); + } +@@ -263,7 +263,7 @@ void driver(vector<FILE*> ref_gtf_files, FILE* sam_out) + vector<vector<shared_ptr<Scaffold> > > ref_mRNA_table; + vector<pair<string, vector<double> > > sample_count_table; + +- foreach (FILE* ref_gtf, ref_gtf_files) ++ for_each (FILE* ref_gtf, ref_gtf_files) + { + vector<shared_ptr<Scaffold> > ref_mRNAs; + ::load_ref_rnas(ref_gtf, rt, ref_mRNAs, false, true); +@@ -314,7 +314,7 @@ int main(int argc, char** argv) + + vector<FILE*> ref_gtf_files; + +- foreach (const string& ref_gtf_in_filename, ref_gtf_filenames) ++ for_each (const string& ref_gtf_in_filename, ref_gtf_filenames) + { + FILE* ref_gtf = NULL; + if (ref_gtf_in_filename != "") +diff --git a/src/hits.cpp b/src/hits.cpp +index 910ba0f..dc81813 100644 +--- a/src/hits.cpp ++++ b/src/hits.cpp +@@ -233,7 +233,7 @@ void collapse_hits(const vector<MateHit>& hits, + non_redundant.erase(new_end, non_redundant.end()); + non_redundant.resize(non_redundant.size()); + +- foreach(MateHit& hit, non_redundant) ++ for_each(MateHit& hit, non_redundant) + hit.collapse_mass(0); + + size_t curr_aln = 0; +@@ -252,7 +252,7 @@ void collapse_hits(const vector<MateHit>& hits, + ++curr_aln; + } + +- //foreach(MateHit& hit, non_redundant) ++ //for_each(MateHit& hit, non_redundant) + //assert(hit.collapse_mass() <= 1 || !hit.is_multi()); + + //non_redundant.erase(remove_if(non_redundant.begin(),non_redundant.end(),has_no_collapse_mass), non_redundant.end()); +diff --git a/src/replicates.cpp b/src/replicates.cpp +index 634f209..ec8ce9c 100644 +--- a/src/replicates.cpp ++++ b/src/replicates.cpp +@@ -236,7 +236,7 @@ fit_dispersion_model_helper(const string& condition_name, + mean /= p.counts.size(); + + double var = 0.0; +- foreach (double d, p.counts) ++ for_each (double d, p.counts) + { + var += (d - mean) * (d - mean); + } +@@ -363,7 +363,7 @@ fit_dispersion_model(const string& condition_name, + ProgressBar p_bar("Modeling fragment count overdispersion.",0); + + int max_transcripts = 0; +- foreach(const LocusCountList& L, sample_count_table) ++ for_each(const LocusCountList& L, sample_count_table) + { + if (L.num_transcripts > max_transcripts) + { +@@ -382,7 +382,7 @@ fit_dispersion_model(const string& condition_name, + if (i != 0) + { + // vector<LocusCountList> sample_count_subtable; +-// foreach(const LocusCountList& L, sample_count_table) ++// for_each(const LocusCountList& L, sample_count_table) + // { + // if (L.num_transcripts == i) + // { +diff --git a/src/replicates.h b/src/replicates.h +index ca4484f..73d339c 100644 +--- a/src/replicates.h ++++ b/src/replicates.h +@@ -99,7 +99,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach (boost::shared_ptr<BundleFactory> fac, _factories) ++ for_each (boost::shared_ptr<BundleFactory> fac, _factories) + { + if (fac->bundles_remain()) + return true; +@@ -115,7 +115,7 @@ public: + std::vector<HitBundle*> bundles; + + bool non_empty_bundle = false; +- foreach (boost::shared_ptr<BundleFactory> fac, _factories) ++ for_each (boost::shared_ptr<BundleFactory> fac, _factories) + { + bundles.push_back(new HitBundle()); + if (fac->next_bundle(*(bundles.back()))) +@@ -126,7 +126,7 @@ public: + + if (non_empty_bundle == false) + { +- foreach (HitBundle* in_bundle, bundles) ++ for_each (HitBundle* in_bundle, bundles) + { + in_bundle->ref_scaffolds().clear(); + in_bundle->clear_hits(); +@@ -149,7 +149,7 @@ public: + // Merge the replicates into a combined bundle of hits. + HitBundle::combine(bundles, bundle_out); + +- foreach (HitBundle* in_bundle, bundles) ++ for_each (HitBundle* in_bundle, bundles) + { + in_bundle->ref_scaffolds().clear(); + in_bundle->clear_hits(); +@@ -163,7 +163,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach (shared_ptr<BundleFactory> fac, _factories) ++ for_each (shared_ptr<BundleFactory> fac, _factories) + { + fac->reset(); + } +@@ -246,7 +246,7 @@ public: + shared_ptr<MassDispersionModel const> disperser; + disperser = fit_dispersion_model(_condition_name,scale_factors, sample_count_table); + +- foreach (shared_ptr<BundleFactory> fac, _factories) ++ for_each (shared_ptr<BundleFactory> fac, _factories) + { + shared_ptr<ReadGroupProperties> rg_props = fac->read_group_properties(); + rg_props->mass_dispersion_model(disperser); +@@ -260,7 +260,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach(shared_ptr<BundleFactory> fac, _factories) ++ for_each(shared_ptr<BundleFactory> fac, _factories) + { + fac->set_ref_rnas(mRNAs); + } +@@ -271,7 +271,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach(shared_ptr<BundleFactory> fac, _factories) ++ for_each(shared_ptr<BundleFactory> fac, _factories) + { + fac->set_mask_rnas(mRNAs); + } +@@ -284,7 +284,7 @@ public: + #if ENABLE_THREADS + boost::mutex::scoped_lock lock(_rep_factory_lock); + #endif +- foreach(shared_ptr<BundleFactory>& fac, _factories) ++ for_each(shared_ptr<BundleFactory>& fac, _factories) + { + fac->read_group_properties()->mass_dispersion_model(disperser); + } +diff --git a/src/scaffolds.cpp b/src/scaffolds.cpp +index 096f58a..c12118e 100644 +--- a/src/scaffolds.cpp ++++ b/src/scaffolds.cpp +@@ -620,7 +620,7 @@ void Scaffold::tile_with_scaffs(vector<Scaffold>& tile_scaffs, int max_len, int + + // genomic_offset actually could be zero - from an exon starting at coord + // 1 in some chromosome of the ref. +-// foreach(const AugmentedCuffOp& op, ops) ++// for_each(const AugmentedCuffOp& op, ops) + // { + // assert (op.genomic_offset != 0); + // } +@@ -819,7 +819,7 @@ void Scaffold::merge(const vector<Scaffold>& s, + if (library_type == "transfrags") + { + double avg_fpkm = 0.0; +- foreach (const Scaffold& sc, s) ++ for_each (const Scaffold& sc, s) + { + avg_fpkm += sc.fpkm(); + } +@@ -871,7 +871,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler) + + vector<AugmentedCuffOp> tmp_filler = filler; + +- foreach(const AugmentedCuffOp& op, orig_ops) ++ for_each(const AugmentedCuffOp& op, orig_ops) + { + assert (op.g_left() < op.g_right()); + +@@ -888,7 +888,7 @@ void Scaffold::fill_gaps(const vector<AugmentedCuffOp>& filler) + AugmentedCuffOp::merge_ops(tmp_filler, padded_filler, false); + + vector<AugmentedCuffOp> overlapping; +- foreach (const AugmentedCuffOp& op, padded_filler) ++ for_each (const AugmentedCuffOp& op, padded_filler) + { + //if (left() <= op.g_left() && right() >= op.g_right() + if(::overlap_in_genome(op.g_left(),op.g_right(), left(), right()) +@@ -1630,7 +1630,7 @@ void Scaffold::get_complete_subscaffolds(vector<Scaffold>& complete) + + // const vector<const MateHit*>& hits = known.mate_hits(); + // bool contains_spliced_hit = false; +- // foreach (const MateHit* h, hits) ++ // for_each (const MateHit* h, hits) + // { + // const ReadHit* left = h->left_alignment(); + // const ReadHit* right = h->right_alignment(); +@@ -1670,7 +1670,7 @@ double Scaffold::internal_exon_coverage() const + int left = augmented_ops()[2].g_left(); + int right = augmented_ops()[augmented_ops().size() - 3].g_right(); + vector<bool> covered(right-left, 0); +- foreach(const MateHit* h, mate_hits()) ++ for_each(const MateHit* h, mate_hits()) + { + if (::overlap_in_genome(h->left(),h->right(), left, right)) + { +@@ -1694,7 +1694,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con + if (has_intron()) + return true; + +- foreach (const MateHit* h, mate_hits()) ++ for_each (const MateHit* h, mate_hits()) + { + if (h->strand() == strand()) + return true; +@@ -1704,7 +1704,7 @@ bool Scaffold::has_strand_support(vector<shared_ptr<Scaffold> >* ref_scaffs) con + if (ref_scaffs == NULL) + return false; + +- foreach (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) ++ for_each (shared_ptr<Scaffold const> ref_scaff, *ref_scaffs) + { + if (ref_scaff->strand() == strand() && exons_overlap(*this, *ref_scaff)) + return true; +@@ -1729,10 +1729,10 @@ bool Scaffold::hits_support_introns() const + { + set<AugmentedCuffOp> hit_introns; + set<AugmentedCuffOp> scaffold_introns; +- foreach(const MateHit* h, _mates_in_scaff) ++ for_each(const MateHit* h, _mates_in_scaff) + { + Scaffold s(*h); +- foreach (AugmentedCuffOp a, s.augmented_ops()) ++ for_each (AugmentedCuffOp a, s.augmented_ops()) + { + if (a.opcode == CUFF_INTRON) + { +@@ -1740,7 +1740,7 @@ bool Scaffold::hits_support_introns() const + } + } + } +- foreach (AugmentedCuffOp a, _augmented_ops) ++ for_each (AugmentedCuffOp a, _augmented_ops) + { + if (a.opcode == CUFF_INTRON) + { +@@ -1751,13 +1751,13 @@ bool Scaffold::hits_support_introns() const + if (hit_introns != scaffold_introns) + { + fprintf(stderr, "********************\n"); +- foreach(const AugmentedCuffOp& a, hit_introns) ++ for_each(const AugmentedCuffOp& a, hit_introns) + { + fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right()); + } + + fprintf(stderr, "####################\n"); +- foreach(const AugmentedCuffOp& a, scaffold_introns) ++ for_each(const AugmentedCuffOp& a, scaffold_introns) + { + fprintf(stderr, "%d - %d\n", a.g_left(), a.g_right()); + } +@@ -1770,7 +1770,7 @@ bool Scaffold::hits_support_introns(set<AugmentedCuffOp>& hit_introns) const + { + set<AugmentedCuffOp> scaffold_introns; + +- foreach (AugmentedCuffOp a, _augmented_ops) ++ for_each (AugmentedCuffOp a, _augmented_ops) + { + if (a.opcode == CUFF_INTRON) + { +diff --git a/src/scaffolds.h b/src/scaffolds.h +index 0f29e80..f8410f7 100644 +--- a/src/scaffolds.h ++++ b/src/scaffolds.h +@@ -314,7 +314,7 @@ public: + if (library_type == "transfrags") + { + double avg_fpkm = 0.0; +- foreach (const Scaffold& sc, hits) ++ for_each (const Scaffold& sc, hits) + { + avg_fpkm += sc.fpkm(); + } diff --git a/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch new file mode 100644 index 000000000000..360e9c1a11b8 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-1.3.0-gcc-4.7.patch @@ -0,0 +1,20 @@ + src/lemon/bits/base_extender.h | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/lemon/bits/base_extender.h b/src/lemon/bits/base_extender.h +index 84bb242..b812247 100644 +--- a/src/lemon/bits/base_extender.h ++++ b/src/lemon/bits/base_extender.h +@@ -359,10 +359,10 @@ namespace lemon { + } + + Node source(const UEdge& edge) const { +- return aNode(edge); ++ return this->aNode(edge); + } + Node target(const UEdge& edge) const { +- return bNode(edge); ++ return this->bNode(edge); + } + + void firstInc(UEdge& edge, bool& dir, const Node& node) const { diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch new file mode 100644 index 000000000000..47784088fab9 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch @@ -0,0 +1,28 @@ + configure.ac | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 96ffbac..e88b8e4 100755 +--- a/configure.ac ++++ b/configure.ac +@@ -61,7 +61,8 @@ AC_CANONICAL_HOST + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024" ++generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized" ++generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024" + ext_CFLAGS="" + debug_CFLAGS="" + #echo "${host_cpu}-${host_os}" +@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with + [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" +-CXXFLAGS="$CFLAGS" +-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" ++CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}" ++CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" + user_LDFLAGS="$LDFLAGS" + LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch new file mode 100644 index 000000000000..3b9abd812680 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch @@ -0,0 +1,16 @@ + ax_bam.m4 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ax_bam.m4 b/ax_bam.m4 +index 7d463b7..95f1bed 100644 +--- a/ax_bam.m4 ++++ b/ax_bam.m4 +@@ -189,7 +189,7 @@ if test "x$want_bam" = "xyes"; then + AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).]) + fi + else +- BAM_LIB="-lbam" ++ BAM_LIB="-lbam -lhts" + AC_SUBST(BAM_CPPFLAGS) + AC_SUBST(BAM_LDFLAGS) + AC_SUBST(BAM_LIB) diff --git a/sci-biology/cufflinks/metadata.xml b/sci-biology/cufflinks/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/cufflinks/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest new file mode 100644 index 000000000000..5c0e901d9aba --- /dev/null +++ b/sci-biology/cutg/Manifest @@ -0,0 +1 @@ +DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93 diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild new file mode 100644 index 000000000000..46163bc2a80f --- /dev/null +++ b/sci-biology/cutg/cutg-160-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Codon usage tables calculated from GenBank" +HOMEPAGE="http://www.kazusa.or.jp/codon/" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + mkdir CODONS || die + ebegin "Indexing CUTG for usage with EMBOSS." + EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \ + "Indexing CUTG failed." + eend + fi +} + +src_install() { + local file + dodoc README CODON_LABEL SPSUM_LABEL + if ! use minimal; then + dodir /usr/share/${PN} + mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \ + "Installing raw CUTG database failed." + fi + + if use emboss; then + dodir /usr/share/EMBOSS/data/CODONS + cd CODONS || die + for file in *; do + mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \ + "Installing the EMBOSS-indexed database failed." + done + fi +} diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml new file mode 100644 index 000000000000..59b110912ca6 --- /dev/null +++ b/sci-biology/cutg/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + Codon usage tables maintained at the Kazusa DNA Research Institute. + Codon usage in individual genes has been calculated using the + nucleotide sequence data obtained from the GenBank Genetic Sequence + Database. The compilation of codon usage is synchronized with each + major release of GenBank. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest new file mode 100644 index 000000000000..de90a59afc93 --- /dev/null +++ b/sci-biology/dialign-tx/Manifest @@ -0,0 +1 @@ +DIST DIALIGN-TX_1.0.2.tar.gz 1765296 SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 WHIRLPOOL 70565aa507f23a4f79affd8bda64e1b2698680e2288718c7518bd1d3782ca51ab747f8860e5513e7b1d480efd065702cc407c8137e96c47c3aad28ecdd345277 diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild new file mode 100644 index 000000000000..c73d043742b8 --- /dev/null +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +MY_P=DIALIGN-TX_${PV} + +DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment" +HOMEPAGE="http://dialign-tx.gobics.de/" +SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \ + -i source/Makefile || die #336533 + epatch "${FILESDIR}"/${P}-implicits.patch +} + +src_compile() { + emake -C source clean + emake -C source CC="$(tc-getCC)" \ + CPPFLAGS="" +} + +src_install() { + dobin "${S}"/source/dialign-tx + insinto /usr/$(get_libdir)/${PN}/conf + doins "${S}"/conf/* +} + +pkg_postinst() { + einfo "The configuration directory is" + einfo "${ROOT}usr/$(get_libdir)/${PN}/conf" + einfo "You will need to pass this to ${PN} on every run." +} diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch new file mode 100644 index 000000000000..a8388d03232f --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch @@ -0,0 +1,18 @@ +--- source/museq.c ++++ source/museq.c +@@ -38,6 +38,7 @@ + //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + // struct prob_dist *pdist); + //extern struct diag_col *create_diag_col(int seq_amount); ++extern void free_diag(struct diag* dg); + extern void free_diag_col(struct diag_col* dcol); + extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, + struct prob_dist *pdist, +@@ -52,6 +53,7 @@ + + // alig.c + extern struct alignment* create_empty_alignment(struct seq_col *scol); ++extern void free_alignment(struct alignment *algn); + //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); + extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol, + struct scr_matrix* smatrix, diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/dialign-tx/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/dialign2/Manifest b/sci-biology/dialign2/Manifest new file mode 100644 index 000000000000..8f3f4080e56f --- /dev/null +++ b/sci-biology/dialign2/Manifest @@ -0,0 +1 @@ +DIST dialign-2.2.1-src.tar.gz 209015 SHA256 046361bb4ca6e4ab2ac5e634cfcd673f964a887006c09c1b8bd3310fac86f519 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 WHIRLPOOL a6c5cd25e8e1f3d3738ae0a7f9eaac2509a17400cc3492b9b0b5991c08df08b586c003bbaa3f92d22ae8dd13a66488e6acbbce0aca798cfd20938cb391a02f84 diff --git a/sci-biology/dialign2/dialign2-2.2.1.ebuild b/sci-biology/dialign2/dialign2-2.2.1.ebuild new file mode 100644 index 000000000000..58557729b529 --- /dev/null +++ b/sci-biology/dialign2/dialign2-2.2.1.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="Multiple sequence alignment" +HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign" +SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-2.2.1-src.tar.gz" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/dialign_package + +src_compile() { + emake -C src \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -I. -DCONS -c" +} + +src_install() { + dobin src/${PN}-2 + insinto /usr/share/${PN} + doins dialign2_dir/* + + cat >> "${T}"/80${PN} <<- EOF + DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" + EOF + doenvd "${T}"/80${PN} +} diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml new file mode 100644 index 000000000000..7bc6ee8ea837 --- /dev/null +++ b/sci-biology/dialign2/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/diya/Manifest b/sci-biology/diya/Manifest new file mode 100644 index 000000000000..fe0ae5f610cb --- /dev/null +++ b/sci-biology/diya/Manifest @@ -0,0 +1 @@ +DIST diya-1.0-rc4.tar.gz 386706 SHA256 13f7dd4dd7f96143948587884954e337552d7491347c2c174e786824880590c7 diff --git a/sci-biology/diya/diya-1.0_rc4.ebuild b/sci-biology/diya/diya-1.0_rc4.ebuild new file mode 100644 index 000000000000..2211525f8af9 --- /dev/null +++ b/sci-biology/diya/diya-1.0_rc4.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit perl-module + +DESCRIPTION="Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotation" +HOMEPAGE="http://gmod.org/wiki/Diya" +SRC_URI="mirror://sourceforge/diyg/files/diya/diya-1.0/diya-${PV/_/-}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="-minimal" +KEYWORDS="~amd64 ~x86" + +DEPEND="sci-biology/bioperl + dev-perl/Data-Utilities + dev-perl/XML-Simple" +RDEPEND="${DEPEND} + !minimal? ( + sci-biology/mummer + sci-biology/glimmer + sci-biology/trnascan-se + sci-biology/infernal )" + +# see ftp://ftp.ncbi.nih.gov/blast/ to check if blast and blast+ are different from ncbi-tools and ncbi-tools++ +# * rfamscan.pl v0.1 (http://www.sanger.ac.uk/Users/sgj/code/) +# * UniRef50 (http://www.ebi.ac.uk/uniref/) +# * Protein Clusters (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/CLUSTERS/) +# The file cddid_all.tbl can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/. + +S="${WORKDIR}/diya-${PV/_/-}" + +SRC_TEST=do + +src_install() { + mydoc="INSTALL README docs/diya.html" + perl-module_src_install + insinto /usr/share/${PN} + doins -r diya.conf docs examples scripts +} diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml new file mode 100644 index 000000000000..d6b9de8b20a7 --- /dev/null +++ b/sci-biology/diya/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">diyg</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest new file mode 100644 index 000000000000..60015030796d --- /dev/null +++ b/sci-biology/elph/Manifest @@ -0,0 +1,2 @@ +DIST ELPH-0.1.5.tar.gz 153150 RMD160 7e60e2cf9a99cb435768cebbcd1506164e8a901c SHA1 1a3820c851ac0d021c9696ba1fd4eec819d82dbc SHA256 6ffa160f85cb2569bdf869cb0514dc624afcef4f2d8a36efbd1228d1a16cf361 +DIST ELPH-1.0.1.tar.gz 113476 RMD160 854bc34aba30f1c7493536e1b2e36dd8143af7e7 SHA1 9c8bf6ac54ade29daa15dc07aeeb94747626298a SHA256 6d944401d2457d75815a34dbb5780f05df569eb1edfd00909b33c4c4c4ff40b9 diff --git a/sci-biology/elph/elph-0.1.5.ebuild b/sci-biology/elph/elph-0.1.5.ebuild new file mode 100644 index 000000000000..5fc361ace8fd --- /dev/null +++ b/sci-biology/elph/elph-0.1.5.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils toolchain-funcs + +DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" +LICENSE="Artistic" +HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="x86" + +S="${WORKDIR}/ELPH/sources" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-usage.patch + sed -i -e "s/CC := g++/CC := $(tc-getCXX)/" \ + -e "s/-fno-exceptions -fno-rtti -D_REENTRANT -g/${CXXFLAGS}/" \ + -e "s/LINKER := g++/LINKER := $(tc-getCXX)/" \ + Makefile || die "Failed to patch Makefile." +} + +src_compile() { + make || die "Compilation failed." +} + +src_install() { + dobin elph || die "Failed to install program." + cd "${WORKDIR}"/ELPH + dodoc VERSION || die "Documentation installation failed." + newdoc Readme.ELPH README || die "Readme installation failed." +} diff --git a/sci-biology/elph/elph-1.0.1.ebuild b/sci-biology/elph/elph-1.0.1.ebuild new file mode 100644 index 000000000000..78476added83 --- /dev/null +++ b/sci-biology/elph/elph-1.0.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils toolchain-funcs + +DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" +LICENSE="Artistic" +HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +S=${WORKDIR}/ELPH/sources + +src_compile() { + emake CC="$(tc-getCXX)" LINKER="$(tc-getCXX)" \ + CFLAGS="${CXXFLAGS} -D_REENTRANT" LDFLAGS="${LDFLAGS}" || die +} + +src_install() { + dobin elph || die "Failed to install program." + cd "${WORKDIR}"/ELPH + dodoc VERSION || die "Documentation installation failed." + newdoc Readme.ELPH README || die "Readme installation failed." +} diff --git a/sci-biology/elph/files/elph-0.1.4-usage.patch b/sci-biology/elph/files/elph-0.1.4-usage.patch new file mode 100644 index 000000000000..be49e2d1ebb8 --- /dev/null +++ b/sci-biology/elph/files/elph-0.1.4-usage.patch @@ -0,0 +1,133 @@ +--- elph.cc~ 2003-06-03 14:45:22.000000000 -0400 ++++ elph.cc 2004-10-30 10:14:49.220415168 -0400 +@@ -26,11 +26,11 @@ + period variable\n\ + -x : print maximum positions within sequences\n\ + -g : find significance of motif\n\ +- -t <matrix> : test if there is significant difference between the two +- input files for a given motif matrix; <matrix> is the file ++ -t <matrix> : test if there is significant difference between the two\n\ ++ input files for a given motif matrix; <matrix> is the file\n\ + containing the motif matrix\n\ +- -l : compute Least Likely Consensus (LLC) for given motif +- -c : in conjunction with -m option: motif is not necessarily in ++ -l : compute Least Likely Consensus (LLC) for given motif\n\ ++ -c : in conjunction with -m option: motif is not necessarily in\n\ + the closest edit distance from input motif\n\ + LEN=n : n = length of motif\n\ + ITERNO=n : n = no of iterations to compute the global maximum;\n\ +@@ -41,7 +41,7 @@ + default = 1000\n\ + " + +-// global variables: ++// global variables: + int ITER_NO=10; + int MAX_LOOP=500; + int printmax=0; +@@ -66,7 +66,7 @@ + seqType t; + + GArgs args(argc, argv, "ho:abglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO="); +- ++ + // == Process arguments. + + int e; +@@ -83,7 +83,7 @@ + + if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files + +- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); ++ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); + M->twofilesignif(gdet,testfile,SignifNo,print,pattern); + + } +@@ -93,11 +93,11 @@ + // given motif + + M = new Motif(infile,outf,t,pattern); +- if(defLLC) { ++ if(defLLC) { + double llc=M->computeLLC(pattern,print); + fprintf(outf,"LLC = %f\n",llc); + } +- ++ + } + else { + +@@ -108,7 +108,7 @@ + } + + double globAlignProb; +- ++ + globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet); + + +@@ -116,13 +116,13 @@ + /*info=M->InfoPar(globAlignProb); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info); + M->printMotif();*/ +- ++ + // optimizing + fprintf(stderr,"Optimizing...\n"); + globAlignProb=M->optimize(globAlignProb,info,closest); + fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n"); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb)); +- ++ + if(runsignif) { + M->runforsignif(SignifNo,print,gdet,pattern); + } +@@ -134,17 +134,17 @@ + + seqType Process_Options(GArgs* args) + { +- +- if (args->startNonOpt()) { //parse the non-options arguments ++ ++ if (args->startNonOpt()) { //parse the non-options arguments + //(usually filenames) + infile=args->nextNonOpt(); + } + +- if (infile.is_empty() || args->getOpt('h')!=NULL) ++ if (infile.is_empty() || args->getOpt('h')!=NULL) + GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input + + testfile=args->nextNonOpt(); +- ++ + GString outfile=args->getOpt('o'); + if (!outfile.is_empty()) { + outf=fopen(outfile, "w"); +@@ -156,7 +156,7 @@ + matrixfile=args->getOpt('t'); + + GString param; +- ++ + pattern=args->getOpt('m'); + if(pattern.is_empty()) { + param=args->getOpt("LEN"); +@@ -200,7 +200,7 @@ + + seqType t; + if(args->getOpt('a')!=NULL) t=aac; else t=nucl; +- ++ + return(t); + + } +@@ -210,7 +210,7 @@ + Motif *M; + + double llcmax=-HUGE_VAL; +- GString seed; ++ GString seed; + for(int i1=0;i1<4;i1++) + for(int i2=0;i2<4;i2++) + for(int i3=0;i3<4;i3++) diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch new file mode 100644 index 000000000000..139b83c1c1c6 --- /dev/null +++ b/sci-biology/elph/files/elph-0.1.5-usage.patch @@ -0,0 +1,133 @@ +--- elph.cc.old 2005-01-11 14:17:47.000000000 -0500 ++++ elph.cc 2005-01-27 19:42:30.218350552 -0500 +@@ -26,11 +26,11 @@ + period variable\n\ + -x : print maximum positions within sequences\n\ + -g : find significance of motif\n\ +- -t <matrix> : test if there is significant difference between the two +- input files for a given motif matrix; <matrix> is the file ++ -t <matrix> : test if there is significant difference between the two\n\ ++ input files for a given motif matrix; <matrix> is the file\n\ + containing the motif matrix\n\ +- -l : compute Least Likely Consensus (LLC) for given motif +- -c : in conjunction with -m option: motif is not necessarily in ++ -l : compute Least Likely Consensus (LLC) for given motif\n\ ++ -c : in conjunction with -m option: motif is not necessarily in\n\ + the closest edit distance from input motif\n\ + LEN=n : n = length of motif\n\ + ITERNO=n : n = no of iterations to compute the global maximum;\n\ +@@ -41,7 +41,7 @@ + default = 1000\n\ + " + +-// global variables: ++// global variables: + int ITER_NO=10; + int MAX_LOOP=500; + int printmax=0; +@@ -66,7 +66,7 @@ + seqType t; + + GArgs args(argc, argv, "ho:abcglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO="); +- ++ + // == Process arguments. + + int e; +@@ -83,7 +83,7 @@ + + if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files + +- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); ++ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); + M->twofilesignif(gdet,testfile,SignifNo,print,pattern); + + } +@@ -93,11 +93,11 @@ + // given motif + + M = new Motif(infile,outf,t,pattern); +- if(defLLC) { ++ if(defLLC) { + double llc=M->computeLLC(pattern,print); + fprintf(outf,"LLC = %f\n",llc); + } +- ++ + } + else { + +@@ -108,7 +108,7 @@ + } + + double globAlignProb; +- ++ + globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet); + + +@@ -116,13 +116,13 @@ + /*info=M->InfoPar(globAlignProb); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info); + M->printMotif();*/ +- ++ + // optimizing + fprintf(stderr,"Optimizing...\n"); + globAlignProb=M->optimize(globAlignProb,info,closest); + fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n"); + fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb)); +- ++ + if(runsignif) { + M->runforsignif(SignifNo,print,gdet,pattern); + } +@@ -134,17 +134,17 @@ + + seqType Process_Options(GArgs* args) + { +- +- if (args->startNonOpt()) { //parse the non-options arguments ++ ++ if (args->startNonOpt()) { //parse the non-options arguments + //(usually filenames) + infile=args->nextNonOpt(); + } + +- if (infile.is_empty() || args->getOpt('h')!=NULL) ++ if (infile.is_empty() || args->getOpt('h')!=NULL) + GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input + + testfile=args->nextNonOpt(); +- ++ + GString outfile=args->getOpt('o'); + if (!outfile.is_empty()) { + outf=fopen(outfile, "w"); +@@ -156,7 +156,7 @@ + matrixfile=args->getOpt('t'); + + GString param; +- ++ + pattern=args->getOpt('m'); + if(pattern.is_empty()) { + param=args->getOpt("LEN"); +@@ -200,7 +200,7 @@ + + seqType t; + if(args->getOpt('a')!=NULL) t=aac; else t=nucl; +- ++ + return(t); + + } +@@ -210,7 +210,7 @@ + Motif *M; + + double llcmax=-HUGE_VAL; +- GString seed; ++ GString seed; + for(int i1=0;i1<4;i1++) + for(int i2=0;i2<4;i2++) + for(int i3=0;i3<4;i3++) diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml new file mode 100644 index 000000000000..469879ba8f5b --- /dev/null +++ b/sci-biology/elph/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + ELPH is a general-purpose Gibbs sampler for finding motifs in a set of + DNA or protein sequences. The program takes as input a set containing + anywhere from a few dozen to thousands of sequences, and searches + through them for the most common motif, assuming that each sequence + contains one copy of the motif. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest new file mode 100644 index 000000000000..408037d6a1ec --- /dev/null +++ b/sci-biology/embassy-cbstools/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-cbstools-1.0.0.tar.gz 343812 SHA256 b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693 +DIST embassy-cbstools-1.0.0.650.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild new file mode 100644 index 000000000000..b2f9738aa495 --- /dev/null +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Applications from the CBS group" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild new file mode 100644 index 000000000000..ca1539905c99 --- /dev/null +++ b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS wrappers for applications from the CBS group" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..d29310efcb47 --- /dev/null +++ b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index a70d4d2..b8f5e79 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 824a03c..9db171d 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -19,9 +19,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -65,5 +63,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-cbstools/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest new file mode 100644 index 000000000000..43c85d868e12 --- /dev/null +++ b/sci-biology/embassy-clustalomega/Manifest @@ -0,0 +1 @@ +DIST embassy-clustalomega-1.1.0.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54 diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild new file mode 100644 index 000000000000..620383da2eb0 --- /dev/null +++ b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Clustal Omega - Scalable multiple protein sequences alignment" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" + +RDEPEND+=" sci-biology/clustal-omega" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch new file mode 100644 index 000000000000..5525d79b525f --- /dev/null +++ b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f12ed19..b143922 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 9135679..c201149 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-clustalomega/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest new file mode 100644 index 000000000000..74ca98eecf1d --- /dev/null +++ b/sci-biology/embassy-domainatrix/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-domainatrix-0.1.0.tar.gz 420983 SHA256 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1 +DIST embassy-domainatrix-0.1.650.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0 diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild new file mode 100644 index 000000000000..ee009ca052f0 --- /dev/null +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein domain analysis add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild new file mode 100644 index 000000000000..9734758ee2ad --- /dev/null +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein domain analysis add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..a932e1ebe21e --- /dev/null +++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index d16cc02..d327a0d 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index d405d00..54be7ca 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -64,5 +62,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-domainatrix/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest new file mode 100644 index 000000000000..87fdc97be669 --- /dev/null +++ b/sci-biology/embassy-domalign/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-domalign-0.1.0.tar.gz 462156 SHA256 c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a +DIST embassy-domalign-0.1.650.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37 diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild new file mode 100644 index 000000000000..8a0e7bb2de92 --- /dev/null +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein domain alignment add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild new file mode 100644 index 000000000000..b26dd2cb35df --- /dev/null +++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein domain alignment add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..033ddf7b6535 --- /dev/null +++ b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch @@ -0,0 +1,101 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 7 ++----- + 2 files changed, 9 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 693eb4d..dc0fda9 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 8785446..fe85f11 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,10 +17,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${embprefix}/include \ +- -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -63,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-domalign/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest new file mode 100644 index 000000000000..76709b452174 --- /dev/null +++ b/sci-biology/embassy-domsearch/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-domsearch-0.1.0.tar.gz 470537 SHA256 fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95 +DIST embassy-domsearch-0.1.650.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 WHIRLPOOL 02afa5cdf4d82b127317537c088b91592f6c4624769b7b13f030fd59590b533fb8ec62189b165bbf885d967069883f5e08f562e7187294468700ce9571a47111 diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild new file mode 100644 index 000000000000..48f945c08d8a --- /dev/null +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein domain search add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild new file mode 100644 index 000000000000..e9c4a6c48fd4 --- /dev/null +++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein domain search add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..d24857c8386d --- /dev/null +++ b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f0f97fa..d419d7d 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 9829ebd..433a5c5 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -62,5 +60,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-domsearch/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest new file mode 100644 index 000000000000..7c67122bbc0a --- /dev/null +++ b/sci-biology/embassy-emnu/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-emnu-1.05.tar.gz 390229 SHA256 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333 +DIST embassy-emnu-1.05.650.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild new file mode 100644 index 000000000000..3163cb635c4c --- /dev/null +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05-r5.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +RDEPEND="sys-libs/ncurses + ${RDEPEND}" + +DEPEND="sys-libs/ncurses + ${DEPEND}" diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild new file mode 100644 index 000000000000..ee617cddf7ca --- /dev/null +++ b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Simple menu of EMBOSS applications" +EBO_EXTRA_ECONF="$(use_enable ncurses curses)" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +IUSE+=" ncurses" + +RDEPEND+=" ncurses? ( sys-libs/ncurses )" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch new file mode 100644 index 000000000000..4e14bac1704a --- /dev/null +++ b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch @@ -0,0 +1,139 @@ + configure.ac | 67 +++++++++++--------------------------------------- + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 7 +++--- + 3 files changed, 18 insertions(+), 58 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 7482ade..b815bdb 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -899,20 +864,16 @@ dnl fi + + + dnl emnu and mse only: uses curses +-dnl Test if --with-curses is given +-AC_ARG_WITH([curses], +-[AS_HELP_STRING([--with-curses], [curses (or ncurses)])]) ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) + +-AC_MSG_CHECKING([for curses]) +- +-AS_IF([test "${with_curses}"], +-[ +- CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" +- LDFLAGS="$LDFLAGS -L${with_curses}/lib" ++AS_IF([test "x$enable_curses" = "xyes"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++ PKG_CHECK_MODULES([FORM], [form]) ++ PKG_CHECK_MODULES([MENU], [menu]) + ]) + +-AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"]) +- + + + +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index b295079..330c76f 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,8 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \ ++ $(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS) + endif + + if ISSHARED +@@ -57,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la -lmenu -lform $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) ++ -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) + endif diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-emnu/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest new file mode 100644 index 000000000000..ade72c4415f8 --- /dev/null +++ b/sci-biology/embassy-esim4/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-esim4-1.0.0.tar.gz 431898 SHA256 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577 +DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62 diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild new file mode 100644 index 000000000000..927f8ab6a202 --- /dev/null +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r5.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild new file mode 100644 index 000000000000..470cb0b299cd --- /dev/null +++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..ead54c91b5f3 --- /dev/null +++ b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 924220a..2c45f46 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 0620938..0304bb8 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -63,5 +61,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-esim4/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest new file mode 100644 index 000000000000..1aeb5559decf --- /dev/null +++ b/sci-biology/embassy-hmmer/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-hmmer-2.3.2.tar.gz 565686 SHA256 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258 +DIST embassy-hmmer-2.3.2.650.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83 diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild new file mode 100644 index 000000000000..a246730c4b22 --- /dev/null +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2-r2.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +RDEPEND="~sci-biology/hmmer-2.3.2" + +src_install() { + embassy_src_install + insinto /usr/include/emboss/hmmer + doins src/*.h +} diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild new file mode 100644 index 000000000000..871d512a172a --- /dev/null +++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Wrappers for HMMER - Biological sequence analysis with profile HMMs" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +RDEPEND+="sci-biology/hmmer" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch new file mode 100644 index 000000000000..90c45632eada --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 037ca00..f539ab6 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index dc789bc..5a8c38e 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -67,5 +65,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-hmmer/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest new file mode 100644 index 000000000000..6d689c8ee615 --- /dev/null +++ b/sci-biology/embassy-iprscan/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-iprscan-4.3.1.tar.gz 339939 SHA256 df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a +DIST embassy-iprscan-4.3.1.650.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8 diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild new file mode 100644 index 000000000000..f8e7380c017c --- /dev/null +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="InterProScan motif detection add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild new file mode 100644 index 000000000000..2ed141470a13 --- /dev/null +++ b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="InterProScan motif detection add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch new file mode 100644 index 000000000000..8c8a1060e30f --- /dev/null +++ b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 9052ca5..c12c268 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 0afc96a..904b41a 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -58,5 +56,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-iprscan/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest new file mode 100644 index 000000000000..13e38d3a79dd --- /dev/null +++ b/sci-biology/embassy-meme/Manifest @@ -0,0 +1 @@ +DIST embassy-meme-4.7.650.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51 diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild new file mode 100644 index 000000000000..bdbc70a3bab2 --- /dev/null +++ b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Wrappers for MEME - Multiple Em for Motif Elicitation" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +RDEPEND+=" sci-biology/meme" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch new file mode 100644 index 000000000000..56f5814e1efa --- /dev/null +++ b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 391989f..d921f25 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 1600399..9f28162 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-meme/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-memenew/Manifest b/sci-biology/embassy-memenew/Manifest new file mode 100644 index 000000000000..f42b89771c56 --- /dev/null +++ b/sci-biology/embassy-memenew/Manifest @@ -0,0 +1,2 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-memenew-0.1.0.tar.gz 450102 SHA256 5411d1445feb1b5e460e598a9d7e670a4357fe7aa350d96531b1aa9c79fab636 diff --git a/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild b/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild new file mode 100644 index 000000000000..58f3852fce08 --- /dev/null +++ b/sci-biology/embassy-memenew/embassy-memenew-0.1.0-r1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS wrappers for MEME - Multiple Em for Motif Elicitation" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +src_install() { + embassy_src_install + insinto /usr/include/emboss/meme + doins src/INCLUDE/*.h +} diff --git a/sci-biology/embassy-memenew/metadata.xml b/sci-biology/embassy-memenew/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-memenew/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-mira/Manifest b/sci-biology/embassy-mira/Manifest new file mode 100644 index 000000000000..6229623c3b0e --- /dev/null +++ b/sci-biology/embassy-mira/Manifest @@ -0,0 +1,2 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-mira-2.8.2.tar.gz 365566 SHA256 33d756bd50fe26c04aff862f34230feaad831cbe538096e4d8e5c8e0b6784fe1 diff --git a/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild b/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild new file mode 100644 index 000000000000..28e3d2587d1e --- /dev/null +++ b/sci-biology/embassy-mira/embassy-mira-2.8.2.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Fragment assembly add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-mira/metadata.xml b/sci-biology/embassy-mira/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-mira/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest new file mode 100644 index 000000000000..15e2c00a0f43 --- /dev/null +++ b/sci-biology/embassy-mse/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-mse-1.0.0.tar.gz 445562 SHA256 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90 +DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b diff --git a/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild b/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild new file mode 100644 index 000000000000..8767aee8f8d3 --- /dev/null +++ b/sci-biology/embassy-mse/embassy-mse-1.0.0-r6.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of MSE - Multiple Sequence Screen Editor" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" + +src_install() { + embassy_src_install + insinto /usr/include/emboss/mse + doins h/*.h +} diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild new file mode 100644 index 000000000000..32b6410620e1 --- /dev/null +++ b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" +EBO_EXTRA_ECONF="$(use_enable ncurses curses)" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" +IUSE+=" ncurses" + +RDEPEND+=" ncurses? ( sys-libs/ncurses )" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) + +src_install() { + autotools-utils_src_install + insinto /usr/include/emboss/mse + doins h/*.h +} diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch new file mode 100644 index 000000000000..c1095b266d60 --- /dev/null +++ b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch @@ -0,0 +1,149 @@ + ckit/Makefile.am | 2 +- + configure.ac | 67 +++++++++++--------------------------------------- + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++--- + 4 files changed, 18 insertions(+), 59 deletions(-) + +diff --git a/ckit/Makefile.am b/ckit/Makefile.am +index f87b131..a670d2b 100644 +--- a/ckit/Makefile.am ++++ b/ckit/Makefile.am +@@ -2,7 +2,7 @@ + + lib_LTLIBRARIES = libckit.la + +-AM_CPPFLAGS = -I../h ++AM_CPPFLAGS = -I$(top_srcdir)/h + + CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ + seqspec.c ttyinterface.c nextseqentry.c \ +diff --git a/configure.ac b/configure.ac +index a20d488..eb208bf 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +@@ -1000,17 +965,13 @@ AS_IF([test "x${enable_savestats}" = "xyes"], + + + +-dnl emnu and mse only: uses curses +-dnl Test if --with-curses is given +-AC_ARG_WITH([curses], +- [AS_HELP_STRING([--with-curses], +- [curses (or ncurses)])]) +-if test "${with_curses}" ; then +-AC_MSG_CHECKING([for curses]) +-CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" +-LDFLAGS="$LDFLAGS -L${with_curses}/lib" +-fi +-AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") ++dnl Test if --enable-curses is given ++AC_ARG_ENABLE([curses], ++[AS_HELP_STRING([--enable-curses], [curses])]) ++ ++AS_IF([test "x$enable_curses" = "xyes"], [ ++ PKG_CHECK_MODULES([NCURSES], [ncurses]) ++]) + + + +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index b44632a..84e89b5 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -18,9 +18,7 @@ AM_CPPFLAGS = -I../h \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../h -I${embprefix}/include \ +- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ +- $(NLINCLUDES) ++AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../ckit/libckit.la \ + $(XLIB) + else + LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) + endif diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-mse/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest new file mode 100644 index 000000000000..638f9da73ac0 --- /dev/null +++ b/sci-biology/embassy-phylipnew/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-phylipnew-3.67.tar.gz 1624802 SHA256 efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945 +DIST embassy-phylipnew-3.69.650.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58 diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild new file mode 100644 index 000000000000..2bc4a956502f --- /dev/null +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.67.ebuild @@ -0,0 +1,14 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of PHYLIP - The Phylogeny Inference Package" +LICENSE="freedist" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild new file mode 100644 index 000000000000..18b8b33c91fb --- /dev/null +++ b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="The Phylogeny Inference Package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +LICENSE+=" freedist" + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch new file mode 100644 index 000000000000..1cba944094a2 --- /dev/null +++ b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch @@ -0,0 +1,111 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 7 ++----- + 3 files changed, 10 insertions(+), 48 deletions(-) + +diff --git a/configure.ac b/configure.ac +index e5bfaf1..09ed517 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -781,21 +754,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -918,6 +876,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 1883ce9..fb1787f 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -16,10 +16,7 @@ AM_CPPFLAGS = -I../include -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../include -I${embprefix}/include \ +- -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -120,5 +117,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + ../../../plplot/libeplplot.la $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-phylipnew/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest new file mode 100644 index 000000000000..8e615337acb6 --- /dev/null +++ b/sci-biology/embassy-signature/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-signature-0.1.0.tar.gz 574940 SHA256 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f +DIST embassy-signature-0.1.650.tar.gz 622294 SHA256 2ab34cc76caaaefe7914e9b00dd12ee81a32d7a7ccca20ba901d67f1e2c2f27e SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 WHIRLPOOL 1a943266ee9092f13fb3ad0779cdfe70e3cb5c1ed7d31164a93da90aaea2df95150970e0ef22df89c3cc97dfe7564092f2cab8aad7fb720e2f456cb363666de3 diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild new file mode 100644 index 000000000000..83f7f8487ee8 --- /dev/null +++ b/sci-biology/embassy-signature/embassy-signature-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein signature add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild new file mode 100644 index 000000000000..b70e05d76087 --- /dev/null +++ b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein signature add-on package" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) +AUTOTOOLS_AUTORECONF=1 +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..32e4d684cbb3 --- /dev/null +++ b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 2f5ddd0..827543f 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index d77e43c..849f17a 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -68,5 +66,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-signature/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest new file mode 100644 index 000000000000..7cd125ec2b29 --- /dev/null +++ b/sci-biology/embassy-structure/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-structure-0.1.0.tar.gz 532035 SHA256 cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23 +DIST embassy-structure-0.1.650.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03 diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild new file mode 100644 index 000000000000..64b653083ff2 --- /dev/null +++ b/sci-biology/embassy-structure/embassy-structure-0.1.0-r3.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="Protein structure add-on package for EMBOSS" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild new file mode 100644 index 000000000000..b6fcd9770e3b --- /dev/null +++ b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Protein structure add-on package" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch new file mode 100644 index 000000000000..bdd9e37714e4 --- /dev/null +++ b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch @@ -0,0 +1,100 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 6 ++---- + 2 files changed, 9 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index ee482ef..e4af4b1 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 81ade5d..2ed0d14 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -66,5 +64,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-structure/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest new file mode 100644 index 000000000000..7da88ac0231b --- /dev/null +++ b/sci-biology/embassy-topo/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-topo-1.0.0.tar.gz 379929 SHA256 a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16 +DIST embassy-topo-2.0.650.tar.gz 443510 SHA256 a8b8b7c1e04be44b5d6982614a9af44b84d0282bb917ed29e23a0a710241ad6f SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 WHIRLPOOL fbe0edadeafe14b4b24be6fd65ed51dc9572f89e12e6f038017e9dd208a867138219350ccde6ca3eeab94ccedf34e5ec672a65cbf30c3819387407e778caeb55 diff --git a/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild b/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild new file mode 100644 index 000000000000..f0ffdd356594 --- /dev/null +++ b/sci-biology/embassy-topo/embassy-topo-1.0.0-r5.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of TOPO - Transmembrane protein display" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild new file mode 100644 index 000000000000..dec34b9db31f --- /dev/null +++ b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Transmembrane protein display" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch new file mode 100644 index 000000000000..3c37879de8c8 --- /dev/null +++ b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch @@ -0,0 +1,110 @@ + configure.ac | 49 +++++++------------------------------------------ + emboss_acd/Makefile.am | 2 +- + src/Makefile.am | 6 ++---- + 3 files changed, 10 insertions(+), 47 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 8eeb8ca..4fd28ac 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -635,33 +635,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -737,21 +710,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -874,6 +832,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss_acd/Makefile.am b/emboss_acd/Makefile.am +index e1c1878..e253c95 100644 +--- a/emboss_acd/Makefile.am ++++ b/emboss_acd/Makefile.am +@@ -1,3 +1,3 @@ + +-pkgdata_DATA = *.acd ++pkgdata_DATA = $(srcdir)/*.acd + pkgdatadir=$(prefix)/share/EMBOSS/acd +diff --git a/src/Makefile.am b/src/Makefile.am +index 1cdb0b1..0e86a4b 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -17,9 +17,7 @@ AM_CPPFLAGS = -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -60,5 +58,5 @@ LDADD = ../../../nucleus/libnucleus.la ../../../ajax/acd/libacd.la \ + $(XLIB) + else + LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ +- -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-topo/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest new file mode 100644 index 000000000000..d7061f3dd813 --- /dev/null +++ b/sci-biology/embassy-vienna/Manifest @@ -0,0 +1,3 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST embassy-6.0.1-vienna-1.7.2.tar.gz 682200 SHA256 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db +DIST embassy-vienna-1.7.2.650.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2 diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild new file mode 100644 index 000000000000..62f1626a26a4 --- /dev/null +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EBO_DESCRIPTION="Vienna RNA package - RNA folding" + +AUTOTOOLS_AUTORECONF=1 + +inherit emboss-r1 + +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +PATCHES=( "${FILESDIR}"/${P}_fix-build-system.patch ) diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild new file mode 100644 index 000000000000..49eac3cdc4d8 --- /dev/null +++ b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.ebuild @@ -0,0 +1,13 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EBOV="6.0.1" + +inherit embassy + +DESCRIPTION="EMBOSS integrated version of the Vienna RNA package - RNA folding" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz + mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" + +KEYWORDS="amd64 ~ppc x86" diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch new file mode 100644 index 000000000000..5ce365ed5497 --- /dev/null +++ b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch @@ -0,0 +1,108 @@ + configure.ac | 49 +++++++------------------------------------------ + src/Makefile.am | 7 +++---- + 2 files changed, 10 insertions(+), 46 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f5a4ecf..bbe0743 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -649,33 +649,6 @@ AS_CASE([${host_os}], + + + +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- +- +- + dnl FIXME: This does no longer seem required with Autoconf 2.67? + dnl Intel MacOSX 10.6 puts X11 in a non-standard place + dnl AS_IF([test "x${with_x}" != "xno"], +@@ -751,21 +724,6 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE +- +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) +- +- +- +- + dnl Test if --enable-localforce given + locallink="no" + embprefix="/usr/local" +@@ -888,6 +846,13 @@ AC_ARG_ENABLE([systemlibs], + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/src/Makefile.am b/src/Makefile.am +index 1f5b756..e178914 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -32,9 +32,7 @@ AM_CPPFLAGS = -I../H -I../../../nucleus -I../../../ajax/pcre \ + -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ + -I../../../ajax/acd -I../../../plplot + else +-AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ +- $(NLINCLUDES) \ +- -I${embprefix}/include/epcre ++AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) + endif + + if ISSHARED +@@ -87,6 +85,7 @@ LINKFLAGS = $(VERS_INF) + endif + + liboviennarna_la_LDFLAGS = $(LINKFLAGS) ++liboviennarna_la_LIBADD = -lajax + + ovrnaalifold_SOURCES = vrnaalifold.c + ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c +@@ -119,5 +118,5 @@ LDADD = liboviennarna.la \ + $(XLIB) + else + LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ +- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) ++ -lensembl -lajaxg -lajax $(NLADD) $(XLIB) + endif diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy-vienna/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/embassy/embassy-6.0.1.ebuild b/sci-biology/embassy/embassy-6.0.1.ebuild new file mode 100644 index 000000000000..3c7c37b20ff6 --- /dev/null +++ b/sci-biology/embassy/embassy-6.0.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" +HOMEPAGE="http://www.emboss.org/" +SRC_URI="" +LICENSE="GPL-2 freedist" + +SLOT="0" +KEYWORDS="amd64 ~ppc x86" +IUSE="" + +RDEPEND="!<sci-biology/emboss-6.0.1 + !sci-biology/embassy-meme + !sci-biology/embassy-phylip + ~sci-biology/emboss-6.0.1 + =sci-biology/embassy-cbstools-1.0.0 + =sci-biology/embassy-domainatrix-0.1.0-r3 + =sci-biology/embassy-domalign-0.1.0-r3 + =sci-biology/embassy-domsearch-0.1.0-r3 + =sci-biology/embassy-emnu-1.05-r5 + =sci-biology/embassy-esim4-1.0.0-r5 + =sci-biology/embassy-hmmer-2.3.2-r2 + =sci-biology/embassy-iprscan-4.3.1 + =sci-biology/embassy-memenew-0.1.0-r1 + =sci-biology/embassy-mira-2.8.2 + =sci-biology/embassy-mse-1.0.0-r6 + =sci-biology/embassy-phylipnew-3.67 + =sci-biology/embassy-signature-0.1.0-r3 + =sci-biology/embassy-structure-0.1.0-r3 + =sci-biology/embassy-topo-1.0.0-r5 + =sci-biology/embassy-vienna-1.7.2" diff --git a/sci-biology/embassy/embassy-6.6.0.ebuild b/sci-biology/embassy/embassy-6.6.0.ebuild new file mode 100644 index 000000000000..d663e22efda3 --- /dev/null +++ b/sci-biology/embassy/embassy-6.6.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" +HOMEPAGE="http://emboss.sourceforge.net/embassy/" + +LICENSE+=" freedist" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" + +RDEPEND+=" + >=sci-biology/embassy-cbstools-1.0.0.650 + >=sci-biology/embassy-clustalomega-1.1.0 + >=sci-biology/embassy-domainatrix-0.1.650 + >=sci-biology/embassy-domalign-0.1.650 + >=sci-biology/embassy-domsearch-0.1.650 + >=sci-biology/embassy-emnu-1.05.650 + >=sci-biology/embassy-esim4-1.0.0.650 + >=sci-biology/embassy-hmmer-2.3.2.650 + >=sci-biology/embassy-iprscan-4.3.1.650 + >=sci-biology/embassy-meme-4.7.650 + >=sci-biology/embassy-mse-3.0.0.650 + >=sci-biology/embassy-phylipnew-3.69.650 + >=sci-biology/embassy-signature-0.1.650 + >=sci-biology/embassy-structure-0.1.650 + >=sci-biology/embassy-topo-2.0.650 + >=sci-biology/embassy-vienna-1.7.2.650 +" diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/embassy/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest new file mode 100644 index 000000000000..c364f2c77e86 --- /dev/null +++ b/sci-biology/emboss/Manifest @@ -0,0 +1,4 @@ +DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d +DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d +DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe +DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild new file mode 100644 index 000000000000..0edfd7a639d0 --- /dev/null +++ b/sci-biology/emboss/emboss-6.0.1.ebuild @@ -0,0 +1,112 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=1 + +inherit eutils + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +HOMEPAGE="http://emboss.sourceforge.net/" +SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz" +LICENSE="GPL-2 LGPL-2" + +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="X png minimal" + +DEPEND=" + X? ( x11-libs/libXt ) + png? ( + sys-libs/zlib + media-libs/libpng + media-libs/gd + ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + )" + +RDEPEND="${DEPEND} + !sys-devel/cons" + +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch + + local link_string="$(pkg-config --libs x11)" + if use png; then + link_string="${link_string} -lgd $(pkg-config --libs libpng)" + fi + sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ + || die "Failed to patch ajax Makefile" +} + +src_compile() { + local myconf + myconf="--includedir=${D}/usr/include/emboss" + use X || myconf="${EXTRA_CONF} --without-x" + use png || myconf="${EXTRA_CONF} --without-pngdriver" + + econf ${myconf} + # Do not install the JEMBOSS component (the --without-java configure option + # does not work). JEMBOSS will eventually be available as a separate package. + sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ + Makefile || die + emake || die +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ + || die "Failed to install documentation." + newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \ + || die "Failed to install Gentoo readme file." + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss || die "Failed to install environment file." + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die + dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die + dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die + dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die + + # Clashes #330507 + mv "${D}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild new file mode 100644 index 000000000000..e8baba4c7752 --- /dev/null +++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild @@ -0,0 +1,117 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit autotools eutils + +MY_PATCH="4" + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +HOMEPAGE="http://emboss.sourceforge.net/" +SRC_URI=" + ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz + ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz" + +LICENSE="GPL-2 LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc minimal mysql pdf png postgres static-libs X" + +DEPEND=" + dev-libs/expat + dev-libs/libpcre:3 + sci-libs/plplot + sys-libs/zlib + mysql? ( virtual/mysql ) + pdf? ( media-libs/libharu ) + png? ( + sys-libs/zlib + media-libs/libpng + media-libs/gd + ) + postgres? ( dev-db/postgresql ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + ) + X? ( x11-libs/libXt )" +RDEPEND="${DEPEND} + !sys-devel/cons" +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}" + +src_prepare() { + epatch "${WORKDIR}"/${P}.patch + epatch \ + "${FILESDIR}"/${PV}-unbundle-libs.patch \ + "${FILESDIR}/${PF}_plcol.patch" + eautoreconf +} + +src_configure() { + econf \ + $(use_with X x) \ + $(use_with png pngdriver "${EPREFIX}/usr") \ + $(use_with doc docroot "${EPREFIX}/usr") \ + $(use_with pdf hpdf "${EPREFIX}/usr") \ + $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \ + $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \ + $(use_enable amd64 64) \ + $(use_enable static-libs static) \ + --without-java \ + --enable-large \ + --enable-systemlibs \ + --includedir="${ED}/usr/include/emboss" +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS + sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ + dodoc README.Gentoo + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals + dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs + dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials + dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html + + # Clashes #330507 + mv "${ED}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild new file mode 100644 index 000000000000..22d650f1107a --- /dev/null +++ b/sci-biology/emboss/emboss-6.6.0.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +inherit autotools-utils emboss-r1 eutils readme.gentoo + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" + +KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE+=" minimal" +LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0" + +RDEPEND+=" !sys-devel/cons" +PDEPEND+=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/primer3 + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + )" + +S="${WORKDIR}"/EMBOSS-${PV} + +DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ ) + +PATCHES=( + "${FILESDIR}"/${P}_fix-build-system.patch + "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch + "${FILESDIR}"/${P}_plplot-declarations.patch + "${FILESDIR}"/${P}_qa-implicit-declarations.patch +) + +src_install() { + # Use autotools-utils_* to remove useless *.la files + autotools-utils_src_install + + readme.gentoo_create_doc + + # Install env file for setting libplplot and acd files path. + cat > 22emboss <<- EOF + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" + EOF + doenvd 22emboss + + # Remove useless dummy files + find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." +} diff --git a/sci-biology/emboss/files/22emboss b/sci-biology/emboss/files/22emboss new file mode 100644 index 000000000000..177643ced11f --- /dev/null +++ b/sci-biology/emboss/files/22emboss @@ -0,0 +1,4 @@ +# plplot libs dir +PLPLOT_LIB="/usr/share/EMBOSS/" +# ACD files location +EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" diff --git a/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch new file mode 100644 index 000000000000..5e463744a739 --- /dev/null +++ b/sci-biology/emboss/files/6.3.1_p4-unbundle-libs.patch @@ -0,0 +1,600 @@ +diff --git a/Makefile.am b/Makefile.am +index 4fe2ed1..7f3a95f 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -5,12 +5,21 @@ ACLOCAL_AMFLAGS = -I m4 + + AUTOMAKE_OPTIONS = gnits + +-SUBDIRS = plplot ajax nucleus emboss test doc jemboss ++if !ESYSTEMLIBS ++EXTRA_DIRS = plplot ++endif ++ ++if GJEMBOSS ++JEMBOSS_DIR = jemboss ++endif ++ ++SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) ++DIST_SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc $(JEMBOSS_DIR) + + # AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\" + + # files with nonstandard names in this directory +-EXTRA_DIST = COMPAT LICENSE KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh ++EXTRA_DIST = COMPAT KNOWN_BUGS ONEWS PROBLEMS FAQ ChangeLog depcomp ltmain.sh + + # tar to pick up the other directories + # then remove any CVS subdirectories +diff --git a/README.fixes b/README.fixes +new file mode 100644 +index 0000000..3c56d79 +--- /dev/null ++++ b/README.fixes +@@ -0,0 +1,9 @@ ++The files in this directory are bugfix replacements for files in ++the EMBOSS-6.3.1 distribution. Just drop the replacement files in ++the location shown and redo the 'make install.' ++ ++Fix 1. EMBOSS-6.3.1/configure ++ EMBOSS-6.3.1/m4/mysql.m4 ++ ++21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of ++ hpdf support prevented inclusion of MySQL support. +diff --git a/ajax/Makefile.am b/ajax/Makefile.am +index 4a44f6f..cf27ff8 100644 +--- a/ajax/Makefile.am ++++ b/ajax/Makefile.am +@@ -1,6 +1,6 @@ + ## Process this file with automake to produce Makefile.in + if !ESYSTEMLIBS +-EXTRA_DIRS = expat zlib ++EXTRA_DIRS = pcre expat zlib + endif + +-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd ++SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd +diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am +index 02bcaa7..368ddfe 100644 +--- a/ajax/acd/Makefile.am ++++ b/ajax/acd/Makefile.am +@@ -13,10 +13,13 @@ CYGWIN_LDACD = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core \ + -I$(top_srcdir)/ajax/graphics \ +@@ -38,3 +41,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libacd_la_LDFLAGS = $(LINKFLAGS) ++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la ../ajaxdb/libajaxdb.la +diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am +index da57727..857ca5f 100644 +--- a/ajax/ajaxdb/Makefile.am ++++ b/ajax/ajaxdb/Makefile.am +@@ -13,11 +13,12 @@ CYGWIN_LDAJAXDB = -L../../plplot -L../pcre -L../expat -L../zlib -L../core \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre + endif + + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl + +@@ -37,3 +38,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajaxdb_la_LDFLAGS = $(LINKFLAGS) ++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la +diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am +index af27cb0..8fa4a3a 100644 +--- a/ajax/core/Makefile.am ++++ b/ajax/core/Makefile.am +@@ -12,13 +12,18 @@ CYGWIN_LDAJAX = -L../../plplot -L../expat -L../pcre -L../zlib \ + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_LIBS = -lexpat -lpcre + endif + ++EXTRA_DIST = ajax-pcre-config.h.in ++DISTCLEAN = ajax-pcre-config.h + + INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \ + -DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \ +--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES) ++$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS) + + AJAXSRC = ajalign.c ajarr.c ajassert.c \ + ajbase.c ajcall.c ajcod.c \ +@@ -44,7 +49,7 @@ ajindex.h ajjava.h ajlist.h \ + ajmath.h ajmatrices.h ajmem.h ajmess.h \ + ajnam.h ajnexus.h ajobo.h \ + ajpat.h ajpdb.h ajpdbio.h ajphylo.h \ +-ajrange.h ajreg.h ajreport.h ajresource.h \ ++ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \ + ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h \ + ajsort.h ajsql.h ajstr.h ajsys.h \ + ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h +@@ -61,3 +66,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajax_la_LDFLAGS = $(LINKFLAGS) ++libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS) +diff --git a/ajax/core/ajax-pcre-config.h.in b/ajax/core/ajax-pcre-config.h.in +new file mode 100644 +index 0000000..b09e4e6 +--- /dev/null ++++ b/ajax/core/ajax-pcre-config.h.in +@@ -0,0 +1 @@ ++@DEFINE_USE_SYSTEM_PCRE@ AJAX_USE_SYSTEM_PCRE +diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h +index 06793be..659f462 100644 +--- a/ajax/core/ajreg.h ++++ b/ajax/core/ajreg.h +@@ -16,9 +16,14 @@ extern "C" + #define ajreg_h + + #include "ajax.h" ++#include "ajax-pcre-config.h" ++#ifndef AJAX_USE_SYSTEM_PCRE + #include "pcre_config.h" + #include "pcre_internal.h" + #include "pcreposix.h" ++#else ++#include <pcre.h> ++#endif + + #define AJREG_OVECSIZE 30 + +@@ -41,7 +46,11 @@ extern "C" + ******************************************************************************/ + + typedef struct AjSRegexp { ++#ifndef AJAX_USE_SYSTEM_PCRE + real_pcre *pcre; ++#else ++ pcre *pcre; ++#endif + pcre_extra *extra; + int *ovector; + const char* orig; +diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am +index ca33a84..87e51bd 100644 +--- a/ajax/ensembl/Makefile.am ++++ b/ajax/ensembl/Makefile.am +@@ -10,12 +10,13 @@ CYGWIN_LDENSEMBL = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplo + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre + endif + + +-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \ +--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core ++INCLUDES = $(EXTRA_INCLUDES) \ ++-I$(top_srcdir)/ajax/core + + ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \ + ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \ +@@ -56,3 +57,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libensembl_la_LDFLAGS = $(LINKFLAGS) ++libensembl_la_LIBADD = ../core/libajax.la +diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am +index ab45afc..f61c605 100644 +--- a/ajax/graphics/Makefile.am ++++ b/ajax/graphics/Makefile.am +@@ -10,11 +10,15 @@ CYGWIN_LDAJAXG = -L../../plplot -L../expat -L../pcre -L../core -lajax -leplplot + endif + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM ++EXTRA_LIBS = $(PLPLOT_LIBS) + endif + + +-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = \ + $(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core + + AJAXGSRC = ajgraph.c ajhist.c +@@ -32,3 +36,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libajaxg_la_LDFLAGS = $(LINKFLAGS) ++libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS) +diff --git a/ajax/graphics/ajgraph.c b/ajax/graphics/ajgraph.c +index 25e75e4..60f2743 100644 +--- a/ajax/graphics/ajgraph.c ++++ b/ajax/graphics/ajgraph.c +@@ -34,10 +34,8 @@ + #include <float.h> + #define AZ 28 + +- + #include "plplotP.h" + +- + static void GraphArray(ajuint numofpoints, + float *x, float *y); + static void GraphArrayGaps(ajuint numofpoints, +@@ -1049,13 +1047,26 @@ static void GraphDefCharSize(float size) + ** @@ + ******************************************************************************/ + ++#define _GNU_SOURCE ++#include <stdio.h> ++ + static void GraphSetName(const AjPGraph thys, + const AjPStr txt, const char *ext) + { + if(!thys->ready) + { ++#ifdef USE_PLXSFNAM_SHIM ++ char *fullname; ++#endif + ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); ++#ifdef USE_PLXSFNAM_SHIM ++ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext); ++ ajDebug("=g= plsfnam ('%S') instead\n", fullname); ++ plsfnam(fullname); ++ free(fullname); ++#else + plxsfnam(ajStrGetPtr(txt), ext); ++#endif + ajStrAssignS(&graphBasename, txt); + ajStrAssignC(&graphExtension, ext); + if(ajStrGetCharFirst(graphExtension) == '.') +diff --git a/configure.in b/configure.in +index ddb4f81..3f4fe5e 100644 +--- a/configure.in ++++ b/configure.in +@@ -235,15 +235,6 @@ AC_PROG_INSTALL + AC_PROG_LN_S + AC_PROG_MAKE_SET + +-dnl Intel MacOSX 10.6 puts X11 in a non-standard place +-if test "${with_x}" != "no" ; then +-if test "`uname -a | grep Darwin`"; then +-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` +-if test ${OSXX} '>' '10.4'; then +-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" +-fi +-fi +-fi + + # Checks for header files. + #as# AC_PATH_X +@@ -292,9 +283,6 @@ AC_CHECK_FUNCS(memmove) + #as# select socket sqrt strchr strcspn strdup strerror strpbrk \ + #as# strrchr strspn strstr strtol]) + +-if test "${with_x}" != "no" ; then +-LF_EMBOSS_PATH_XLIB +-fi + + dnl Library checks + AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket") +@@ -316,14 +304,16 @@ CHECK_PNGDRIVER + CHECK_AUTH + CHECK_AMD64 + ++AM_CONDITIONAL(GJEMBOSS, test "$JAVA_OK" = "yes") ++ + AX_LIB_MYSQL + AX_LIB_POSTGRESQL + + CFLAGS="$CFLAGS $MYSQL_CFLAGS" + LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS" + +-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS" +-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS" ++CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS" ++LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS" + + + dnl Check for 'ant' for packaging Jemboss and export result +@@ -443,13 +433,36 @@ fi + + dnl Test if --enable-systemlibs given + have_systemlibs=no ++DEFINE_USE_SYSTEM_PCRE="#undef" + AC_ARG_ENABLE(systemlibs, + AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])) ++AC_MSG_CHECKING(for systemlib usage) + if test "${enable_systemlibs}" = "yes" ; then + have_systemlibs=yes ++ DEFINE_USE_SYSTEM_PCRE="#define" ++ PKG_CHECK_MODULES([PLPLOT], [plplotd]) ++ PKG_CHECK_MODULES([ZLIB], [zlib]) ++else ++ dnl X11 is only used by plplot ++ dnl Intel MacOSX 10.6 puts X11 in a non-standard place ++ if test "${with_x}" != "no" ; then ++ if test "`uname -a | grep Darwin`"; then ++ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` ++ if test ${OSXX} '>' '10.4'; then ++ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" ++ fi ++ fi ++ fi ++ if test "${with_x}" != "no" ; then ++ LF_EMBOSS_PATH_XLIB ++ fi ++ AC_MSG_NOTICE(USING bundled LIBS) + fi + AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") + AC_SUBST(ESYSTEMLIBS) ++AC_SUBST(DEFINE_USE_SYSTEM_PCRE) ++AC_SUBST(PLPLOT_CFLAGS) ++AC_SUBST(PLPLOT_LIBS) + + + +@@ -457,7 +470,6 @@ AC_SUBST(ESYSTEMLIBS) + + dnl Test if purify exists and if --enable-purify given if so + dnl set "-g" +- + AC_MSG_CHECKING(for purify) + dnl if(purify -version) < /dev/null > /dev/null 2>&1; then + AC_ARG_ENABLE(purify, +@@ -683,6 +695,7 @@ CHECK_THREADS + + + AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ++ajax/core/ajax-pcre-config.h + ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile + ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile + ajax/acd/Makefile +diff --git a/emboss/Makefile.am b/emboss/Makefile.am +index 0820517..a0257b2 100644 +--- a/emboss/Makefile.am ++++ b/emboss/Makefile.am +@@ -79,14 +79,17 @@ wordcount wordfinder wordmatch wossname \ + yank + + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + +-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = -I$(top_srcdir)/nucleus \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ +- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot ++ -I$(top_srcdir)/ajax/acd + + + aaindexextract_SOURCES = aaindexextract.c +@@ -319,7 +322,7 @@ testplot_SOURCES = testplot.c + treetypedisplay_SOURCES = treetypedisplay.c + + if !ESYSTEMLIBS +-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ++EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la ../plplot/libeplplot.la ../ajax/pcre/libepcre.la + endif + + +@@ -327,7 +330,6 @@ LDADD = ../nucleus/libnucleus.la ../ajax/acd/libacd.la \ + ../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \ + ../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \ + $(EXTRA_LDS) \ +- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \ + $(XLIB) + + pkgdata_DATA = emboss.default.template +diff --git a/m4/mysql.m4 b/m4/mysql.m4 +index fe413af..ebea25c 100644 +--- a/m4/mysql.m4 ++++ b/m4/mysql.m4 +@@ -1,4 +1,6 @@ +-##### http://autoconf-archive.cryp.to/ax_lib_mysql.html ++# =========================================================================== ++# http://www.gnu.org/software/autoconf-archive/ax_lib_mysql.html ++# =========================================================================== + # + # SYNOPSIS + # +@@ -6,19 +8,18 @@ + # + # DESCRIPTION + # +-# This macro provides tests of availability of MySQL client library +-# of particular version or newer. ++# This macro provides tests of availability of MySQL client library of ++# particular version or newer. + # +-# AX_LIB_MYSQL macro takes only one argument which is optional. If +-# there is no required version passed, then macro does not run +-# version test. ++# AX_LIB_MYSQL macro takes only one argument which is optional. If there ++# is no required version passed, then macro does not run version test. + # + # The --with-mysql option takes one of three possible values: + # + # no - do not check for MySQL client library + # +-# yes - do check for MySQL library in standard locations +-# (mysql_config should be in the PATH) ++# yes - do check for MySQL library in standard locations (mysql_config ++# should be in the PATH) + # + # path - complete path to mysql_config utility, use this option if + # mysql_config can't be found in the PATH +@@ -33,27 +34,23 @@ + # + # HAVE_MYSQL + # +-# LAST MODIFICATION ++# LICENSE + # +-# 2006-07-16 +-# 2007-01-09 MS: mysql_config --cflags may set gcc -fomit-frame-pointers, +-# which prevents gdb from displaying stack traces. +-# Changed mysql_config --cflags to mysql_config --include ++# Copyright (c) 2008 Mateusz Loskot <mateusz@loskot.net> + # +-# COPYLEFT +-# +-# Copyright (c) 2006 Mateusz Loskot <mateusz@loskot.net> +-# +-# Copying and distribution of this file, with or without +-# modification, are permitted in any medium without royalty provided +-# the copyright notice and this notice are preserved. ++# Copying and distribution of this file, with or without modification, are ++# permitted in any medium without royalty provided the copyright notice ++# and this notice are preserved. This file is offered as-is, without any ++# warranty. ++ ++#serial 12 + + AC_DEFUN([AX_LIB_MYSQL], + [ + AC_ARG_WITH([mysql], +- [AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], ++ AS_HELP_STRING([--with-mysql=@<:@ARG@:>@], + [use MySQL client library @<:@default=yes@:>@, optionally specify path to mysql_config] +- )], ++ ), + [ + if test "$withval" = "no"; then + want_mysql="no" +@@ -66,19 +63,20 @@ AC_DEFUN([AX_LIB_MYSQL], + ], + [want_mysql="yes"] + ) ++ AC_ARG_VAR([MYSQL_CONFIG], [Full path to mysql_config program]) + + MYSQL_CFLAGS="" + MYSQL_LDFLAGS="" + MYSQL_VERSION="" + + dnl +- dnl Check MySQL libraries (libpq) ++ dnl Check MySQL libraries + dnl + + if test "$want_mysql" = "yes"; then + +- if test -z "$MYSQL_CONFIG" -o test; then +- AC_PATH_PROG([MYSQL_CONFIG], [mysql_config], [no]) ++ if test -z "$MYSQL_CONFIG" ; then ++ AC_PATH_PROGS([MYSQL_CONFIG], [mysql_config mysql_config5], [no]) + fi + + if test "$MYSQL_CONFIG" != "no"; then +@@ -90,35 +88,8 @@ dnl MYSQL_CFLAGS="`$MYSQL_CONFIG --cflags`" + + MYSQL_VERSION=`$MYSQL_CONFIG --version` + +-dnl It isn't enough to just test for mysql_config as Fedora +-dnl provides it in the mysql RPM even though mysql-devel may +-dnl not be installed +- +- EMBCFLAGS=$CFLAGS +- EMBLDFLAGS=$LDFLAGS +- CFLAGS=$MYSQL_CFLAGS +- LDFLAGS=$MYSQL_LDFLAGS +- +- AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h> +- #include "mysql.h"]], +- [[mysql_info(NULL)]])], +- [havemysql=yes], +- [havemysql=no]) +- +- CFLAGS=$EMBCFLAGS +- LDFLAGS=$EMBLDFLAGS +- +- if test "$havemysql" = yes; then +- AC_DEFINE([HAVE_MYSQL], [1], +- [Define to 1 if MySQL libraries are available]) +- found_mysql="yes" +- AC_MSG_RESULT([yes]) +- else +- MYSQL_CFLAGS="" +- MYSQL_LDFLAGS="" +- found_mysql="no" +- AC_MSG_RESULT([no]) +- fi ++ found_mysql="yes" ++ AC_MSG_RESULT([yes]) + else + found_mysql="no" + AC_MSG_RESULT([no]) +@@ -170,6 +141,11 @@ dnl not be installed + fi + fi + ++ if test "$found_mysql" = "yes" ; then ++ AC_DEFINE([HAVE_MYSQL], [1], ++ [Define to 1 if MySQL libraries are available]) ++ fi ++ + AC_SUBST([MYSQL_VERSION]) + AC_SUBST([MYSQL_CFLAGS]) + AC_SUBST([MYSQL_LDFLAGS]) +diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am +index c244786..ff301b9 100644 +--- a/nucleus/Makefile.am ++++ b/nucleus/Makefile.am +@@ -19,13 +19,16 @@ CYGWIN_LIBS = -L../plplot -L../ajax/pcre -L../ajax/expat -L../ajax/zlib \ + -lezlib -leplplot + else + if !ESYSTEMLIBS +-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib ++EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \ ++-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre ++else ++EXTRA_INCLUDES = $(PLPLOT_CFLAGS) + endif + endif + + +-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \ +- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \ ++INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \ ++ -I$(top_srcdir)/ajax \ + $(EXTRA_INCLUDES) \ + -I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \ + -I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \ +@@ -55,3 +58,4 @@ LINKFLAGS = $(VERS_INF) + endif + + libnucleus_la_LDFLAGS = $(LINKFLAGS) ++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la ../ajax/acd/libacd.la diff --git a/sci-biology/emboss/files/README.Gentoo b/sci-biology/emboss/files/README.Gentoo new file mode 100644 index 000000000000..ce37576f0fc4 --- /dev/null +++ b/sci-biology/emboss/files/README.Gentoo @@ -0,0 +1,28 @@ +Using EMBOSS on Gentoo systems + +Codon data files location + +The codon data files that are distributed with EMBOSS are installed in the +"/usr/share/EMBOSS/data/CODONS.orig" directory instead of the usual +"/usr/share/EMBOSS/data/CODONS". This is done to avoid confusion between these +codon files and those installed with the CUTG database. The names of these files +sometimes vary only by their case. Having both sets of files in the same directory +is also impossible on systems such as MacOSX, where the root filesystem is case +insensitive. If you do not have the CUTG database installed and want to use the +codon files distributed with EMBOSS, you can symlink the "CODONS.orig" directory +to "CODONS": + + cd /usr/share/EMBOSS/data + ln -s CODONS.orig CODONS + +Restriction enzymes equivalence file location + +The restriction enzymes equivalence file distributed with EMBOSS is installed as +"/usr/share/EMBOSS/data/embossre.equ.orig" rather than the usual +"/usr/share/EMBOSS/data/embossre.equ". This is done to avoid a file collision +with the equivalence file provided by the Rebase database. If you do not have the +Rebase database installed and want to use the equivalence file distributed with +EMBOSS, you can symlink the "embossre.equ.orig" file to "embossre.equ": + + cd /usr/share/EMBOSS/data + ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo new file mode 100644 index 000000000000..d1879bd0811c --- /dev/null +++ b/sci-biology/emboss/files/README.gentoo @@ -0,0 +1,34 @@ +Administrating EMBOSS on Gentoo systems +======================================= + + +Codon data files location +------------------------- + +The codon data files that are distributed with EMBOSS are installed in the +``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual +``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between +these codon files and those installed with the CUTG database. The names of +these files sometimes vary only by their case. Having both sets of files in +the same directory is also impossible on systems such as MacOSX, where the +root filesystem is case insensitive. If you do not have the CUTG database +installed and want to use the codon files distributed with EMBOSS, you can +symlink the ``CODONS.orig`` directory to ``CODONS``:: + + # cd ${EPREFIX}/usr/share/EMBOSS/data + # ln -s CODONS.orig CODONS + + +Restriction enzymes equivalence file location +--------------------------------------------- + +The restriction enzymes equivalence file distributed with EMBOSS is installed +as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual +``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file +collision with the equivalence file provided by the Rebase database. If you do +not have the Rebase database installed and want to use the equivalence file +distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to +``embossre.equ``:: + + # cd ${EPREFIX}/usr/share/EMBOSS/data + # ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch new file mode 100644 index 000000000000..9915f95376d0 --- /dev/null +++ b/sci-biology/emboss/files/emboss-5.0.0-as-needed.patch @@ -0,0 +1,24 @@ +diff -Naur EMBOSS-5.0.0.old/ajax/Makefile.in EMBOSS-5.0.0/ajax/Makefile.in +--- EMBOSS-5.0.0.old/ajax/Makefile.in 2007-07-12 05:53:32.000000000 -0500 ++++ EMBOSS-5.0.0/ajax/Makefile.in 2008-01-25 16:43:51.000000000 -0500 +@@ -244,7 +244,7 @@ + top_srcdir = @top_srcdir@ + @ISCYGWIN_FALSE@lib_LTLIBRARIES = libajax.la libajaxg.la + @ISCYGWIN_TRUE@lib_LTLIBRARIES = libajax.la +-@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = ++@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = -lm -L../plplot/.libs -leplplot + @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm + @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm + @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot +diff -Naur EMBOSS-5.0.0.old/plplot/Makefile.in EMBOSS-5.0.0/plplot/Makefile.in +--- EMBOSS-5.0.0.old/plplot/Makefile.in 2007-07-12 05:53:36.000000000 -0500 ++++ EMBOSS-5.0.0/plplot/Makefile.in 2008-01-25 16:42:51.000000000 -0500 +@@ -229,7 +229,7 @@ + lib_LTLIBRARIES = libeplplot.la + @AMPNG_FALSE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lX11 + @AMPNG_TRUE@@ISAIXIA64_TRUE@@ISSHARED_TRUE@AM_CFLAGS = -Wl,-G -lgd -lpng -lz -lX11 -lm +-@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = ++@ISAIXIA64_FALSE@@ISSHARED_TRUE@AM_CFLAGS = PATCH_PLPLOT + @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -lX11 -lgd -lpng -lz + INCLUDES = $(X_CFLAGS) -I$(srcdir)/ -I/usr/include/gd -DPREFIX=\"$(prefix)\" -DBUILD_DIR=\"$(srcdir)\" -DDRV_DIR=\"$(srcdir)\" -DEMBOSS_TOP=\"$(EMBOSS_TOP)\" + PLPLOTSRC = pdfutils.c plargs.c plbox.c plcont.c plcore.c \ diff --git a/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch new file mode 100644 index 000000000000..0f5e592b77f1 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.3.1_p4-r1_plcol.patch @@ -0,0 +1,112 @@ +--- EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2012-07-19 23:29:05.000000000 +0200 ++++ /tmp/ajgraph.c 2012-07-19 23:25:00.000000000 +0200 +@@ -1645,14 +1645,14 @@ + ** @return [void] + ** @@ + ******************************************************************************/ + + static void GraphSetPen(ajint colour) + { +- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); +- plcol((PLINT)colour); ++ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); ++ plcol0((PLINT)colour); + + return; + } + + + +--- EMBOSS-6.3.1/plplot/plcore.c 2007-10-24 15:14:43.000000000 +0200 ++++ /tmp/plcore.c 2012-07-19 23:25:00.000000000 +0200 +@@ -1709,13 +1709,13 @@ + if (plsc->zdigmax == 0) + plsc->zdigmax = 3; + + /* Switch to graphics mode and set color and arrow style*/ + + plgra(); +- plcol(1); ++ plcol0(1); + + plstyl(0, &mk, &sp); + plpat(1, &inc, &del); + + plsvect(def_arrow_x, def_arrow_y, 6, 0); + +--- EMBOSS-6.3.1/plplot/plstripc.c 2007-05-08 11:09:37.000000000 +0200 ++++ /tmp/plstripc.c 2012-07-19 23:25:00.000000000 +0200 +@@ -153,17 +153,17 @@ + + plgchr(&sc, &dy); + sc = dy = dy/100; + plwind(-0.01, 1.01, -0.01, 1.01); + for (i=0; i<PEN; i++) { + if (mystripc->npts[i] || first) { +- plcol(mystripc->colline[i]); ++ plcol0(mystripc->colline[i]); + pllsty(mystripc->styline[i]); + pljoin(mystripc->xlpos, mystripc->ylpos - sc, + mystripc->xlpos + 0.1, mystripc->ylpos - sc); +- plcol(mystripc->collab); ++ plcol0(mystripc->collab); + plptex(mystripc->xlpos + 0.11, mystripc->ylpos - sc, + 0., 0., 0, mystripc->legline[i]); + sc += dy; + } + } + plwind(mystripc->xmin, mystripc->xmax, mystripc->ymin, mystripc->ymax); +@@ -184,34 +184,34 @@ + PLFLT x[]={0.,1.,1.,0.}, y[]={0.,0.,1.,1.}; + + /* Set up window */ + + plvpor(0,1,0,1); + plwind(0,1,0,1); +- plcol(0);plpsty(0); ++ plcol0(0);plpsty(0); + plfill(4, &x[0], &y[0]); + plvsta(); + + /* Draw box and same window dimensions */ + mystrip->wxmin=mystrip->xmin; + mystrip->wxmax=mystrip->xmax; + mystrip->wymin=mystrip->ymin; + mystrip->wymax=mystrip->ymax; /* FIXME - can exist some redundancy here */ + + plwind(mystrip->xmin, mystrip->xmax, mystrip->ymin, mystrip->ymax); + + pllsty(1); +- plcol(mystrip->colbox); ++ plcol0(mystrip->colbox); + plbox(mystrip->xspec, 0.0, 0, mystrip->yspec, 0.0, 0); + +- plcol(mystrip->collab); ++ plcol0(mystrip->collab); + pllab(mystrip->labx, mystrip->laby, mystrip->labtop); + + for (i=0; i<PEN; i++) { + if (mystrip->npts[i] > 0) { +- plcol(mystrip->colline[i]);pllsty(mystrip->styline[i]); ++ plcol0(mystrip->colline[i]);pllsty(mystrip->styline[i]); + plline(mystrip->npts[i], mystrip->x[i], mystrip->y[i]); + } + } + + plstrip_legend(mystrip,0); + } +@@ -269,13 +269,13 @@ + if (stripc->xmax - stripc->xmin < stripc->xlen) { + if( yasc == 0) { + + /* If user has changed subwindow, make shure we have the correct one */ + plvsta(); + plwind(stripc->wxmin, stripc->wxmax, stripc->wymin, stripc->wymax); /* FIXME - can exist some redundancy here */ +- plcol(stripc->colline[p]); pllsty(stripc->styline[p]); ++ plcol0(stripc->colline[p]); pllsty(stripc->styline[p]); + if ((stripc->npts[p]-2) < 0) + plP_movwor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); + else + plP_movwor(stripc->x[p][stripc->npts[p]-2], stripc->y[p][stripc->npts[p]-2]); + plP_drawor(stripc->x[p][stripc->npts[p]-1], stripc->y[p][stripc->npts[p]-1]); + plflush(); diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch new file mode 100644 index 000000000000..7704873e9d26 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch @@ -0,0 +1,11 @@ +--- EMBOSS-6.6.0/emboss/embossversion.c ++++ EMBOSS-6.6.0/emboss/embossversion.c +@@ -415,7 +415,7 @@ + ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING); + #endif + #ifdef _FORTIFY_SOURCE +- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE); ++ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL); + #endif + ajFmtPrintF(outfile, "\n"); + ajFmtPrintF(outfile, "Sizes (bytes):\n"); diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch new file mode 100644 index 000000000000..266bddd95a37 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch @@ -0,0 +1,411 @@ + Makefile.am | 9 +++--- + ajax/Makefile.am | 4 +-- + ajax/acd/Makefile.am | 8 +++-- + ajax/ajaxdb/Makefile.am | 6 ++-- + ajax/core/Makefile.am | 6 ++-- + ajax/core/ajreg.h | 7 ++-- + ajax/ensembl/Makefile.am | 6 ++-- + ajax/graphics/Makefile.am | 8 +++-- + configure.ac | 82 ++++++++++++++++++++++++++--------------------- + emboss/Makefile.am | 13 +++++--- + jemboss/lib/Makefile.am | 2 +- + m4/idxdbs.m4 | 17 +++------- + nucleus/Makefile.am | 8 +++-- + 13 files changed, 100 insertions(+), 76 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 177dec5..18dd99a 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -12,8 +12,11 @@ LICENSE \ + ONEWS \ + PROBLEMS + +-SUBDIRS = \ +-plplot \ ++SUBDIRS = ++if !ESYSTEMLIBS ++SUBDIRS += plplot ++endif ++SUBDIRS += \ + ajax \ + nucleus \ + emboss \ +@@ -33,5 +36,3 @@ dist-hook: + tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) + tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) + +-install-exec-hook: +- $(bindir)/embossupdate +diff --git a/ajax/Makefile.am b/ajax/Makefile.am +index f27472c..de34e17 100644 +--- a/ajax/Makefile.am ++++ b/ajax/Makefile.am +@@ -1,7 +1,7 @@ + ## Process this file with automake to produce Makefile.in + +-SUBDIRS = pcre ++SUBDIRS = + if !ESYSTEMLIBS +-SUBDIRS += expat zlib ++SUBDIRS += pcre expat zlib + endif + SUBDIRS += core graphics ensembl ajaxdb acd +diff --git a/ajax/acd/Makefile.am b/ajax/acd/Makefile.am +index 9f0f700..3295a1d 100644 +--- a/ajax/acd/Makefile.am ++++ b/ajax/acd/Makefile.am +@@ -3,16 +3,20 @@ + lib_LTLIBRARIES = libacd.la + + libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la + + libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb ++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics +-libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + if !ESYSTEMLIBS ++libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot ++else ++libacd_la_CFLAGS += $(PLPLOT_CFLAGS) ++endif + libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) + + libacd_la_LDFLAGS = -version-info 6:5:0 +diff --git a/ajax/ajaxdb/Makefile.am b/ajax/ajaxdb/Makefile.am +index c2b0c00..9de14fe 100644 +--- a/ajax/ajaxdb/Makefile.am ++++ b/ajax/ajaxdb/Makefile.am +@@ -3,14 +3,16 @@ + lib_LTLIBRARIES = libajaxdb.la + + libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la + + libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl +-libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre ++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot ++endif + libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) + libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) + +diff --git a/ajax/core/Makefile.am b/ajax/core/Makefile.am +index 2906837..3189c34 100644 +--- a/ajax/core/Makefile.am ++++ b/ajax/core/Makefile.am +@@ -3,13 +3,15 @@ + lib_LTLIBRARIES = libajax.la + + libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) + +-libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libajax_la_CPPFLAGS = + if !ESYSTEMLIBS ++libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot ++endif + libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) + libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) + libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) +diff --git a/ajax/core/ajreg.h b/ajax/core/ajreg.h +index 1623c82..5d928cf 100644 +--- a/ajax/core/ajreg.h ++++ b/ajax/core/ajreg.h +@@ -39,9 +39,8 @@ + #include "ajdefine.h" + #include "ajstr.h" + +-#include "pcre_config.h" +-#include "pcre_internal.h" +-#include "pcreposix.h" ++#include <pcre.h> ++#include <pcreposix.h> + + AJ_BEGIN_DECLS + +@@ -84,7 +83,7 @@ AJ_BEGIN_DECLS + + typedef struct AjSRegexp + { +- real_pcre *pcre; ++ struct real_pcre *pcre; + pcre_extra *extra; + int *ovector; + const char* orig; +diff --git a/ajax/ensembl/Makefile.am b/ajax/ensembl/Makefile.am +index 0d1250b..5484c02 100644 +--- a/ajax/ensembl/Makefile.am ++++ b/ajax/ensembl/Makefile.am +@@ -3,13 +3,15 @@ + lib_LTLIBRARIES = libensembl.la + + libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libensembl_la_LIBADD = ../core/libajax.la + +-libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif + libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot ++endif + libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) + + libensembl_la_LDFLAGS = -version-info 6:5:0 +diff --git a/ajax/graphics/Makefile.am b/ajax/graphics/Makefile.am +index a4f202b..1114c2c 100644 +--- a/ajax/graphics/Makefile.am ++++ b/ajax/graphics/Makefile.am +@@ -3,12 +3,16 @@ + lib_LTLIBRARIES = libajaxg.la + + libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) + +-libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre ++libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat +-endif + libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot ++else ++libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS) ++endif + libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) + + libajaxg_la_LDFLAGS = -version-info 6:5:0 +diff --git a/configure.ac b/configure.ac +index a7bd9c6..9ba3121 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -629,32 +629,6 @@ AS_CASE([${host_os}], + + + +- +-dnl PCRE library definitions - see the MAJOR and MINOR values +-dnl to see which version's configure.in these lines come from +- +-dnl Provide the current PCRE version information. Do not use numbers +-dnl with leading zeros for the minor version, as they end up in a C +-dnl macro, and may be treated as octal constants. Stick to single +-dnl digits for minor numbers less than 10. There are unlikely to be +-dnl that many releases anyway. +- +-PCRE_MAJOR="7" +-PCRE_MINOR="9" +-PCRE_DATE="11-Apr-2009" +-PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" +- +-dnl Default values for miscellaneous macros +- +-POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" +- +-dnl Provide versioning information for libtool shared libraries that +-dnl are built by default on Unix systems. +- +-PCRE_LIB_VERSION="0:1:0" +-PCRE_POSIXLIB_VERSION="0:0:0" +- +- + dnl Define where the EMBOSS package is located + AC_SUBST([AJAX_FIXED_ROOT]) + AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" +@@ -743,17 +717,7 @@ AX_LIB_POSTGRESQL + + + +-dnl "Export" these variables for PCRE + +-AC_SUBST([HAVE_MEMMOVE]) +-AC_SUBST([HAVE_STRERROR]) +-AC_SUBST([PCRE_MAJOR]) +-AC_SUBST([PCRE_MINOR]) +-AC_SUBST([PCRE_DATE]) +-AC_SUBST([PCRE_VERSION]) +-AC_SUBST([PCRE_LIB_VERSION]) +-AC_SUBST([PCRE_POSIXLIB_VERSION]) +-AC_SUBST([POSIX_MALLOC_THRESHOLD]) + + + +@@ -849,7 +813,53 @@ AC_ARG_ENABLE([systemlibs], + + AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) + ++AS_IF([test "x${enable_systemlibs}" = "xyes"], ++[ ++dnl using system libraries ++ PKG_CHECK_MODULES([PCRE], [libpcre]) ++ PKG_CHECK_MODULES([EXPAT], [expat]) ++ PKG_CHECK_MODULES([ZLIB], [zlib]) ++ PKG_CHECK_MODULES([PLPLOT], [plplotd], ++ [],[PKG_CHECK_MODULES([PLPLOT], [plplot])] ++ ) ++], ++[ ++dnl using bundled libraries ++ dnl PCRE library definitions - see the MAJOR and MINOR values ++ dnl to see which version's configure.ac these lines come from + ++ dnl Provide the current PCRE version information. Do not use numbers ++ dnl with leading zeros for the minor version, as they end up in a C ++ dnl macro, and may be treated as octal constants. Stick to single ++ dnl digits for minor numbers less than 10. There are unlikely to be ++ dnl that many releases anyway. ++ ++ PCRE_MAJOR="7" ++ PCRE_MINOR="9" ++ PCRE_DATE="11-Apr-2009" ++ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" ++ ++ dnl Default values for miscellaneous macros ++ ++ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" ++ ++ dnl Provide versioning information for libtool shared libraries that ++ dnl are built by default on Unix systems. ++ ++ PCRE_LIB_VERSION="0:1:0" ++ PCRE_POSIXLIB_VERSION="0:0:0" ++ ++ dnl "Export" these variables for PCRE ++ AC_SUBST([HAVE_MEMMOVE]) ++ AC_SUBST([HAVE_STRERROR]) ++ AC_SUBST([PCRE_MAJOR]) ++ AC_SUBST([PCRE_MINOR]) ++ AC_SUBST([PCRE_DATE]) ++ AC_SUBST([PCRE_VERSION]) ++ AC_SUBST([PCRE_LIB_VERSION]) ++ AC_SUBST([PCRE_POSIXLIB_VERSION]) ++ AC_SUBST([POSIX_MALLOC_THRESHOLD]) ++]) + + + # Enable the purify tool: --enable-purify, sets CC and LIBTOOL +diff --git a/emboss/Makefile.am b/emboss/Makefile.am +index 89ada78..f987d40 100644 +--- a/emboss/Makefile.am ++++ b/emboss/Makefile.am +@@ -28,15 +28,18 @@ endif + + AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd + AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb ++AM_CPPFLAGS += -I$(top_srcdir)/ajax/core + AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl + AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics ++if !ESYSTEMLIBS + AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre +-if !ESYSTEMLIBS + AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat + AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib +-endif +-AM_CPPFLAGS += -I$(top_srcdir)/nucleus + AM_CPPFLAGS += -I$(top_srcdir)/plplot ++else ++AM_CFLAGS += $(PLPLOT_CFLAGS) ++endif ++AM_CPPFLAGS += -I$(top_srcdir)/nucleus + AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) + AM_CPPFLAGS += $(JAVA_CPPFLAGS) + +@@ -49,9 +52,11 @@ LDADD += ../ajax/core/libajax.la + if !ESYSTEMLIBS + LDADD += ../ajax/zlib/libezlib.la + LDADD += ../ajax/expat/libeexpat.la +-endif + LDADD += ../ajax/pcre/libepcre.la + LDADD += ../plplot/libeplplot.la ++else ++LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS) ++endif + LDADD += $(XLIB) + + #if PURIFY +diff --git a/jemboss/lib/Makefile.am b/jemboss/lib/Makefile.am +index 5f7e21e..8b45ce2 100644 +--- a/jemboss/lib/Makefile.am ++++ b/jemboss/lib/Makefile.am +@@ -12,7 +12,7 @@ mail.jar \ + jalviewApplet.jar \ + jemboss.jar + +-jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java ++jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java + if JAVA_BUILD + $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; + endif +diff --git a/m4/idxdbs.m4 b/m4/idxdbs.m4 +index 0ca7ea9..9b54f2a 100644 +--- a/m4/idxdbs.m4 ++++ b/m4/idxdbs.m4 +@@ -1,17 +1,8 @@ + AC_DEFUN([CHECK_IDXDBS], + [ +-AC_MSG_CHECKING(for EMBOSS pre-indexed databases) ++AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) + +- +-if test -f ./emboss/index/edam.xac; then +-AC_MSG_RESULT(yes) +-else +-AC_MSG_RESULT(no) +-echo "" +-echo "Pre-indexed edam, taxon + drcat databases not found." +-echo "Please download them from within this directory using:" +-echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." +-echo "and then repeat the configure step." +-exit 1 +-fi ++AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], ++ [], ++ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) + ]) +diff --git a/nucleus/Makefile.am b/nucleus/Makefile.am +index 37b8543..5819c89 100644 +--- a/nucleus/Makefile.am ++++ b/nucleus/Makefile.am +@@ -3,6 +3,7 @@ + lib_LTLIBRARIES = libnucleus.la + + libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) ++libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la + + if ISSHARED + if ISAIXIA64 +@@ -10,11 +11,14 @@ libnucleus_la_CFLAGS += -Wl,-G -lm + endif + endif + +-libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot +-libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre ++libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core + if !ESYSTEMLIBS ++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot ++libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib ++else ++libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS) + endif + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics + libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch new file mode 100644 index 000000000000..15f5f967a07d --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch @@ -0,0 +1,61 @@ +--- EMBOSS-6.6.0/ajax/graphics/ajgraph.c ++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c +@@ -49,7 +49,7 @@ + + #define GRAPH_DEBUG 1 + +-#include "plplotP.h" ++#include <plplotP.h> + + + static void GraphArray(ajuint numofpoints, +@@ -964,10 +964,10 @@ + if(!thys->ready) + { + #if GRAPH_DEBUG +- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); ++ ajDebug("=g= plsfnam ('%S')\n", txt); + #endif + +- plxsfnam(ajStrGetPtr(txt), ext); ++ plsfnam(ajStrGetPtr(txt)); + ajStrAssignS(&graphBasename, txt); + ajStrAssignC(&graphExtension, ext); + if(ajStrGetCharFirst(graphExtension) == '.') +@@ -1213,10 +1213,10 @@ + void ajGraphicsSetPenwidth(float penwidth) + { + #if GRAPH_DEBUG +- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); ++ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth); + #endif + +- plwid((PLINT)penwidth); ++ c_plwidth((PLINT)penwidth); + + return; + } +@@ -1538,10 +1538,10 @@ + static void GraphSetPen(ajint colour) + { + #if GRAPH_DEBUG +- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); ++ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); + #endif + +- plcol((PLINT)colour); ++ plcol0((PLINT)colour); + + return; + } +--- EMBOSS-6.6.0/ajax/graphics/ajgraph.h ++++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h +@@ -32,7 +32,7 @@ + /* ========================================================================= */ + + #include "ajdefine.h" +-#include "plplot.h" ++#include <plplot.h> + #include "ajgraphstruct.h" + #include "ajdefine.h" + #include "ajstr.h" diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch new file mode 100644 index 000000000000..eff10b2e6700 --- /dev/null +++ b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch @@ -0,0 +1,74 @@ +--- EMBOSS-6.6.0/ajax/core/ajfeatread.c ++++ EMBOSS-6.6.0/ajax/core/ajfeatread.c +@@ -45,6 +45,7 @@ + + #include <limits.h> + #include <math.h> ++#include <string.h> + #include <errno.h> + + #ifdef WIN32 +--- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c ++++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c +@@ -43,7 +43,7 @@ + + #include <limits.h> + #include <math.h> +- ++#include <string.h> + + static AjPRegexp featoutRegUfoFmt = NULL; + static AjPRegexp featoutRegUfoFile = NULL; +--- EMBOSS-6.6.0/ajax/core/ajpdbio.c ++++ EMBOSS-6.6.0/ajax/core/ajpdbio.c +@@ -37,7 +37,7 @@ + + #include <limits.h> + #include <math.h> +- ++#include <string.h> + + + +--- EMBOSS-6.6.0/ajax/core/ajreg.c ++++ EMBOSS-6.6.0/ajax/core/ajreg.c +@@ -32,6 +32,7 @@ + #include "ajlib.h" + + #include "ajreg.h" ++#include <string.h> + + + +--- EMBOSS-6.6.0/ajax/core/ajseqtype.c ++++ EMBOSS-6.6.0/ajax/core/ajseqtype.c +@@ -32,7 +32,7 @@ + #include "ajfeat.h" + #include "ajfile.h" + #include "ajreg.h" +- ++#include <string.h> + + + +--- EMBOSS-6.6.0/nucleus/embindex.c ++++ EMBOSS-6.6.0/nucleus/embindex.c +@@ -35,6 +35,7 @@ + #include "ajnam.h" + + #include <errno.h> ++#include <string.h> + + #define BTENTRYFILE ".ent" + #define KWLIMIT 12 +--- EMBOSS-6.6.0/nucleus/embword.c ++++ EMBOSS-6.6.0/nucleus/embword.c +@@ -36,7 +36,7 @@ + #include "ajutil.h" + + #include <math.h> +- ++#include <string.h> + + + diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-1 b/sci-biology/emboss/files/emboss-README.Gentoo-1 new file mode 100644 index 000000000000..81e71988ae80 --- /dev/null +++ b/sci-biology/emboss/files/emboss-README.Gentoo-1 @@ -0,0 +1,34 @@ +Administrating EMBOSS on Gentoo systems +======================================= + + +Codon data files location +------------------------- + +The codon data files that are distributed with EMBOSS are installed in the +``/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual +``/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between +these codon files and those installed with the CUTG database. The names of +these files sometimes vary only by their case. Having both sets of files in +the same directory is also impossible on systems such as MacOSX, where the +root filesystem is case insensitive. If you do not have the CUTG database +installed and want to use the codon files distributed with EMBOSS, you can +symlink the ``CODONS.orig`` directory to ``CODONS``:: + + # cd /usr/share/EMBOSS/data + # ln -s CODONS.orig CODONS + + +Restriction enzymes equivalence file location +--------------------------------------------- + +The restriction enzymes equivalence file distributed with EMBOSS is installed +as ``/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual +``/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file +collision with the equivalence file provided by the Rebase database. If you do +not have the Rebase database installed and want to use the equivalence file +distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to +``embossre.equ``:: + + # cd /usr/share/EMBOSS/data + # ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/files/emboss-README.Gentoo-2 b/sci-biology/emboss/files/emboss-README.Gentoo-2 new file mode 100644 index 000000000000..72fa3662c9a8 --- /dev/null +++ b/sci-biology/emboss/files/emboss-README.Gentoo-2 @@ -0,0 +1,34 @@ +Administrating EMBOSS on Gentoo systems +======================================= + + +Codon data files location +------------------------- + +The codon data files that are distributed with EMBOSS are installed in the +``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual +``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between +these codon files and those installed with the CUTG database. The names of +these files sometimes vary only by their case. Having both sets of files in +the same directory is also impossible on systems such as MacOSX, where the +root filesystem is case insensitive. If you do not have the CUTG database +installed and want to use the codon files distributed with EMBOSS, you can +symlink the ``CODONS.orig`` directory to ``CODONS``:: + + # cd EPREFIX/usr/share/EMBOSS/data + # ln -s CODONS.orig CODONS + + +Restriction enzymes equivalence file location +--------------------------------------------- + +The restriction enzymes equivalence file distributed with EMBOSS is installed +as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual +``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file +collision with the equivalence file provided by the Rebase database. If you do +not have the Rebase database installed and want to use the equivalence file +distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to +``embossre.equ``:: + + # cd EPREFIX/usr/share/EMBOSS/data + # ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml new file mode 100644 index 000000000000..3af936dc1564 --- /dev/null +++ b/sci-biology/emboss/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + EMBOSS is "The European Molecular Biology Open Software Suite". + EMBOSS is a free Open Source software analysis package specially + developed for the needs of the molecular biology (e.g. EMBnet) user + community. The software automatically copes with data in a variety + of formats and even allows transparent retrieval of sequence data + from the web. Also, as extensive libraries are provided with the + package, it is a platform to allow other scientists to develop and + release software in true open source spirit. EMBOSS also integrates + a range of currently available packages and tools for sequence + analysis into a seamless whole. EMBOSS breaks the historical trend + towards commercial software packages. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest new file mode 100644 index 000000000000..015da1fb031b --- /dev/null +++ b/sci-biology/eugene/Manifest @@ -0,0 +1 @@ +DIST eugene-4.1.tar.gz 7393361 SHA256 faff769f68e1ab1fdec61be34ec7fef3c73805734199765ba11cf1ea9c02f800 SHA512 f4bcf63103754f8fb577d311d181375732411fa926fb0cef86fcd00c373ed5cc5637f1b55fa375a4bb14c5181f7de1dc244570f74cdd1887b6107d5c6cea37b3 WHIRLPOOL 32f4539456c243dd3c6a9d5a986fea210e53e5566aaa0849a26f34832957100623570a0814193059420d53e553247584360635706844ed0ec55c4cc65e235ad4 diff --git a/sci-biology/eugene/eugene-4.1.ebuild b/sci-biology/eugene/eugene-4.1.ebuild new file mode 100644 index 000000000000..088ecc7a1a8b --- /dev/null +++ b/sci-biology/eugene/eugene-4.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools eutils + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://www.inra.fr/mia/T/EuGene/" +SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1157/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND=" + media-libs/gd[png] + media-libs/libpng:0= + " +RDEPEND="${DEPEND}" + +RESTRICT="test" + +src_prepare() { + # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170 + epatch \ + "${FILESDIR}"/${PN}-3.6-overflow.patch \ + "${FILESDIR}"/${PN}-3.6-plugins.patch \ + "${FILESDIR}"/${P}-format-security.patch + sed \ + -e '/SUBDIRS/ s/doc//' \ + -e '/INSTALL.*doc/ s/\(.*\)//' \ + -i Makefile.am || die + eautoreconf +} diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch new file mode 100644 index 000000000000..7222530ad771 --- /dev/null +++ b/sci-biology/eugene/files/eugene-3.6-overflow.patch @@ -0,0 +1,13 @@ +http://bugs.gentoo.org/show_bug.cgi?id=336607 + +--- eugene-3.6/src/Sensor.cc ++++ eugene-3.6/src/Sensor.cc +@@ -224,7 +224,7 @@ + //-------------------------- + void Signals :: PrintS () + { +- char t[7]; ++ char t[10]; + char s = '+'; + + switch (type) { diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch new file mode 100644 index 000000000000..1e910a13d5b1 --- /dev/null +++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch @@ -0,0 +1,43 @@ +http://bugs.gentoo.org/show_bug.cgi?id=297536 + +--- eugene-3.6/src/Makefile.am ++++ eugene-3.6/src/Makefile.am +@@ -20,7 +20,7 @@ + + SUBDIRS = Parametrization GDIF . SensorPlugins + +-AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" ++AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\" + AM_CFLAGS = + + bin_PROGRAMS = eugene +--- eugene-3.6/src/MSensor.cc ++++ eugene-3.6/src/MSensor.cc +@@ -97,7 +97,7 @@ + std::string use_name; + + if (!IsInitialized) { +- PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/"; ++ PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/"; + + // On rcupre les couples nom de sensor/priorit du .par + PAR.ResetIter(); +--- eugene-3.6/Makefile.am ++++ eugene-3.6/Makefile.am +@@ -125,7 +125,7 @@ + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images +- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM +@@ -144,6 +144,6 @@ + $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images + $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg +- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval + $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch new file mode 100644 index 000000000000..e6e4a6cc8bd7 --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1-format-security.patch @@ -0,0 +1,16 @@ + src/Hits.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/Hits.cc b/src/Hits.cc +index edfe178..b228be6 100755 +--- a/src/Hits.cc ++++ b/src/Hits.cc +@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int + while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin, + &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8) + { +- if (HSP) fprintf(stderr,HSP); ++ if (HSP) fprintf(stderr, "%s", HSP); + if (phase < 0 && deb > fin) + { + int tmp = deb; diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/eugene/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest new file mode 100644 index 000000000000..3619350ee4d0 --- /dev/null +++ b/sci-biology/exonerate/Manifest @@ -0,0 +1 @@ +DIST exonerate-2.2.0.tar.gz 509870 SHA256 0ea2720b1388fa329f889522f43029b416ae311f57b229129a65e779616fe5ff SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c WHIRLPOOL dd7ba7a94b93f41d5ddbc66cc14740973dde20e875f37814229614c85312dcc1de031faab5153bc28be3284144d0f8451bd5e5115f8d9e312e4f88d771ce620c diff --git a/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild new file mode 100644 index 000000000000..966f7c2f8e01 --- /dev/null +++ b/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils toolchain-funcs + +DESCRIPTION="Generic tool for pairwise sequence comparison" +HOMEPAGE="http://www.ebi.ac.uk/~guy/exonerate/" +SRC_URI="http://www.ebi.ac.uk/~guy/exonerate/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" +IUSE="utils test threads" + +REQUIRED_USE="test? ( utils )" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) + +src_prepare() { + tc-export CC + sed \ + -e 's: -O3 -finline-functions::g' \ + -i configure.in || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable utils utilities) + $(use_enable threads pthreads) + --enable-largefile + --enable-glib2 + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + doman doc/man/man1/*.1 +} diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch new file mode 100644 index 000000000000..3268055cd544 --- /dev/null +++ b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch @@ -0,0 +1,15 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- configure.in ++++ configure.in +@@ -289,7 +289,7 @@ + if test "$enable_pthreads" = yes; then + echo "Using PTHREADS" + CFLAGS="$CFLAGS -DUSE_PTHREADS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + elif test "$enable_pthreads" = no; then + echo "Not using pthreads" + else diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml new file mode 100644 index 000000000000..711d805d77e7 --- /dev/null +++ b/sci-biology/exonerate/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> + exonerate is a generic tool for pairwise sequence comparison + </longdescription> + <use> + <flag name="utils">Install all utilities</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest new file mode 100644 index 000000000000..6edb1d9f6603 --- /dev/null +++ b/sci-biology/express/Manifest @@ -0,0 +1,2 @@ +DIST express-0.9.5-src.tgz 766024 SHA256 e17250d62750560c2dc9cb579f58784b5076afb74088f36523ddd623e08bc022 SHA512 3a7360ffbe57f4f712b6db38d551d31384d995050a86238d79299edb12f0e7f5dca6f362b7858b5051ea2879af2b3559f78f9780d75ef2ef6fdad7398f781403 WHIRLPOOL 290772dceca2465f922f5d5fe548dc8fd460422589697173c58f98dc3afa2e91175fe1fa52e5f29458ea6af74c8da609776fa583bf5efcb2d5771c4c9ad51cde +DIST express-1.5.1-src.tgz 931166 SHA256 0c5840a42da830fd8701dda8eef13f4792248bab4e56d665a0e2ca075aff2c0f SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee WHIRLPOOL 2c75385b2a2ec8f7b77df760344affc108e827eb9f59014f08af0cee0ca8806beeba101d13ed8b43883a25fc9486bd405f402339f0e4e394d3895694c75a4e2a diff --git a/sci-biology/express/express-0.9.5-r1.ebuild b/sci-biology/express/express-0.9.5-r1.ebuild new file mode 100644 index 000000000000..608ade0766ea --- /dev/null +++ b/sci-biology/express/express-0.9.5-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=dev-libs/boost-1.52.0:= + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +CMAKE_USE_DIR="${S}/src" + +src_prepare() { + sed \ + -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \ + -e '1 a find_package(Boost 1.52 COMPONENTS filesystem program_options system thread)' \ + -e '1 a find_package(ZLIB)' \ + -e '/add_executable/ a include_directories("/usr/include/bamtools")' \ + -i src/CMakeLists.txt || die + + cmake-utils_src_prepare +} diff --git a/sci-biology/express/express-0.9.5.ebuild b/sci-biology/express/express-0.9.5.ebuild new file mode 100644 index 000000000000..a4fcff4be4f5 --- /dev/null +++ b/sci-biology/express/express-0.9.5.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-libs/boost + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +CMAKE_USE_DIR="${S}/src" + +src_prepare() { + sed \ + -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \ + -e '1 a find_package(Boost 1.46 COMPONENTS filesystem program_options thread)' \ + -e '1 a find_package(ZLIB)' \ + -e '/add_executable/ a include_directories("/usr/include/bamtools")' \ + -i src/CMakeLists.txt || die +} diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild new file mode 100644 index 000000000000..231b1f878ba3 --- /dev/null +++ b/sci-biology/express/express-1.5.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Streaming RNA-Seq Analysis" +HOMEPAGE="http://bio.math.berkeley.edu/eXpress/" +SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + >=dev-libs/boost-1.52.0:= + dev-libs/protobuf + dev-util/google-perftools + sys-libs/zlib + sci-biology/bamtools" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${P}-src" + +PATCHES=( + "${FILESDIR}"/${P}-buildsystem.patch +) + +src_configure() { + local mycmakeargs=( + -DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools" + ) + cmake-utils_src_configure +} diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch new file mode 100644 index 000000000000..fca5feadd111 --- /dev/null +++ b/sci-biology/express/files/express-1.5.1-buildsystem.patch @@ -0,0 +1,55 @@ + CMakeLists.txt | 8 +++----- + src/CMakeLists.txt | 4 ++-- + 2 files changed, 5 insertions(+), 7 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index c768e28..65d5633 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1) + set(${PROJECT_NAME}_VERSION_MINOR 5) + set(${PROJECT_NAME}_VERSION_PATCH 1) + +-set(CMAKE_CXX_FLAGS "-Wall") +- + set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}") + + set(CMAKE_BUILD_TYPE Release) +-set(Boost_USE_STATIC_LIBS ON) ++set(Boost_USE_STATIC_LIBS OFF) + + find_package(Boost 1.39 + COMPONENTS +@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB) + + find_package(Protobuf) + if (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 1) + else (PROTOBUF_FOUND) +- include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") ++ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE}) + set(PROTO_INT 0) + endif(PROTOBUF_FOUND) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 1cc0c01..8929d1f 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC) + if(WIN32) + set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib") + else(WIN32) +- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread") ++ set(LIBRARIES ${LIBRARIES} "bamtools" "pthread") + endif(WIN32) + + if (PROTOBUF_FOUND) +- set(LIBRARIES ${LIBRARIES} "libprotobuf.a") ++ set(LIBRARIES ${LIBRARIES} "protobuf") + endif(PROTOBUF_FOUND) + + target_link_libraries(express ${LIBRARIES}) diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/express/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest new file mode 100644 index 000000000000..734131ee7f78 --- /dev/null +++ b/sci-biology/fasta/Manifest @@ -0,0 +1,2 @@ +DIST fasta-35.4.10.tar.gz 618971 SHA256 60616963093784d2e41ff9c125d68d7a43bbe411cdef8dc37ce922b4c3aec758 SHA512 f04268f0eea59cd40985c86597ab68bef40ee28e6ca914a7182c0edfe943ec8fb2a860558f422f210a4c03f3c34f36c677bd3971bc240cb87695826c755f5a47 WHIRLPOOL 87eb008bc507923ceaebe93c5eb2ab367ca184c0fa2304491ba8edf09e5f6eabe16a8823a1b6a11d5157355406157d1c97da9bd1e194dc26709188b995a386ce +DIST fasta-36.3.5e.tar.gz 943763 SHA256 92f44a0e0e13bcd6782489f2db42044d7109a9071d775fb0435df24288be90c2 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812 WHIRLPOOL 803cee2c7da8487811b6aa9776bfa737ab35c4de2f76887915ab285802a738cb073059f4122379512195bd54ad63db42c61059587b6a2aa34550774e57f9f5fa diff --git a/sci-biology/fasta/fasta-35.4.10.ebuild b/sci-biology/fasta/fasta-35.4.10.ebuild new file mode 100644 index 000000000000..3fb4fb923a98 --- /dev/null +++ b/sci-biology/fasta/fasta-35.4.10.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" +SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="debug cpu_flags_x86_sse2 test" + +DEPEND="test? ( app-shells/tcsh )" +RDEPEND="" + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + use debug && append-flags -DDEBUG + + if [[ $(tc-getCC) == *icc* ]]; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT=$(tc-getCC) + use x86 && ALT="32" + use amd64 && ALT="64" + fi + + if use cpu_flags_x86_sse2 ; then + ALT="${ALT}_sse2" + append-flags -msse2 + [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math + fi + + export CC_ALT="${CC_ALT}" + export ALT="${ALT}" + + epatch "${FILESDIR}"/${PV}-ldflags.patch +} + +src_compile() { + cd src + emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all || die +} + +src_install() { + dobin bin/* || die + doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die + dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die +} diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild new file mode 100644 index 000000000000..a9466820c4e8 --- /dev/null +++ b/sci-biology/fasta/fasta-36.3.5e.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" +SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="debug cpu_flags_x86_sse2 test" + +DEPEND="test? ( app-shells/tcsh )" +RDEPEND="" + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + use debug && append-flags -DDEBUG + + if [[ $(tc-getCC) == *icc* ]]; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT=$(tc-getCC) + use x86 && ALT="32" + use amd64 && ALT="64" + fi + + if use cpu_flags_x86_sse2 ; then + ALT="${ALT}_sse2" + append-flags -msse2 + [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math + fi + + export CC_ALT="${CC_ALT}" + export ALT="${ALT}" + + epatch "${FILESDIR}"/${P}-ldflags.patch + + sed \ + -e 's:-ffast-math::g' \ + -i make/Makefile* || die + +} + +src_compile() { + cd src || die + emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all +} + +src_test() { + cd test || die + FASTLIBS="../conf" bash test.sh || die +} + +src_install() { + local bin + dobin bin/* + + pushd bin > /dev/null || die + for bin in *36; do + dosym ${bin} /usr/bin/${bin%36} || die + done + popd + + insinto /usr/share/${PN} + doins -r conf/* data seq + + doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} + dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} +} diff --git a/sci-biology/fasta/files/35.4.10-ldflags.patch b/sci-biology/fasta/files/35.4.10-ldflags.patch new file mode 100644 index 000000000000..c3b7a9b56904 --- /dev/null +++ b/sci-biology/fasta/files/35.4.10-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/make/Makefile.pcom b/make/Makefile.pcom +index a808667..405be95 100644 +--- a/make/Makefile.pcom ++++ b/make/Makefile.pcom +@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm + + res_stats : res_stats.o scale_se.o +- $(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch new file mode 100644 index 000000000000..a6eeabfdf46c --- /dev/null +++ b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch @@ -0,0 +1,74 @@ + make/Makefile.pcom | 8 ++++---- + make/Makefile.pcom_s | 8 ++++---- + make/Makefile.pcom_t | 8 ++++---- + 3 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/make/Makefile.pcom b/make/Makefile.pcom +index 9c5f801..33fc001 100644 +--- a/make/Makefile.pcom ++++ b/make/Makefile.pcom +@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm +diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s +index dc53001..8a45044 100644 +--- a/make/Makefile.pcom_s ++++ b/make/Makefile.pcom_s +@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm +diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t +index 8a71438..5b08a50 100644 +--- a/make/Makefile.pcom_t ++++ b/make/Makefile.pcom_t +@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml new file mode 100644 index 000000000000..b98c9919d241 --- /dev/null +++ b/sci-biology/fasta/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> + </longdescription> +</pkgmetadata> diff --git a/sci-biology/fasttree/Manifest b/sci-biology/fasttree/Manifest new file mode 100644 index 000000000000..da5370b6e7de --- /dev/null +++ b/sci-biology/fasttree/Manifest @@ -0,0 +1,6 @@ +DIST FastTree-2.1.7.c 383551 SHA256 da148297bb64711e43e38481186228496d418bb4ec0166e09df62a72248085a0 SHA512 e88916e6586885e095948e78e6654081f966c78fbf637cfdac01970f5337bfe5616efcd165fb5f9718af0831ff45047b165944f5da9c5931d9725ea6f49cb59e WHIRLPOOL c4b267d8c3d92f0e76110eed31fcbdb4c142a967c3df31ca30ef816716231e1a9867094d183173af28fc3e7cb9acba81a55d455fcb8833539b2cad0667683775 +DIST FastTree-2.1.8.c 385231 SHA256 b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 SHA512 39a7d284412a602208c2a5df3d0a9a30fe3a584f7f7788d741fb1463b698692017f47bb23f70046d0873e9c8fd27c84ec23f6ca48adb0594193765ac732e6559 WHIRLPOOL 31331c85584c2030f56955e79250c6d6c06147007c6dd10f324c207fdebd4a1b89c87dcce52e5bab6e8d89cc69656d95a51bd808f52b8d61f6d29af40a5d4976 +DIST FastTreeUPGMA-2.1.7.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496 +DIST FastTreeUPGMA-2.1.8.c 95271 SHA256 199acc84910ca899dae9dd96d2ea133b651e76bbd855363cf620bf1b3cbd3abd SHA512 4d6a8e2cb28b8ee201091172a3baa59d432420839c6d2244b5fb8230ed9daa626b6bed22cb692393ca3d78b8f2d071fe18fbb4f9bdcdc47ef149c31e3f45546c WHIRLPOOL 538b44382137e6055452c901c76007b1c388a541c193c37f7baff26e59eb477450ce8acf7466d5debe0bc973fecc645d1f88d54f6f871670826bb151fd5b7496 +DIST MOTreeComparison-2.1.7.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475 +DIST MOTreeComparison-2.1.8.tar.gz 13523 SHA256 aea482d47aca528026cdf86fc96dc59b7a9f66ea33b9e974f5c007b46335d174 SHA512 24d2247650d7728942bd1d987b548cefd65a16b433a3810876613e9fd1cff223d4349ee720b3d8d10a73af220c2c9f59a24d77ad34ff009325fe9f22aa35c72b WHIRLPOOL 7ed1009d622ce77c59cf79078a08a08dafb281e87a6ae99be7b7fba9451f2748bfd7a51036c041e3667ea8e29f7545276b799d708aabb7ea1988ea443f73f475 diff --git a/sci-biology/fasttree/fasttree-2.1.7.ebuild b/sci-biology/fasttree/fasttree-2.1.7.ebuild new file mode 100644 index 000000000000..522d09f60400 --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.7.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +SRC_URI=" + http://www.microbesonline.org/fasttree/FastTree-${PV}.c + http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c + http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="double-precision openmp cpu_flags_x86_sse3" + +REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )" + +DOCS=( README ) + +PATCHES=( "${FILESDIR}"/${P}-format-security.patch ) + +src_unpack() { + mkdir "${S}" || die + cd "${S}" || die + unpack ${A} + cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die +} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DVERSION="${PV}" + $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) + $(cmake-utils_use_use openmp) + $(cmake-utils_use_use double-precision double) + ) + cmake-utils_src_configure +} diff --git a/sci-biology/fasttree/fasttree-2.1.8.ebuild b/sci-biology/fasttree/fasttree-2.1.8.ebuild new file mode 100644 index 000000000000..fea83a4d7696 --- /dev/null +++ b/sci-biology/fasttree/fasttree-2.1.8.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Fast inference of approximately-maximum-likelihood phylogenetic trees" +HOMEPAGE="http://www.microbesonline.org/fasttree/" +SRC_URI=" + http://www.microbesonline.org/fasttree/FastTree-${PV}.c + http://www.microbesonline.org/fasttree/FastTreeUPGMA.c -> FastTreeUPGMA-${PV}.c + http://www.microbesonline.org/fasttree/MOTreeComparison.tar.gz -> MOTreeComparison-${PV}.tar.gz +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="double-precision openmp cpu_flags_x86_sse3" + +REQUIRED_USE="?? ( double-precision cpu_flags_x86_sse3 )" + +DOCS=( README ) + +PATCHES=( "${FILESDIR}"/${P}-format-security.patch ) + +src_unpack() { + mkdir "${S}" || die + cd "${S}" || die + unpack ${A} + cp "${DISTDIR}"/{FastTreeUPGMA-${PV}.c,FastTree-${PV}.c} . || die +} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DVERSION="${PV}" + $(cmake-utils_use_has cpu_flags_x86_sse3 sse3) + $(cmake-utils_use_use openmp) + $(cmake-utils_use_use double-precision double) + ) + cmake-utils_src_configure +} diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt new file mode 100644 index 000000000000..e7c53afdaf36 --- /dev/null +++ b/sci-biology/fasttree/files/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required (VERSION 2.6) +project(fasttree C) + +option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON) +option(USE_DOUBLE "Use double precission" OFF) +option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON) + +if(USE_OPENMP) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) + SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) +endif(USE_OPENMP) + +if(USE_DOUBLE) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) +endif(USE_DOUBLE) + +if(NOT HAS_SSE3) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) +endif(NOT HAS_SSE3) + + +add_executable(FastTree FastTree-${VERSION}.c) +add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) + +target_link_libraries(FastTree m) +target_link_libraries(FastTreeUPGMA m) + +install (TARGETS FastTree FastTreeUPGMA DESTINATION bin) + +install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree) diff --git a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch new file mode 100644 index 000000000000..31dafdad46de --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.7.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.7.c ++++ b/FastTreeUPGMA-2.1.7.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch new file mode 100644 index 000000000000..15f5c174ec40 --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.8.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.8.c ++++ b/FastTreeUPGMA-2.1.8.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml new file mode 100644 index 000000000000..5ee1f51e55df --- /dev/null +++ b/sci-biology/fasttree/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="double-precision"> + use double precision instead of single-precision floating point + (2x memroy required) + </flag> + </use> +</pkgmetadata> diff --git a/sci-biology/finchtv/Manifest b/sci-biology/finchtv/Manifest new file mode 100644 index 000000000000..618173a8779c --- /dev/null +++ b/sci-biology/finchtv/Manifest @@ -0,0 +1 @@ +DIST finchtv_1_3_1.tar.gz 6706911 SHA256 03fccbf1ab09b571bbf55d0b71dd86975513b7a6c8d54795055a184b4eda8858 SHA512 813217a6d44cbd60fff061da94f70adadcc803b77352b278246711bf1b952b592a0fdb6bfc9d74264d896cb816078e809bdc633981d4009c422f59f74aca5bc8 WHIRLPOOL 3b6de1673b69bfb41f1416e7758ccafcf97f10bd4f348a88e8498d04c408caf2ac316d8e1a20bf1abe2d6487f38c3b9875af54ecb1d2b1a2ff813b436de90988 diff --git a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild new file mode 100644 index 000000000000..8f89b5cbc873 --- /dev/null +++ b/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PV="${PV//./_}" +MY_P=${PN}_${MY_PV} + +DESCRIPTION="Graphical viewer for chromatogram files" +HOMEPAGE="http://www.geospiza.com/finchtv/" +SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz" + +LICENSE="finchtv" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MY_P}" + +QA_PREBUILT="opt/bin/*" + +src_install() { + exeinto /opt/bin + doexe finchtv + dodoc ReleaseNotes.txt + dohtml -r Help/* + insinto /usr/share/doc/${PN} + doins -r SampleData +} diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml new file mode 100644 index 000000000000..e487463fc00b --- /dev/null +++ b/sci-biology/finchtv/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>je_fro@gentoo.org</email> + <name>Jeff Gardner</name> + </maintainer> + <longdescription lang="en"> +A cross-platform graphical viewer for chromatogram files. +</longdescription> +</pkgmetadata> diff --git a/sci-biology/flower/Manifest b/sci-biology/flower/Manifest new file mode 100644 index 000000000000..727ec9661be4 --- /dev/null +++ b/sci-biology/flower/Manifest @@ -0,0 +1 @@ +DIST flower-0.7.2.tar.gz 10455 SHA256 0b8d60e8af5114e496e401af344c3f7338ecb42c1b8b8a96220efa19d21a3465 SHA512 1c96173b8e3a881b2c65f3dcabd27e71a9341a73e56c056534e7d8eb53bc3222d8d32c6397a3a80413ee361bce42a40f20d7280d5e9748a1c1b828d42fefba74 WHIRLPOOL 8fec1ce45acb41e3da63eee27911fa7a738c7b9e259cecdc01df1f1c06974099b50505a0e51c041e8ae96f60cff9a283aa2b887d12cf7a800b1a129d2cc0ad0c diff --git a/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch b/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch new file mode 100644 index 000000000000..90dfb2326918 --- /dev/null +++ b/sci-biology/flower/files/flower-0.7.2-ghc-7.8.patch @@ -0,0 +1,27 @@ +diff --git a/src/Flower.hs b/src/Flower.hs +index fca5814..9424222 100644 +--- a/src/Flower.hs ++++ b/src/Flower.hs +@@ -25,6 +25,7 @@ import qualified Data.ByteString.Lazy as L1 + + import Data.Array.Unboxed + import Data.Array.ST ++import qualified Data.Array.Unsafe as U + import Control.Monad.ST + import Control.Monad.State + +@@ -238,10 +239,10 @@ histogram fl scores = runST $ do + ins1 (x,_) = error ("Illegal character "++show x++" in flow!") + bump ar i = readArray ar i >>= \x -> writeArray ar i (x+1) + mapM_ ins1 (zip (cycle fl) (map (\x->if x>9999 || x<0 then 9999 else x) $ concat scores)) +- a' <- unsafeFreeze a +- c' <- unsafeFreeze c +- g' <- unsafeFreeze g +- t' <- unsafeFreeze t ++ a' <- U.unsafeFreeze a ++ c' <- U.unsafeFreeze c ++ g' <- U.unsafeFreeze g ++ t' <- U.unsafeFreeze t + return (a',c',g',t') + + showHist :: (Hist,Hist,Hist,Hist) -> String diff --git a/sci-biology/flower/flower-0.7.2.ebuild b/sci-biology/flower/flower-0.7.2.ebuild new file mode 100644 index 000000000000..25e24c3aa26f --- /dev/null +++ b/sci-biology/flower/flower-0.7.2.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +# ebuild generated by hackport 0.2.17.9999 + +EAPI=5 + +CABAL_FEATURES="bin" +inherit eutils haskell-cabal + +DESCRIPTION="Analyze 454 flowgrams (.SFF files)" +HOMEPAGE="http://biohaskell.org/Applications/Flower" +SRC_URI="mirror://hackage/packages/archive/${PN}/${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + >=dev-haskell/binary-0.4 <dev-haskell/binary-0.8 + >=dev-haskell/bio-0.4.9 + >=dev-haskell/cabal-1.6 + >=dev-haskell/cmdargs-0.5 + dev-haskell/mtl + dev-haskell/random + >=dev-lang/ghc-6.10.1" + +src_prepare() { + epatch "${FILESDIR}"/${P}-ghc-7.8.patch + cabal_chdeps \ + 'binary == 0.4.*' 'binary >= 0.4 && <0.8' +} diff --git a/sci-biology/flower/metadata.xml b/sci-biology/flower/metadata.xml new file mode 100644 index 000000000000..dcaae2095b0e --- /dev/null +++ b/sci-biology/flower/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>haskell</herd> + <maintainer> + <email>haskell@gentoo.org</email> + </maintainer> + <longdescription> + flower - FLOWgram ExtractoR tools + + The flower executable reads files in SFF-format and produces various output, + including sequences with quality, or flowgram data in tabular format. By default, + it outputs a textual representation of the data in the SFF-file, much like + 'sffinfo' from Roche does. + + The fselect executable extracts reads from SFF-files, generating a new + SFF-file with a subset of the reads based on various criteria. + + Sometimes SFF files will appear to be corrupted, with all-zero blocks in the + file. The frecover program ignores these and tries to resync with the file after an + invalid region. This was likely a one-time bug in the 454 software, so this program + is probably not so useful any more. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest new file mode 100644 index 000000000000..46799da48482 --- /dev/null +++ b/sci-biology/foldingathome/Manifest @@ -0,0 +1,4 @@ +DIST fahclient_7.3.6-32bit-release.tar.bz2 4014455 SHA256 c8415aa5a64d6b26e7684327d51f9133d524777d4123ea47138ba86595c37f12 SHA512 0a49e9cb26659357b4855f5aaf7ef5c078f172af16777d74fb566e7faa61ac0e41185dcd6f06841bf4efe047017e8dc783eae7682a40b921acb436e4d81e6639 WHIRLPOOL 0cd8f0b6dcfce297cb70b307887f1d44278c07435f5a067d9f1e83399b3913710d481982033023faf1b9056b63f14eca3b53babe698633de24544c6cdbce5f82 +DIST fahclient_7.3.6-64bit-release.tar.bz2 4349503 SHA256 e3d48b0d1b64da96601f741e0b9164ea633f1be3fe4407086679bc7c72742079 SHA512 9995a72549e38724830c403eef188786b137c8669b6121c0ec6c3d29539db9b0f67876adf5c3af64c818ada05f57a0f2ea88a58b73bdfd852c1ed8f09a327583 WHIRLPOOL 4e5bccb175dc042a1380c06b96a5d803f36ede50e429d3b1f13b33c872f753bda5acd7f5a3d60a522cb82c7da47313ef95e0c55778cbe94d579a9ecaa22c49cc +DIST fahclient_7.4.4-32bit-release.tar.bz2 4313096 SHA256 81f1a1d161d1302a08638f23ebcfd7a163046a5427c49c70651fc8e2f6d8d60e SHA512 6a660b99c97c83518863ef671ae760b15e3ca33cacfde6485c11b29e98fab15a9d27833ba307c95b39e6ffb7f271cd0c7a47060ec5b8614961e9a5ee46494b3f WHIRLPOOL 6c6c25446e8e118b7931c58643827739691bcb9f1ae67461e6dd72cfc8556f86d49c533669897f6711537ce920680c23d0d496ba75a21047a88708cc93fec314 +DIST fahclient_7.4.4-64bit-release.tar.bz2 4451080 SHA256 4642ed9b5a06c8ab63106293f6a5ce547f6a96efe85fcd3b8c19d9065ab582df SHA512 40fc93c4ec682342040a4c7a9fd92dc9d1727ef60af6d3fa3191575719c7e595868f289727561f6902f8374061f7b51dfcf565ac047706336ef4ae9a589ff9a8 WHIRLPOOL 4feea83f1e826430943dec0495ce7658408cdaa4671bf1e4d1ec338991dbeb1599f25a4835f3960bea135fe4af7c4e415be6767ea5a0a13f63201c64e6ce6f6e diff --git a/sci-biology/foldingathome/files/7.3/fah-init b/sci-biology/foldingathome/files/7.3/fah-init new file mode 100644 index 000000000000..1c1a232fb697 --- /dev/null +++ b/sci-biology/foldingathome/files/7.3/fah-init @@ -0,0 +1,30 @@ +#!/sbin/runscript +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $ + +extra_commands="unitinfo" + +unitinfo() { + einfo "$(head -n1 /opt/foldingathome/unitinfo.txt):" + sed -e '1,2d' /opt/foldingathome/unitinfo.txt +} + +start() { + ebegin "Starting Folding@Home" + cd /opt/foldingathome + start-stop-daemon --chdir ${PWD} --user foldingathome --nicelevel 19 \ + --make-pidfile --pidfile "${PIDFILE}" \ + --start --background --exec ./FAHClient -- ${FOLD_OPTS} + eend $? +} + +stop() { + ebegin "Stopping Folding@Home" + start-stop-daemon --stop --user foldingathome --pidfile "${PIDFILE}" + if [ $? -ne 0 ]; then + killall --user foldingathome --signal SIGKILL + ewarn "killing all processes running as user 'foldingathome' ..." + fi + eend $? +} diff --git a/sci-biology/foldingathome/files/7.3/folding-conf.d b/sci-biology/foldingathome/files/7.3/folding-conf.d new file mode 100644 index 000000000000..b4e0448226a6 --- /dev/null +++ b/sci-biology/foldingathome/files/7.3/folding-conf.d @@ -0,0 +1,10 @@ +# Config file for /etc/init.d/foldingathome +# +# The f@h client configuration can be found in /opt/foldingathome/config.xml +# Run /opt/foldingathome/initfolding to reconfigure that. +# +# The options that may be passed to the Folding client can be obtained +# by running /opt/foldingathome/FAHClient --help +# +FOLD_OPTS="" +PIDFILE=/run/folding diff --git a/sci-biology/foldingathome/files/7.3/initfolding b/sci-biology/foldingathome/files/7.3/initfolding new file mode 100644 index 000000000000..240b7fa2f17b --- /dev/null +++ b/sci-biology/foldingathome/files/7.3/initfolding @@ -0,0 +1,5 @@ +#!/bin/sh + +cd /opt/foldingathome +/opt/foldingathome/FAHClient --configure +/bin/chown -R foldingathome:nogroup /opt/foldingathome diff --git a/sci-biology/foldingathome/foldingathome-7.3.6-r2.ebuild b/sci-biology/foldingathome/foldingathome-7.3.6-r2.ebuild new file mode 100644 index 000000000000..d55a4d1c9140 --- /dev/null +++ b/sci-biology/foldingathome/foldingathome-7.3.6-r2.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit versionator user + +MY_BASEURI="https://fah.stanford.edu/file-releases/public/release/fahclient" +MY_64B_URI="${MY_BASEURI}/centos-5.3-64bit/v$(get_version_component_range 1-2)/fahclient_${PV}-64bit-release.tar.bz2" +MY_32B_URI="${MY_BASEURI}/centos-5.5-32bit/v$(get_version_component_range 1-2)/fahclient_${PV}-32bit-release.tar.bz2" + +DESCRIPTION="Folding@Home is a distributed computing project for protein folding" +HOMEPAGE="http://folding.stanford.edu/FAQ-SMP.html" +SRC_URI="x86? ( ${MY_32B_URI} ) + amd64? ( ${MY_64B_URI} )" + +RESTRICT="mirror bindist strip" + +LICENSE="FAH-EULA-2009 FAH-special-permission" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +# Expressly listing all deps, as this is a binpkg and it is doubtful whether +# i.e. uclibc or clang can provide what is necessary at runtime +RDEPEND="app-arch/bzip2 + sys-devel/gcc + sys-libs/glibc + sys-libs/zlib" + +S="${WORKDIR}" + +I="opt/foldingathome" + +QA_PREBUILT="${I}/*" + +pkg_setup() { + I="${EROOT}/${I}" + einfo "" + cat "${PORTDIR}"/licenses/FAH-special-permission + einfo "" +} + +src_install() { + local myS="fahclient_${PV}-64bit-release" + use x86 && myS="${myS//64bit/32bit}" + exeinto "${I}" + doexe "${FILESDIR}"/$(get_version_component_range 1-2)/initfolding + doexe "${myS}"/{FAHClient,FAHCoreWrapper} + newconfd "${FILESDIR}"/$(get_version_component_range 1-2)/folding-conf.d foldingathome + newinitd "${FILESDIR}"/$(get_version_component_range 1-2)/fah-init foldingathome +} + +pkg_preinst() { + # the bash shell is important for "su -c" in init script + enewuser foldingathome -1 /bin/bash /opt/foldingathome +} + +pkg_postinst() { + chown -R foldingathome:nogroup "${I}" + einfo "To run Folding@home in the background at boot:" + einfo "\trc-update add foldingathome default" + einfo "" + if [ ! -e "${I}"/config.xml ]; then + elog "No configuration found -- please run ${I}/initfolding or" + elog "emerge --config ${P} to configure your client and edit" + elog "${EROOT}/etc/conf.d/foldingathome for options" + fi + einfo "" + einfo "The original author encourages you to acquire a username and join team 36480." + einfo "http://folding.stanford.edu/English/Download#ntoc2" + einfo "" +} + +pkg_postrm() { + elog "Folding@home data files were not removed." + elog "Remove them manually from ${I}" +} + +pkg_config() { + "${I}"/initfolding +} diff --git a/sci-biology/foldingathome/foldingathome-7.4.4.ebuild b/sci-biology/foldingathome/foldingathome-7.4.4.ebuild new file mode 100644 index 000000000000..2a48c1b03554 --- /dev/null +++ b/sci-biology/foldingathome/foldingathome-7.4.4.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit versionator user + +MY_BASEURI="https://fah.stanford.edu/file-releases/public/release/fahclient" +MY_64B_URI="${MY_BASEURI}/centos-5.3-64bit/v$(get_version_component_range 1-2)/fahclient_${PV}-64bit-release.tar.bz2" +MY_32B_URI="${MY_BASEURI}/centos-5.5-32bit/v$(get_version_component_range 1-2)/fahclient_${PV}-32bit-release.tar.bz2" + +DESCRIPTION="Folding@Home is a distributed computing project for protein folding" +HOMEPAGE="http://folding.stanford.edu/FAQ-SMP.html" +SRC_URI="x86? ( ${MY_32B_URI} ) + amd64? ( ${MY_64B_URI} )" + +RESTRICT="mirror bindist strip" + +LICENSE="FAH-EULA-2014 FAH-special-permission" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +# Expressly listing all deps, as this is a binpkg and it is doubtful whether +# i.e. uclibc or clang can provide what is necessary at runtime +RDEPEND="app-arch/bzip2 + sys-devel/gcc + sys-libs/glibc + sys-libs/zlib" + +S="${WORKDIR}" + +I="opt/foldingathome" + +QA_PREBUILT="${I}/*" + +pkg_setup() { + I="${EROOT}/${I}" + einfo "" + cat "${PORTDIR}"/licenses/FAH-special-permission + einfo "" +} + +src_install() { + local myS="fahclient_${PV}-64bit-release" + use x86 && myS="${myS//64bit/32bit}" + exeinto "${I}" + doexe "${FILESDIR}"/7.3/initfolding + doexe "${myS}"/{FAHClient,FAHCoreWrapper} + newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome + newinitd "${FILESDIR}"/7.3/fah-init foldingathome +} + +pkg_preinst() { + # the bash shell is important for "su -c" in init script + enewuser foldingathome -1 /bin/bash /opt/foldingathome +} + +pkg_postinst() { + chown -R foldingathome:nogroup "${I}" + einfo "To run Folding@home in the background at boot (with openrc):" + einfo "\trc-update add foldingathome default" + einfo "" + if [ ! -e "${I}"/config.xml ]; then + elog "No configuration found -- please run ${I}/initfolding or" + elog "emerge --config ${P} to configure your client and edit" + elog "${EROOT}/etc/conf.d/foldingathome for options" + fi + einfo "" + einfo "The original author encourages you to acquire a username and join team 36480." + einfo "http://folding.stanford.edu/English/Download#ntoc2" + einfo "" +} + +pkg_postrm() { + elog "Folding@home data files were not removed." + elog "Remove them manually from ${I}" +} + +pkg_config() { + "${I}"/initfolding +} diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml new file mode 100644 index 000000000000..63d767b84f60 --- /dev/null +++ b/sci-biology/foldingathome/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-biology</herd> +<maintainer> + <email>axs@gentoo.org</email> + <name>Ian Stakenvicius</name> +</maintainer> +</pkgmetadata> diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest new file mode 100644 index 000000000000..6cd4e325d33f --- /dev/null +++ b/sci-biology/gatk/Manifest @@ -0,0 +1 @@ +DIST gatk-2.4.tar.gz 9106774 SHA256 db0be90ef5182866a1f936742fba20b317ce582556e19acb69de2a8894f7383a SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace WHIRLPOOL 1fa7a73f317db82c313ea112ffaa6466c2b17384f1ad8d06c74a3f4764dfd822f036cc2dc99890c157fc2c32ce299a4a7d0c73cafc72dd7ad955d75053745b2c diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild new file mode 100644 index 000000000000..53bc0dc1b50b --- /dev/null +++ b/sci-biology/gatk/gatk-2.4.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EANT_BUILD_TARGET="dist" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" + +inherit java-pkg-2 java-ant-2 vcs-snapshot + +DESCRIPTION="The Genome Analysis Toolkit" +HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit" +SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64" + +COMMON_DEPS="" +DEPEND=" + >=virtual/jdk-1.6 + ${COMMON_DEPS}" +RDEPEND=" + >=virtual/jre-1.6 + ${COMMON_DEPS}" + +src_prepare() { + sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar dist/*.jar + java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar + java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar +} diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild new file mode 100644 index 000000000000..9a705487d658 --- /dev/null +++ b/sci-biology/gatk/gatk-9999.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +EANT_BUILD_TARGET="dist" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" + +inherit git-2 java-pkg-2 java-ant-2 + +DESCRIPTION="The Genome Analysis Toolkit" +HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit" +SRC_URI="" +EGIT_REPO_URI="https://github.com/broadgsa/gatk.git" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="" + +COMMON_DEPS="" +DEPEND=" + >=virtual/jdk-1.6 + dev-vcs/git + ${COMMON_DEPS}" +RDEPEND=" + >=virtual/jre-1.6 + ${COMMON_DEPS}" + +src_prepare() { + sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar dist/*.jar + java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar + java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar +} diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/gatk/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest new file mode 100644 index 000000000000..affcfb9f045f --- /dev/null +++ b/sci-biology/gibbs/Manifest @@ -0,0 +1 @@ +DIST gibbs-3.1.tar.gz 563300 RMD160 063de85a7f1a62bcd63c0838db62cb344ff27abd SHA1 9e6fcddd6036ea0c19259820dcfffa9286cd4e1f SHA256 e8bd62b7d2580b00fc0cdf32ed75ac1ffac29747c75227269a75fd587ba77b69 diff --git a/sci-biology/gibbs/files/gibbs-demo b/sci-biology/gibbs/files/gibbs-demo new file mode 100644 index 000000000000..c58ae3b88e04 --- /dev/null +++ b/sci-biology/gibbs/files/gibbs-demo @@ -0,0 +1,7 @@ +#!/bin/bash + +gibbs /usr/share/gibbs/examples/porins.b185 11 100 -R2000 -s230 +gibbs /usr/share/gibbs/examples/iomps.b58 11 125 -s1 +gibbs /usr/share/gibbs/examples/Igfold.b60x 12,12,12 90,90,90 -s1 +gibbs /usr/share/gibbs/examples/hth90seqs 12 150 -s1 +gibbs /usr/share/gibbs/examples/hth90seqs 18,18,18 20,20,20 -s1 diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild new file mode 100644 index 000000000000..9ed11b435129 --- /dev/null +++ b/sci-biology/gibbs/gibbs-3.1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils multilib + +DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences" +HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html" +SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="mpi" +KEYWORDS="amd64 x86" + +DEPEND=" + mpi? ( + virtual/mpi + sys-cluster/mpe2 )" +RDEPEND="${DEPEND}" + +src_prepare() { + sed \ + -e 's/CFLAGS="$OPTFLAGS/CFLAGS="$CFLAGS $OPTFLAGS/' \ + -e 's/-Werror//' \ + -i configure.in || die + autotools-utils_src_prepare +} + +src_configure() { + if use mpi; then export CC=mpicc; fi + local myeconfargs=( $(use_enable mpi) ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + exeinto /usr/$(get_libdir)/${PN} + doexe *.pl + dodoc README ChangeLog +} + +pkg_postinst() { + einfo "Supplementary Perl scripts for Gibbs have been installed into /usr/$(get_libdir)/${PN}." + einfo "These scripts require installation of sci-biology/bioperl." +} diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml new file mode 100644 index 000000000000..c31e2db70216 --- /dev/null +++ b/sci-biology/gibbs/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + The Gibbs motif sampler stochastically examines candidate alignments + in an effort to find the best alignment as measured by the maximum + a posteriori (MAP) log-likelihood ratio. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/glimmer/Manifest b/sci-biology/glimmer/Manifest new file mode 100644 index 000000000000..7071ac856370 --- /dev/null +++ b/sci-biology/glimmer/Manifest @@ -0,0 +1,2 @@ +DIST glimmer302.tar.gz 5637075 SHA256 a1e422ee56f495f9f99e1741ba2043f026fc8182afcc47cb20cfd2d989537221 SHA512 c28e5902bffab00566560fa0bcf61909921932935f8298f098361aeb58eb67a40403c23709cf5075fb47dc87bcf54e25572840f110bb15cd21325a072050407c WHIRLPOOL c3eedb4a3a65043a69d632360608f04382117b8f7f3718eae328a1aa14f9f5d6d9ae6f05e0a83a09af5eb9e6b0c7b0ae26cb820813341aa5d7fa3f6002938ce8 +DIST glimmer302b.tar.gz 5637975 SHA256 ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6 SHA512 00d44a02a8099ceac4b4d2a1cd5d69cc2b787942bb87f612cd63edacf7e502bc9a65cdf9b9270ad789981a84c940cc01e187882d21d2c9de4dcc12b492b041a6 WHIRLPOOL bbce6f57546e6cc77801ac7f5e783510feafc2e120a8727e848a95dd9e2d966538e56cb7be597c2a463d9b372c8586a389d639e1377708a27bd56f81b37fea1f diff --git a/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch new file mode 100644 index 000000000000..f6051ec82054 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-glibc210.patch @@ -0,0 +1,24 @@ +diff -durr glimmer3.02-orig/src/Common/gene.cc glimmer3.02/src/Common/gene.cc +--- glimmer3.02-orig/src/Common/gene.cc 2009-12-28 13:34:21.577437056 +0000 ++++ glimmer3.02/src/Common/gene.cc 2009-12-28 13:36:06.914974685 +0000 +@@ -443,7 +443,7 @@ + // Return a subscript corresponding to character ch . + + { +- char * p; ++ const char * p; + + p = strchr (CONVERSION_STRING, tolower (ch)); + if (p == NULL) +diff -durr glimmer3.02-orig/src/ICM/icm.cc glimmer3.02/src/ICM/icm.cc +--- glimmer3.02-orig/src/ICM/icm.cc 2009-12-28 13:34:21.577437056 +0000 ++++ glimmer3.02/src/ICM/icm.cc 2009-12-28 13:36:44.649451803 +0000 +@@ -1981,7 +1981,7 @@ + // model) for character ch . + + { +- char * p; ++ const char * p; + + p = strchr (ALPHA_STRING, tolower (Filter (ch))); + if (p == NULL) diff --git a/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch new file mode 100644 index 000000000000..91498b116d12 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-jobserver-fix.patch @@ -0,0 +1,22 @@ +diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile +--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100 +@@ -2,12 +2,12 @@ + + + all: +- @ TGT=objs +- @ $(dosubdirs) +- @ TGT=libs +- @ $(dosubdirs) +- @ TGT=progs +- @ $(dosubdirs) ++ @+ TGT=objs ++ @+ $(dosubdirs) ++ @+ TGT=libs ++ @+ $(dosubdirs) ++ @+ TGT=progs ++ @+ $(dosubdirs) + + + install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch new file mode 100644 index 000000000000..0a04fbef1dcc --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02-ldflags.patch @@ -0,0 +1,88 @@ +diff --git a/src/c_make.gen b/src/c_make.gen +index 414dead..84c3030 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc + #### Do not redefine if (a) passed in on command line, or (b) + #### defined in an environment variable. + +-ifneq "$(origin CC)" "environment" +-CC = cc +-endif +- +-ifneq "$(origin CPPFLAGS)" "environment" +-CPPFLAGS= +-endif +- +-ifneq "$(origin CFLAGS)" "environment" +-CFLAGS = +-endif +- +-ifneq "$(origin CDEFS)" "environment" +-CDEFS = +-endif +- +-ifneq "$(origin CXX)" "environment" +-CXX = g++ +-endif +- +-ifneq "$(origin CXXFLAGS)" "environment" +-CXXFLAGS= +-endif +- +-ifneq "$(origin CXXDEFS)" "environment" +-CXXDEFS= -D__cplusplus +-endif +- +-ifneq "$(origin AR)" "environment" +-AR = ar +-endif +- +-ifneq "$(origin ARFLAGS)" "environment" +-ARFLAGS = rvs +-endif +- +-ifneq "$(origin LDFLAGS)" "environment" +-LDFLAGS = +-endif ++CC ?= cc ++CXX ?= g++ ++CXXFLAGS ?= ++CXXDEFS = -D__cplusplus ++AR ?= ar ++ARFLAGS ?= rvs + + #### Delete default suffix rules + .SUFFIXES: +@@ -359,13 +326,13 @@ $(PROGS): + cd $(LOCAL_OBJ); \ + if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + else \ + cd $(LOCAL_OBJ); \ + if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + fi ; + +diff --git a/src/c_make.glm b/src/c_make.glm +index 0decc17..b82131c 100644 +--- a/src/c_make.glm ++++ b/src/c_make.glm +@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen + + SUBDIRS = Common ICM Glimmer Util + +-CFLAGS = -g -Wall +-CXXFLAGS = -g -Wall +- +-LDFLAGS = -g -lm ++LIBS = -lm + + + #AS_BUILD_DIR =$(LOCAL_WORK) diff --git a/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch new file mode 100644 index 000000000000..91498b116d12 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-jobserver-fix.patch @@ -0,0 +1,22 @@ +diff -ru glimmer3.02-orig/src/Makefile glimmer3.02/src/Makefile +--- glimmer3.02-orig/src/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Makefile 2010-03-18 14:30:15.000000000 +0100 +@@ -2,12 +2,12 @@ + + + all: +- @ TGT=objs +- @ $(dosubdirs) +- @ TGT=libs +- @ $(dosubdirs) +- @ TGT=progs +- @ $(dosubdirs) ++ @+ TGT=objs ++ @+ $(dosubdirs) ++ @+ TGT=libs ++ @+ $(dosubdirs) ++ @+ TGT=progs ++ @+ $(dosubdirs) + + + install: all diff --git a/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch new file mode 100644 index 000000000000..0a04fbef1dcc --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch @@ -0,0 +1,88 @@ +diff --git a/src/c_make.gen b/src/c_make.gen +index 414dead..84c3030 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc + #### Do not redefine if (a) passed in on command line, or (b) + #### defined in an environment variable. + +-ifneq "$(origin CC)" "environment" +-CC = cc +-endif +- +-ifneq "$(origin CPPFLAGS)" "environment" +-CPPFLAGS= +-endif +- +-ifneq "$(origin CFLAGS)" "environment" +-CFLAGS = +-endif +- +-ifneq "$(origin CDEFS)" "environment" +-CDEFS = +-endif +- +-ifneq "$(origin CXX)" "environment" +-CXX = g++ +-endif +- +-ifneq "$(origin CXXFLAGS)" "environment" +-CXXFLAGS= +-endif +- +-ifneq "$(origin CXXDEFS)" "environment" +-CXXDEFS= -D__cplusplus +-endif +- +-ifneq "$(origin AR)" "environment" +-AR = ar +-endif +- +-ifneq "$(origin ARFLAGS)" "environment" +-ARFLAGS = rvs +-endif +- +-ifneq "$(origin LDFLAGS)" "environment" +-LDFLAGS = +-endif ++CC ?= cc ++CXX ?= g++ ++CXXFLAGS ?= ++CXXDEFS = -D__cplusplus ++AR ?= ar ++ARFLAGS ?= rvs + + #### Delete default suffix rules + .SUFFIXES: +@@ -359,13 +326,13 @@ $(PROGS): + cd $(LOCAL_OBJ); \ + if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + else \ + cd $(LOCAL_OBJ); \ + if $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \ + $(LD_DIRS) $(filter-out lib%.a, $+) \ +- $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) ; then \ ++ $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LIBS) ; then \ + true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \ + fi ; + +diff --git a/src/c_make.glm b/src/c_make.glm +index 0decc17..b82131c 100644 +--- a/src/c_make.glm ++++ b/src/c_make.glm +@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen + + SUBDIRS = Common ICM Glimmer Util + +-CFLAGS = -g -Wall +-CXXFLAGS = -g -Wall +- +-LDFLAGS = -g -lm ++LIBS = -lm + + + #AS_BUILD_DIR =$(LOCAL_WORK) diff --git a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch new file mode 100644 index 000000000000..6eebc5610414 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch @@ -0,0 +1,196 @@ +diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex +--- glimmer3.02.old/docs/notes.tex 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/docs/notes.tex 2015-05-25 22:41:39.450340098 +0200 +@@ -306,7 +306,7 @@ + The script would then run the commands: + \BSV\begin{verbatim} + long-orfs -n -t 1.15 genom.seq run1.longorfs +- extract -t genom.seq run1.longorfs > run1.train ++ glimmer_extract -t genom.seq run1.longorfs > run1.train + build-icm -r run1.icm < run1.train + glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1 + \end{verbatim}\ESV +@@ -330,9 +330,9 @@ + \end{verbatim}\ESV + The script would then run the commands: + \BSV\begin{verbatim} +- extract -t genom.seq train.coords > run2.train ++ glimmer_extract -t genom.seq train.coords > run2.train + build-icm -r run2.icm < run2.train +- upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream ++ upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream + elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif + set startuse = `start-codon-distrib -3 genom.seq train.coords` + glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2 +@@ -358,11 +358,11 @@ + The script would then run the commands: + \BSV\begin{verbatim} + long-orfs -n -t 1.15 genom.seq run3.longorfs +- extract -t genom.seq run3.longorfs > run3.train ++ glimmer_extract -t genom.seq run3.longorfs > run3.train + build-icm -r run3.icm < run3.train + glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1 + tail +2 run3.run1.predict > run3.coords +- upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream ++ upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream + elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif + set startuse = `start-codon-distrib -3 genom.seq run3.coords` + glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3 +@@ -1081,12 +1081,12 @@ + \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords} + \eq + +-\subsubsection{\Pg{extract} Program} ++\subsubsection{\Pg{glimmer_extract} Program} + This program reads a genome sequence and a list of coordinates + for it and outputs a multi-fasta file of the regions specified + by the coordinates. Output goes to standard output. + \bq +- \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords} ++ \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords} + \eq + + \subsubsection{\Pg{multi-extract} Program} +diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh +--- glimmer3.02.old/sample-run/g3-from-scratch.csh 2006-06-12 21:46:35.000000000 +0200 ++++ glimmer3.02/sample-run/g3-from-scratch.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -50,7 +50,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh +--- glimmer3.02.old/sample-run/g3-from-training.csh 2006-06-12 21:46:35.000000000 +0200 ++++ glimmer3.02/sample-run/g3-from-training.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -42,7 +42,7 @@ + step1: + # Extract the training sequences from the genome file + echo "Step 1 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $coords > $tag.train ++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -66,7 +66,7 @@ + # upstream of the start locations in $coords + echo "Step 3 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh +--- glimmer3.02.old/sample-run/g3-iterated.csh 2006-06-13 14:15:28.000000000 +0200 ++++ glimmer3.02/sample-run/g3-iterated.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -57,7 +57,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -103,7 +103,7 @@ + # upstream of the start locations in $tag.coords + echo "Step 6 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $tag.coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh +--- glimmer3.02.old/scripts/g3-from-scratch.csh 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/scripts/g3-from-scratch.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -50,7 +50,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh +--- glimmer3.02.old/scripts/g3-from-training.csh 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/scripts/g3-from-training.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -42,7 +42,7 @@ + step1: + # Extract the training sequences from the genome file + echo "Step 1 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $coords > $tag.train ++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -66,7 +66,7 @@ + # upstream of the start locations in $coords + echo "Step 3 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh +--- glimmer3.02.old/scripts/g3-iterated.csh 2006-06-13 14:15:46.000000000 +0200 ++++ glimmer3.02/scripts/g3-iterated.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -57,7 +57,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -103,7 +103,7 @@ + # upstream of the start locations in $tag.coords + echo "Step 6 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $tag.coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile +--- glimmer3.02.old/src/Util/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200 +@@ -8,7 +8,7 @@ + SOURCES = $(UTIL_SRCS) + OBJECTS = $(UTIL_OBJS) + +-PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \ ++PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \ + uncovered window-acgt + + LIBRARIES = +diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc +--- glimmer3.02.old/src/Util/extract.cc 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Util/extract.cc 2015-05-25 22:44:01.760342470 +0200 +@@ -297,7 +297,7 @@ + + { + fprintf (stderr, +- "USAGE: extract [options] <sequence-file> <coords>\n" ++ "USAGE: glimmer_extract [options] <sequence-file> <coords>\n" + "\n" + "Read fasta-format <sequence-file> and extract from it the\n" + "subsequences specified by <coords>. By default, <coords>\n" +--- glimmer3.02.old/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200 ++++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile 2015-05-25 23:13:34.230372010 +0200 +@@ -21,7 +21,7 @@ + + entropy-score: entropy-score.o libGLMcommon.a + +-extract: extract.o libGLMcommon.a ++glimmer_extract: extract.o libGLMcommon.a + + multi-extract: multi-extract.o libGLMcommon.a + diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild new file mode 100644 index 000000000000..acc0eb98e18b --- /dev/null +++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit eutils toolchain-funcs + +MY_PV=${PV//./} + +DESCRIPTION="An HMM-based microbial gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/" +SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="app-shells/tcsh" + +S="${WORKDIR}/${PN}${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-glibc210.patch + "${FILESDIR}"/${P}-jobserver-fix.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${PN}-3.02b-rename_extract.patch +) + +src_prepare() { + sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ + -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" + # Fix Makefile to die on failure + sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die + epatch "${PATCHES[@]}" +} + +src_compile() { + emake \ + -C src \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + AR=$(tc-getAR) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/test || die + dobin bin/* + + insinto /usr/share/${PN} + doins -r scripts + + dodoc glim302notes.pdf +} diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild new file mode 100644 index 000000000000..0ebbbabe0c99 --- /dev/null +++ b/sci-biology/glimmer/glimmer-3.02b.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +inherit eutils toolchain-funcs + +MY_PV=${PV//./} + +DESCRIPTION="An HMM-based microbial gene finding system from TIGR" +HOMEPAGE="http://ccb.jhu.edu/software/glimmer" +SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="app-shells/tcsh + sci-biology/elph" + +#S="${WORKDIR}/${PN}${PV}" +S="${WORKDIR}/${PN}3.02" + +PATCHES=( + "${FILESDIR}"/${P}-jobserver-fix.patch + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${P}-rename_extract.patch +) + +src_prepare() { + sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \ + -e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths" + # Fix Makefile to die on failure + sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die + # GCC 4.3 include fix + sed -i 's/include <string>/include <string.h>/' src/Common/delcher.hh || die + # + sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die + sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die + sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die + sed -i "s/@ if/if/" src/c_make.gen || die + # avoid file collision on /usr/bin/extract #247394 + epatch "${PATCHES[@]}" +} + +src_compile() { + emake \ + -C src \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + AR=$(tc-getAR) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/test || die + dobin bin/* + + insinto /usr/share/${PN} + doins -r scripts + + dodoc glim302notes.pdf +} diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/glimmer/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest new file mode 100644 index 000000000000..fd4e75d3fee9 --- /dev/null +++ b/sci-biology/glimmerhmm/Manifest @@ -0,0 +1 @@ +DIST GlimmerHMM-3.0.1.tar.gz 45475952 SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7 WHIRLPOOL f2cc0f6cea083c223273dd59f9474a054c049b697fc122925d4f5820170ade67bfa76c6dd218ab10be5675fe0a2a2a9fa5172be540509770332cc5a1d6862ff7 diff --git a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch new file mode 100644 index 000000000000..949a4fe3e92d --- /dev/null +++ b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch @@ -0,0 +1,153 @@ + sources/makefile | 15 +++++-------- + train/makefile | 59 +++++++++++++++++++++++++++++++---------------------- + 2 files changed, 40 insertions(+), 34 deletions(-) + +diff --git a/sources/makefile b/sources/makefile +index f287d71..c560f48 100644 +--- a/sources/makefile ++++ b/sources/makefile +@@ -2,25 +2,22 @@ + + + +-CC=g++ +-CFLAGS=-g +- + all: glimmerhmm + + glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o +- $(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm + + glimmerhmm.o: glimmerhmm.c +- $(CC) $(CFLAGS) -c glimmerhmm.c ++ $(CXX) $(CXXFLAGS) -c glimmerhmm.c + + graph.o: graph.c +- $(CC) $(CFLAGS) -c graph.c ++ $(CXX) $(CXXFLAGS) -c graph.c + + sites.o: sites.c +- $(CC) $(CFLAGS) -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c + + tree_util_prob.o: tree_util_prob.c +- $(CC) $(CFLAGS) -c tree_util_prob.c ++ $(CXX) $(CXXFLAGS) -c tree_util_prob.c + + util.o: util.c +- $(CC) $(CFLAGS) -c util.c ++ $(CXX) $(CXXFLAGS) -c util.c +diff --git a/train/makefile b/train/makefile +index 2383f18..d5a7107 100644 +--- a/train/makefile ++++ b/train/makefile +@@ -2,9 +2,6 @@ + + # C compiler + +-C = gcc +-CC = g++ +-CFLAGS = -O1 ${SEARCHDIRS} + #CFLAGS = -O3 -g -Wall + LIBS = -lm + +@@ -15,64 +12,76 @@ all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco + + + misc.o: misc.c +- ${C} ${CFLAGS} -c misc.c ++ $(CC) $(CFLAGS) -c misc.c + + build-icm.o: build-icm.c +- ${C} ${CFLAGS} -c build-icm.c ++ $(CC) $(CFLAGS) -c build-icm.c + + build-icm: build-icm.o misc.o +- $(C) -o $@ build-icm.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS) + + build-icm-noframe.o: build-icm-noframe.c +- ${C} ${CFLAGS} -c build-icm-noframe.c ++ $(CC) $(CFLAGS) -c build-icm-noframe.c + + build-icm-noframe: build-icm-noframe.o misc.o +- $(C) -o $@ build-icm-noframe.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS) + + build1: build1.o +- ${CC} build1.c -o build1 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS) + + build2: build2.o +- ${CC} build2.c -o build2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS) + + falsecomp: falsecomp.o +- ${CC} falsecomp.c -o falsecomp $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS) + + findsites: findsites.o +- ${CC} findsites.c -o findsites $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS) + + karlin: karlin.o +- ${CC} karlin.c -o karlin $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS) + + score: score.o +- ${CC} score.c -o score $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS) + + score2: score2.o +- ${CC} score2.c -o score2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS) + + scoreATG: scoreATG.o +- ${CC} scoreATG.c -o scoreATG $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS) + + scoreATG2: scoreATG2.o +- ${CC} scoreATG2.c -o scoreATG2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS) + + scoreSTOP: scoreSTOP.o +- ${CC} scoreSTOP.c -o scoreSTOP $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS) + + escoreSTOP2: scoreSTOP2.o +- ${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS) + +-rfapp: erfapp.o +- ${CC} erfapp.c -o erfapp $(LIBS) ++erfapp: erfapp.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS) + + sites.o: sites.c +- ${CC} ${CFLAGS} -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c ++ ++scoreATG.o: scoreATG.c ++ $(CXX) $(CXXFLAGS) -c scoreATG.c ++ ++scoreSTOP.o: scoreSTOP.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP.c ++ ++scoreSTOP2.o: scoreSTOP2.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP2.c ++ ++scoreATG2.o: scoreATG2.c ++ $(CXX) $(CXXFLAGS) -c scoreATG2.c + + utils.o: utils.c +- ${CC} ${CFLAGS} -c utils.c ++ $(CXX) $(CXXFLAGS) -c utils.c + + splicescore.o: splicescore.c +- ${CC} ${CFLAGS} -c splicescore.c ++ $(CXX) $(CXXFLAGS) -c splicescore.c + + splicescore: splicescore.o sites.o utils.o +- ${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS) diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild new file mode 100644 index 000000000000..bbddc6bdc8ad --- /dev/null +++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P=GlimmerHMM + +DESCRIPTION="A eukaryotic gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +src_unpack() { + unpack ${A} + mv GlimmerHMM ${P} +} + +src_prepare() { + sed \ + -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \ + -e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \ + -i "${S}/train/trainGlimmerHMM" || die + + epatch "${FILESDIR}"/${PV}-gentoo.patch + tc-export CC CXX +} + +src_compile() { + emake -C "${S}/sources" + emake -C "${S}/train" +} + +src_install() { + dobin sources/glimmerhmm train/trainGlimmerHMM + + insinto /usr/share/${PN}/lib + doins train/*.pm + insinto /usr/share/${PN}/models + doins -r trained_dir/* + exeinto /usr/libexec/${PN}/training_utils + doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} + + dodoc README.first train/readme.train +} diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/glimmerhmm/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/gmap/Manifest b/sci-biology/gmap/Manifest new file mode 100644 index 000000000000..b15b9200188f --- /dev/null +++ b/sci-biology/gmap/Manifest @@ -0,0 +1,2 @@ +DIST gmap-gsnap-2011-10-07.tar.gz 3404351 SHA256 e508009592d5dd3442345dc5ce6fd9930366e008efa32e4c72dc243a495f3f20 SHA512 6546be4da41c45e41bdab71dcda69cbf172bc186ca64a2543461eb050f383641a13fea0cfcc6bb76b87cc4faa4c593944b029ee1ca2ba68dbaf7d939d0bf02e1 WHIRLPOOL 9f5cd62fb9cbb2cc73d6b971f29d8816e67e1b4b1b9906d8b06ddf99ffd9356bcdf19869066fb14ca5d3ad93a3b70527d05237be2f438da4db86898103bd2bf2 +DIST gmap-gsnap-2012-07-20.tar.gz 3623122 SHA256 4cd0c0a313cb7a35b8c7afd45b545e6062b343739f9ef522a09001d448aeb5ec SHA512 bbc22509fc63814a102f96ce0da6a1119c78de7fc2fc4fe17cc4d97881313a77818eaedc51bb6d4ce2426560925fe5ffa121acf972d7b3b097e8d3d65efb7b95 WHIRLPOOL 7318377e4cf80db5c5a9495bf68653fbc48051d6fa5748ed796e18888b6e20215d2714b753358fb4cc97aa9c8e441d53ef616ded6ee0923fe78312e78ee91e82 diff --git a/sci-biology/gmap/gmap-2011.10.07.ebuild b/sci-biology/gmap/gmap-2011.10.07.ebuild new file mode 100644 index 000000000000..fb20296c2654 --- /dev/null +++ b/sci-biology/gmap/gmap-2011.10.07.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +MY_PV=${PV//./-} + +DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" +HOMEPAGE="http://www.gene.com/share/gmap/" +SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz" + +LICENSE="gmap" +SLOT="0" +IUSE="+samtools +goby" +KEYWORDS="~amd64 ~x86" + +DEPEND="samtools? ( sci-biology/samtools ) + goby? ( sci-biology/goby-cpp )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/gmap-${MY_PV}" + +src_configure() { + econf $(use_with samtools) \ + $(use_with goby goby /usr) +} + +src_install() { + einstall || die + dodoc AUTHORS ChangeLog README +} + +src_test() { + emake check || die +} diff --git a/sci-biology/gmap/gmap-2012.07.20.ebuild b/sci-biology/gmap/gmap-2012.07.20.ebuild new file mode 100644 index 000000000000..cd20c09b57f8 --- /dev/null +++ b/sci-biology/gmap/gmap-2012.07.20.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +MY_PV=${PV//./-} + +DESCRIPTION="A Genomic Mapping and Alignment Program for mRNA and EST Sequences" +HOMEPAGE="http://research-pub.gene.com/gmap/" +SRC_URI="http://research-pub.gene.com/gmap/src/gmap-gsnap-${MY_PV}.tar.gz" + +LICENSE="gmap" +SLOT="0" +IUSE="+samtools +goby" +KEYWORDS="~amd64 ~x86" + +DEPEND="samtools? ( sci-biology/samtools ) + goby? ( sci-biology/goby-cpp )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/gmap-${MY_PV}" + +src_configure() { + econf $(use_with samtools) \ + $(use_with goby goby /usr) +} + +src_install() { + einstall || die + dodoc AUTHORS ChangeLog README +} + +src_test() { + emake check || die +} diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml new file mode 100644 index 000000000000..7d62e2f44e07 --- /dev/null +++ b/sci-biology/gmap/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="samtools">Enable support for samtools</flag> + <flag name="goby">Enable support for goby</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/goby-cpp/Manifest b/sci-biology/goby-cpp/Manifest new file mode 100644 index 000000000000..b9ab55a817cd --- /dev/null +++ b/sci-biology/goby-cpp/Manifest @@ -0,0 +1,3 @@ +DIST goby_1.9.7.3-cpp.zip 127215 SHA256 8493daa7c850732c6c48d4512bd26b7eec411a729b39d9861a4a6aae08faa674 +DIST goby_1.9.8.1-cpp.zip 134904 SHA256 2f1bd87f2870af178f34a8e7c11819aa9e42f35e20f1985d2ceb054f452e2a97 SHA512 d31cd7f0be19074bfe8da74d9f2510f0e0f15fe6c485bbed8520052468d2cd2f1bc5fcad8b0d6a1586f5acde73db326059f45994ecfbb5fb6c09692d8e155190 WHIRLPOOL 6ce51c46f8802d31068f510f6da13b2920086eafdae24506830b42d79e48eb6ed9cac48a96090a81964daebf4a0c8f21c490ca3b0af2f589ac57647bde1be79f +DIST goby_2.0.1-cpp.zip 177718 SHA256 5ec57b833cb1a0f53e975112d1c360b14a9b17cfff3fb0ad77dd70672c1881db SHA512 992bd10d5538dec1478820f26151dd311f4de13e7947b49f0b06d6cbdd4b71deeb3aa8a4c6a598fb92fbcb9cbf4ff97bf81205c9389d4a0da4443317e48aea9f WHIRLPOOL ab94cf674703917b6f0cde812d0fbcd94e18fb6055b30d6a1eefa1e4cb5b76bbe18c67388c66e25e87e522df9a9946b0eae5a164428abe874a382f5bc39a13d0 diff --git a/sci-biology/goby-cpp/files/Alignments.proto b/sci-biology/goby-cpp/files/Alignments.proto new file mode 100644 index 000000000000..fe7f56647644 --- /dev/null +++ b/sci-biology/goby-cpp/files/Alignments.proto @@ -0,0 +1,597 @@ +package goby; + +option java_package = "edu.cornell.med.icb.goby.alignments"; + +option optimize_for = SPEED; + +/* + This message is written to 'basename'.entries as a very large chunked collection. +*/ +message AlignmentCollection { + repeated AlignmentEntry alignment_entries = 1; +} + + +message AlignmentEntry { + /* Multiplicity of this entry. The number of times this alignment entry would be repeated exactly the same if + query redundancy had not been removed by read factorization. + */ + optional uint32 multiplicity = 7; + + /* + Compressed stream of data. Removed since Goby 2.0 supports chunk codecs. Do not reuse field index 23 + optional bytes compressed_data = 23; + */ + + /* An integer that uniquely identifies the query (a short read) in a set of alignment runs. When several + alignment runs are made with the same set of query sequences, equality of query index means that the query + sequences were the same. (Comparing integers for equality is much faster than comparing strings.) + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 query_index = 1; + /* An integer that uniquely identifies the target (e.g., a chromosome) in a set of alignment runs. When several + alignment runs are made with the same set of target sequences, equality of target index means that the target + sequence was the same across the runs. (Comparing integers for equality is much faster than comparing strings.) + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 target_index = 2; + /* + The position on the target of the start of the alignment between the query and the target. + In the following example, position is 3 because the third base of the query 'C' was aligned with + position 3 of the reference (two read bases were soft clipped: "ct"). This example shows that the + alignment can start at a mismatch if it was so constructed by the aligner. + + 0123456789 + AAAAGTCAAA target + ctCGTC query + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 position = 3; + + /* + True when the query matches the target on the reverse strand + */ + optional bool matching_reverse_strand = 6; + + /* + The position on the query where the alignment starts. This value is different from zero + when some bases/residues of the query could not be aligned with the target. + TODO: Rename this to left_trim. Add a right_trim property. + */ + optional uint32 query_position = 5; + + /* + The score of the alignment, where larger scores indicate better matches between the query and the target. + If an aligner outputs only the number of mismatches between query and target, the score is taken to be + -(#mismatches(query,target)). + */ + optional float score = 4; + + /* + Number of bases/residues that differ in the alignment between query and target sequences. + */ + optional uint32 number_of_mismatches = 8; + + /* + Cumulative number of insertions and/or deletions present in the alignment. + */ + optional uint32 number_of_indels = 9; + + /* + Number of bases that have been aligned for the query. Please note that query_aligned_length must be + less or equal to query_length. + */ + optional uint32 query_aligned_length = 11; + + /* + Number of bases that have been aligned for the target. + */ + optional uint32 target_aligned_length = 12; + + repeated SequenceVariation sequence_variations = 13; + + /* + Length of the query sequence. + */ + optional uint32 query_length = 10; + /* + Mapping Quality (phred-scaled posterior probability that the mapping + position of this read is incorrect). Please note that different aligners + may estimate mapping quality with different approaches, resulting in aligner + specific differences in the distribution of mapping quality. It is recommended + to condition mapping quality on the aligner that produced the specific alignment + being processed. See aligner name and version in the header. + Note that the following description is preliminary. A clear specification is + needed: + The mapping quality should be proportional to the + log of the probability that the given mapping is the "correct" one. + So if there are five equally good mappings of a read to the genome, + the probability of each would be 0.2, and the mapping quality would be + something like -10*log10(1-0.2) = 1. If a mapping is highly likely, + say a 1e-4 of it being wrong, then the mapping quality would be + -10*log10(1e-4) = 40. + */ + optional int32 mapping_quality = 14; + + /* + If this read was aligned with a pair, the flags for the pair alignment (based on SAM): + 000000001 paired + 000000010 properly paired + 000000100 read unmapped + 000001000 mate unmapped + 000010000 read reverse strand + 000100000 mate reverse strand + 001000000 first in pair + 010000000 second in pair + 100000000 not primary alignment + */ + optional uint32 pair_flags = 15; + + /* + If there is an alignment entry for the paired read (the paired read was mapped), a link to the entry is given. + */ + optional RelatedAlignmentEntry pair_alignment_link = 16; + + /* Index of the read fragment from which this alignment was obtained. */ + optional uint32 fragment_index = 17; + + /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more + alignment entries, one for each matching part of the read, and link these entries with + spliced_alignment_links. The field spliced_forward_alignment_link points to the next + AlignmentEntry in the chain of spliced alignments. + */ + optional RelatedAlignmentEntry spliced_forward_alignment_link = 18; + + /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more + alignment entries, one for each matching part of the read, and link these entries with + spliced_alignment_links. The field spliced_backward_alignment_link points to the previous + AlignmentEntry in the chain of spliced alignments. + */ + optional RelatedAlignmentEntry spliced_backward_alignment_link = 22; + + /* + If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two alignment entries, one for each + matching part of the read, and flag describes the spliced_alignment_link with these + binary flags: + 000000001 normal + 000000010 novel + */ + optional uint32 spliced_flags = 19; + + /* The size of the insert used when making the sequence library. This is the total size of the DNA + fragment to sequence, without the adapters. This is not the length of sequence that separates the reads. + See http://seqanswers.com/forums/showthread.php?t=8730 for details. Insert size is inferred for each pair + of reads by the aligner and is recorded here if was estimated (i.e., for paired-end reads). + */ + optional sint32 insert_size = 20; + + /* + The sample index. Uniquely identifies the aligned sample this read was read from. Storing the sample index in the + alignment entry makes it possible to concat alignments from different origins and track what sample originally + contained each entry. + */ + optional uint32 sample_index = 21; + /* + The total number of times the query index associated with this entry occurs across the entire alignment file. + + This field is used to purge queryIndex->smallIndex associations after all instances of a queryindex have + been seen (see QueryIndexPermutation class). When each entry has a value for this field, the header field + query_index_occurrences is true. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 query_index_occurrences = 25; + /* + The total number of times the read matches the reference across the entire alignment file. This differs from + query_index_occurrences because reads that are matching through splice and pair links count as one for ambiguity. + The field can be used to filter by ambiguity-threshold on the fly after an alignment has been done (to restrict + entries to more smaller thresholds). When each entry has a value for this field, the header field + ambiguity_stored_in_entries is true. + + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 ambiguity = 27; + /* + List of BAM attributes, if the alignment was imported from BAM. The attributes are stored in exactly the format + allowed for BAM. For instance, X0:i:9 X1:i:1 MD:Z:68 RG:Z:SRR084825 will be stored as four strings: + "X0:i:9", "X1:i:1", "MD:Z:68", "RG:Z:SRR084825". Note that sam-to-compact will interpret some BAM attributes + and populate goby native fields. Such tags do not appear in bam_attributes, and are instead re-generated from + the corresponding goby native fields. + Since Goby 2.0. + */ + repeated string bam_attributes = 50; + /* + Quality scores for all bases of the read. + Since Goby 2.0. + */ + optional bytes read_quality_scores = 55; + + /* + Origin index. An integer that references a ReadOriginInfo message in the alignment header and + makes it possible to track the origin of the read (especially useful after several alignments + have been merged/concatenated). + (Since Goby 2.0). + */ + optional uint32 read_origin_index = 26; + /* + Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially + erroneous bases, or bases that belong to a different part of the reference genome. Left clipped bases are + stored in this field as character bases, or as an equal sign character '=' when the clipped base did match + the reference base. For instance "A=G" for three soft-clipped bases, the middle one matching the genome at + this position. The number of bases in softClippedBasesLeft is exactly equal to queryPosition. + */ + optional string softClippedBasesLeft = 30; + /* + Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially + erroneous bases, or bases that belong to a different part of the reference genome. Right clipped bases are + stored in this field as character bases, or as an equal sign character '=' when the clipped base did match + the reference base. The number of bases in softClippedBasesRight is exactly equal + to queryLength - queryAlignedLength - queryPosition. + */ + optional string softClippedBasesRight = 31; + + /* + Quality scores for bases in softClippedBasesLeft. Stored in Phred Units. + */ + optional bytes softClippedQualityLeft = 32; + /* + Quality scores for bases in softClippedBasesRight. Stored in Phred Units. + */ + optional bytes softClippedQualityRight = 33; + /* + Sequence for a read placed near this entry, but unmapped to the reference sequence. For instance, used to record + the sequence of a mate that did not map to the reference. We know that the mate maps in the proximity of this entry + (it is placed) but are unable to map it to a specific genomic position. The sequence is always given as obtained + from the reads file. + */ + optional string placedUnmappedSequence=40; + /* + Quality scores for a read placed near this entry. Phred units. + */ + optional bytes placedUnmappedQuality=41; + + /* + Read name. In SAM/BAM this is referred to as QNAME. Paired and segmented reads will have the same Read name. + */ + optional string readName=42; +} + +/* A link to another alignment entry. This message type is used to represent relations + between alignments, such as the relation between the two read fragments in a paired-end protocol, + or the relation between parts of reads that align through an exon exon junction and map in + different locations of the genome. + */ +message RelatedAlignmentEntry { + /* Target index of the location where the other alignment entry is mapped. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 target_index = 1; + + /* Position on the reference where the other alignment entry is mapped. * + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 position = 2; + + /* Index of the fragment for the related alignment entry. This index + makes it possible to identify which of the read fragments mapped to the given + location is related to the source alignment entry. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 fragment_index = 3; + + optional uint32 optimized_index=50; +} + +/* + Represents sequence variations between the query and the reference sequences. Many variations can be represented. + For instance, an insertion at position 5 in the reference would be represented as from="A", to="" position=5. + A mutation T->G at position 6 would be rendered as from="T", to="G" position=6. Padded alignments (see SAM description) + can be described by a combination of pair-wise alignments, where the gap character '-' is used to indicate that no + base exists in the sequence considered for the alignment position, for instance: + + - Padding example: + + 123 (<-positions) +ref A-C + A-T [from="-" to="" position=2] [from="C" to="T" position=3] + ACT [from="" to="C" position=2] [from="C" to="T" position=3] + A-T [from="-" to="" position=2] [from="C" to="T" position=3] + + - Mutation example: + 123 (<-positions) +ref ATT + ACT [from="T" to="C" position=2] + + -- Example of deletion in a read: + 123 (<-positions) +ref ATT + A-T [from="T" to="-" position=2] + + -- Example of insertion of two base pairs in a read: + 12345 (<-positions) +ref A--TT + ACCTT [from="" to="CC" position=2] + + */ +message SequenceVariation { + /* The reference bases. Can include one or more gap characters '-', to indicate that the reference sequence has + no base at this alignment position. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional string from = 2; + /* The read bases that differ from the reference sequence. Can include one or more gap characters '-', to indicate + that the query sequence has no base at this alignment position. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional string to = 1; + /* + The position of the variation on the read, as if the read always matched on the forward strand. + Adding position to the index where the reference starts aligning the read yields the position of the variation + in reference/target sequence space. Since position starts at one the resulting position will also be one based. + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 position = 3; + /* + The position of the variation, starting from the beginning of the aligned read (position 1), and up to the length + of the read (inclusive). Use this index if you need to know how far the variation is observed from the beginning + of the sequenced read. When the read has an insertion, this index records the position immediately before the base + where the bases are inserted (these bases are in the to field). + When the read has a deletion, read_index records the position in the read after which the bases that would align + in the reference are missing (these bases are in the from field). + This field is required (enforced by semantic validation in Goby 2.0+). + */ + optional uint32 read_index = 5; + + /** + The read base quality scores for those bases that are given in the to field. This field + is populated when the reads used to perform the search include quality scores, and when + the alignment parser can extract the information from the aligner's output. + (this option is currently not implemented in Goby.) + */ + optional bytes to_quality = 4; + +} +/* + This message is written to 'basename'.header +*/ + +message AlignmentHeader { + /* + The smallest possible query index in this alignment. Data stored as an array where + queryIndex is the array index will be stored with only the elements in the inclusive + range [smallestSplitQueryIndex largestSplitQueryIndex] + Such data structures include queryLength and some arrays in the TooManyHits data + structure. + */ + optional uint32 smallest_split_query_index = 9; + /* + The largest possible query index in this alignment. Data stored as an array where + queryIndex is the array index will be stored with only the elements in the inclusive + range [smallestSplitQueryIndex largestSplitQueryIndex] + Such data structures include queryLength and some arrays in the TooManyHits data + structure. + */ + optional uint32 largest_split_query_index = 11; + + /* Mapping from query identifier name to query index (as used in alignment entries). + */ + optional IdentifierMapping query_name_mapping = 1; + + /* Mapping from target identifier name to target index (as used in alignment entries). + */ + optional IdentifierMapping target_name_mapping = 2; + + /* + The number of query sequences + */ + optional uint32 number_of_queries = 5; + /* + The number of target sequences + */ + optional uint32 number_of_targets = 6; + /* + The number of reads that were aligned to the reference and are represented in this alignment archive. + */ + optional uint32 number_of_aligned_reads = 7; + + /* + Length of the query sequences. One number per query, in the order of increasing query index. + This information has been moved to the individual alignment entries. + */ + repeated uint32 query_length = 3 [deprecated = true]; + /* + If query length is constant across all the queries, this field contains the constant length. + In such cases, query_length will be empty. + */ + optional uint32 constant_query_length = 10; + + /* + Length of the target sequences. One number per target, in the order of increasing target index. + The target indexes must be 0..(number of targets - 1). + */ + repeated uint32 target_length = 8; + /* + Indicates whether this alignment is sorted by position. True: the alignment entries occur in sorted + order, such that entry a occurs before entry b if a.targetIndex< b.targetIndex or, when entries + have the same target, when a.position < b.position. + */ + optional bool sorted = 13; + + /* + Indicates whether this alignment is indexed by position. When this attribute is true, a file called + 'basename'.index exists that contains the AlignmentIndex message (GZip compressed). + */ + optional bool indexed = 14; + /* + True when query lengths are stored in alignment entries (Goby 1.7+). + */ + optional bool query_lengths_stored_in_entries = 15; + /* + Name of the aligner that produced this alignment. + */ + optional string aligner_name = 17; + /* + Version number for the aligner implementation that produced this alignment. + */ + optional string aligner_version = 18; + /* + The version of Goby that created this alignment file. + */ + optional string version = 25; + + /* + Sample basenames, in the order of increasing sampleIndex, starting with sampleIndex=0. + */ + + repeated string sample_basename = 30; + + /* + This field is true when the query indices of alignment entries were permuted to smaller indices. Only sorted + alignments can have query_indices_were_permuted=true. When the field is true, and you need to retrieve the + original query-index of an alignment (because you want to retrieve the specific read(s) from a read file for + instance), you will need the information in the permutation file (extension basename.perm) and transform back + each small index of interest to the original query index. + */ + optional bool query_indices_were_permuted = 26; + /* + This field is true when entries in the alignment .entries file all have the query_index_occurrences field populated + (Since Goby 2.0). + */ + optional bool query_index_occurrences = 35; + + /* + This field is true when entries in the alignment .entries file all have the ambiguity field populated + (Since Goby 2.0). + */ + optional bool ambiguity_stored_in_entries = 36; + /* + This field is true when entries in the alignment .entries file all have the read_quality_score field populated. + (Since Goby 2.0). + */ + optional bool all_read_quality_scores = 40; + /* + A description of the origin of sets of reads. Serves a similar function to BAM read groups, but more flexible and + efficient. Instead of storing strings, we use integers in the entries. + Alignemnt entries will link to a specific ReadOriginInfo with the origin_index field. + (Since Goby 2.0). + */ + repeated ReadOriginInfo read_origin = 27; +} + +message IdentifierMapping { + repeated IdentifierInfo mappings = 1; +} + +message IdentifierInfo { + required string name = 1; + required uint32 index = 2; +} + + +/* + A description of the origin of sets of reads. Stored in the Goby alignment header and linked + from alignment entries. Goby makes it possible to adapt origin equivalence rules on the fly + efficiently. To do this, it is sufficient to read the header of the alignment, decide which + ReadOriginInfo instances are equivalent (e.g., by looking at sample, platform, library, or + other fields in the message), then construct a function e(a):int. This function takes + one originIndex parameter and returns another integer that maps to an equivalent class. The + equivalence class can be used to estimate error models for entries that belong to each class, + for instance. + (Since Goby 2.0). + */ +message ReadOriginInfo { + /* + Origin index. An integer that links alignment entries to their origin information. + */ + required uint32 origin_index = 1; + /* + Identifier that describes the origin of the reads. This field is compatible with the ID/platform field of BAM read + groups. Free text. + */ + required string origin_id = 2; + /* + The sample from which the reads were sequenced. This field is compatible with the SM/sample field of BAM read + groups. Free text. + */ + optional string sample = 4; + /* + The platform on which the reads were sequenced. This field is compatible with the PL/platform field of BAM read + groups. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO. + */ + optional string platform = 5; + /* + The library from which the reads were sequenced. This field is compatible with the LB/library field of BAM read + groups. Free text. + */ + optional string library = 8; + /* + The platform unit on which the reads were sequenced. This field for compatibility with samtools. + */ + optional string platform_unit = 12; + /* + The date the reads were sequenced. Useful to identify batch effects, in the format dd:MMM:yyyy. + The month is Jan, Feb, etc. to avoid all confusion with days when day<=12. + */ + optional string run_date = 6; +} + +/* + This message is written to 'basename'.tmh +*/ + +message AlignmentTooManyHits { + /* + The threshold used by the aligner to determine that a query is ambiguous and should be dropped. + Referred to as parameter k below. + */ + required uint32 aligner_threshold = 2; + /* + The hits that are assigned to several (>k) reference location. + */ + repeated AmbiguousLocation hits = 1; + +} + +message AmbiguousLocation { + /* + The index of the query that matched too many times. + */ + required uint32 query_index = 1; + /* + The number of hits that triggered membership in the too many hits list. The query may hit more + locations than reported here, since some alignment tools will just drop queries that match above + a threshold and stop counting. This number can be >=k. + */ + required uint32 at_least_number_of_hits = 2; + /** +The length of the part of the query sequence that could be matched to the target (also called depth). +May be less than the length of the query sequence, in which case the match was not perfect. When merging +alignments produced by searching different reference sequences, consider only at_least_number_of_hits +from alignments that have exactly the longer depth for the query. */ + optional uint32 length_of_match = 3; +} + +/* + This message is written to 'basename'.index + */ +message AlignmentIndex { + /* + Stores one element by target sequence. Each element is the cumulative target length for the target + stored at index i. Assume there are four target sequences, with lengths {10, 12, 15, 34}. The field + targetPositionOffsets will contain: {0,10,22,37}. Such offsets can be used to calculate the absolute + position of a genomic location. Given targetIndex and positionOnReference, the absolute location + is defined as targetPositionOffsets[targetIndex]+positionOnReference. + */ + repeated uint32 target_position_offsets = 1 [packed = true]; + /* + The byte offsets into the compressed entries file. Byte offsets are matched with absolute position + by index. There should be as many elements in offsets as there are in absolutePosition + where chunks start which represent entries whose absolute positions are less than + */ + repeated uint64 offsets = 2 [packed = true]; + /* + The absolute positions of the first entry in the chunk that immediately start at offset. One element + per chunk in the 'basename'.entries file. + */ + repeated uint64 absolute_positions = 3 [packed = true]; + +} diff --git a/sci-biology/goby-cpp/files/Reads.proto b/sci-biology/goby-cpp/files/Reads.proto new file mode 100644 index 000000000000..32c1244a3eb3 --- /dev/null +++ b/sci-biology/goby-cpp/files/Reads.proto @@ -0,0 +1,96 @@ +package goby; + +option java_package = "edu.cornell.med.icb.goby.reads"; +option optimize_for = SPEED; + +message ReadCollection { + repeated ReadEntry reads = 1; +} + +message ReadEntry { + /* + Index of a read. + */ + required uint32 read_index = 1; + /* + Index of the barcode, if any. + */ + optional uint32 barcode_index = 10; + /* + Read identifier/name may be present. + */ + optional string read_identifier = 23; + /* + Additional description about the read (from Fasta/Q format). + */ + optional string description = 22; + /* + Length of the sequence. + */ + required uint32 read_length = 2; + /* + Sequence, encoded as ascii characters stored in single bytes. + */ + optional bytes sequence = 3; + /* + The second sequence in a pair. Stored the same way as the sequence attribute. + */ + optional bytes sequence_pair = 5; + /* + Length of the second sequence in a pair. + */ + optional uint32 read_length_pair = 6; + /* + Quality scores in Phred units, stored as single bytes (0-255). + */ + optional bytes quality_scores = 4; + /* + Quality scores for the second sequence in a pair. Stored as the 'qualityScores' attribute. + */ + optional bytes quality_scores_pair = 7; + /* + Compressed stream of data. The first byte indicates the compression/decompression method (codec). The remaining bytes are + content compressed with the codec. + */ + optional bytes compressed_data = 8; + /* + Stores meta-data about the reads. Typically meta-data is stored in the very first read of a + read collection, with the understanding that the meta-data applies to all the reads in the + collection. Meta-data can be used to store information about when the sample was sequenced, + or other information of interest. The key-value pair format is sufficiently flexible to + accomodate a variety of needs. The following keys are pre-defined. Please use pre-defined + keys so that automated tools can use metadata in relatively standard way. Please note that + some keys provide a format for the value. This format should also be followed to garantee + that meta data can be used computationally in fully automatic manner. + + key="sequencing-run-start-date" value="MM/DD/YYYY" Used to record when the sequencing run + was initiated on the instrument. Can be used to detect batch effect in a large set of samples. + key="platform" value="<free-text>". Value is free text, but the following terms are pre-defined. + Illumina GaIIx + Illumina HiSeq 1000 + Illumina HiSeq 2000 + Helicos Heliscope + LifeTech 5500 SOLiD + LifeTech 5500xl SOLiD + Roche 454 GS FLX Ti + + key="organism" value="species name" + Since Goby 1.9.1 + */ + repeated MetaData meta_data = 25; + +} +/* + A message to store a key/value pair and represent metadata about reads. + Since Goby 1.9.1 + */ +message MetaData { + /* + Provides the key. See examples in the documentation of meta_data for ReadEntry. + */ + required string key=1; + /* + Describes the value associated with the key. See examples in the documentation of meta_data for ReadEntry. + */ + required string value=2; +} diff --git a/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch new file mode 100644 index 000000000000..415785466af7 --- /dev/null +++ b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch @@ -0,0 +1,16 @@ + src/Makefile.am | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/Makefile.am b/src/Makefile.am +index 1033382..33ca906 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -84,7 +84,7 @@ GobyReadsStats_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_D + GobyReadsStats_SOURCES = \ + GobyReadsStats.cc + +-GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} ++GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} -lz + GobyFastaToCompact_SOURCES = \ + GobyFastaToCompact.cc + diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild new file mode 100644 index 000000000000..1b15aaac3ac6 --- /dev/null +++ b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools + +DESCRIPTION="A DNA sequencing data management framework - C/C++ API" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND=">=dev-libs/protobuf-2.4.1 + >=dev-libs/libpcre-8.12" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/goby_${PV}/cpp" + +src_prepare() { + eautoreconf +} diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild new file mode 100644 index 000000000000..c74f57306255 --- /dev/null +++ b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools + +DESCRIPTION="A DNA sequencing data management framework - C/C++ API" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND=">=dev-libs/protobuf-2.4.1 + >=dev-libs/libpcre-8.12" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/goby_${PV}/cpp" + +src_prepare() { + eautoreconf +} diff --git a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild new file mode 100644 index 000000000000..2cadda103999 --- /dev/null +++ b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="A DNA sequencing data management framework - C/C++ API" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=" + >=dev-libs/protobuf-2.4.1 + >=dev-libs/libpcre-8.12" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${PV}/cpp" + +PATCHES=( + "${FILESDIR}"/${P}-underlinking.patch +) + +src_prepare() { + sed \ + -e '/BUILD_TIMESTAMP/s:\(goby/timestamp.h\):$(top_srcdir)/src/\1:g' \ + -i src/Makefile.am || die + + pushd src/goby > /dev/null || die + cp "${FILESDIR}"/*.proto . || die + protoc --cpp_out=. *.proto || die + popd > /dev/null || die + + autotools-utils_src_prepare +} diff --git a/sci-biology/goby-cpp/metadata.xml b/sci-biology/goby-cpp/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/goby-cpp/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/goby/Manifest b/sci-biology/goby/Manifest new file mode 100644 index 000000000000..9e3b65fbcbaa --- /dev/null +++ b/sci-biology/goby/Manifest @@ -0,0 +1,4 @@ +DIST goby_1.9.7.3-deps.zip 19959489 SHA256 3932c61f001fc1d06ef298043d5206041e47175fa28d755efd01148de35b567a +DIST goby_1.9.7.3-src.zip 15642000 SHA256 fe32a6720fcc0858811e40b744c9bcfffbb6cf277be50102446ff8798fd9ab24 +DIST goby_1.9.8.1-deps.zip 20820943 SHA256 eb11916408a7978a1e90967783b8167b96c6d0dd60ae58cf1dab915a519d1bbb +DIST goby_1.9.8.1-src.zip 15748880 SHA256 e2489a815a38bd10b1ec59b4e262a023f97994d9953f97bcc6571cadd05919c3 diff --git a/sci-biology/goby/goby-1.9.7.3.ebuild b/sci-biology/goby/goby-1.9.7.3.ebuild new file mode 100644 index 000000000000..20622d49ffa7 --- /dev/null +++ b/sci-biology/goby/goby-1.9.7.3.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby" +EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2" +EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar" + +JAVA_ANT_REWRITE_CLASSPATH="true" + +#inherit java-pkg-2 java-ant-2 subversion +inherit java-pkg-2 java-ant-2 + +MY_P="${PN}_${PV}" + +DESCRIPTION="A DNA sequencing data management framework" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip + http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="+cpp" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPS="dev-java/commons-logging + dev-java/commons-lang:2.1 + dev-java/commons-io:1 + dev-libs/protobuf[java] + dev-java/fastutil:5.0 + dev-java/log4j + dev-java/jsap + dev-java/commons-configuration + dev-java/commons-math:2" +DEPEND=">=virtual/jdk-1.6 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6 + ${COMMON_DEPS} + cpp? ( ~sci-biology/goby-cpp-${PV} )" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i '/sge/ d' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar goby*.jar + java-pkg_dolauncher goby --jar goby.jar + + insinto /usr/share/${PN} + doins -r python + dodoc CHANGES.txt +} diff --git a/sci-biology/goby/goby-1.9.8.1.ebuild b/sci-biology/goby/goby-1.9.8.1.ebuild new file mode 100644 index 000000000000..5039b96941b3 --- /dev/null +++ b/sci-biology/goby/goby-1.9.8.1.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby" +EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2" +EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar" + +JAVA_ANT_REWRITE_CLASSPATH="true" + +#inherit java-pkg-2 java-ant-2 subversion +inherit java-pkg-2 java-ant-2 + +MY_P="${PN}_${PV}" + +DESCRIPTION="A DNA sequencing data management framework" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip + http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="+cpp" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPS="dev-java/commons-logging + dev-java/commons-lang:2.1 + dev-java/commons-io:1 + dev-libs/protobuf[java] + dev-java/fastutil:5.0 + dev-java/log4j + dev-java/jsap + dev-java/commons-configuration + dev-java/commons-math:2" +DEPEND=">=virtual/jdk-1.6 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6 + ${COMMON_DEPS} + cpp? ( ~sci-biology/goby-cpp-${PV} )" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i '/sge/ d' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar goby*.jar + java-pkg_dolauncher goby --jar goby.jar + + insinto /usr/share/${PN} + doins -r python + dodoc CHANGES.txt +} diff --git a/sci-biology/goby/metadata.xml b/sci-biology/goby/metadata.xml new file mode 100644 index 000000000000..3bc02ac6b32e --- /dev/null +++ b/sci-biology/goby/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="cpp">Compile C/C++ API</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest new file mode 100644 index 000000000000..4ab0094769a2 --- /dev/null +++ b/sci-biology/hmmer/Manifest @@ -0,0 +1,2 @@ +DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 +DIST hmmer-3.0.tar.gz 3952015 SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83 diff --git a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch new file mode 100644 index 000000000000..983827b0bd46 --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch @@ -0,0 +1,23 @@ +--- easel/Makefile.in ++++ easel/Makefile.in +@@ -26,8 +26,7 @@ + LDFLAGS = @LDFLAGS@ + SIMDFLAGS= @SIMD_CFLAGS@ + CPPFLAGS = @CPPFLAGS@ +-LIBGSL = @LIBGSL@ +-LIBS = @LIBS@ @PTHREAD_LIBS@ ++LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ + + # Other tools + # +@@ -252,8 +251,8 @@ + else \ + DFILE=${srcdir}/esl_$${BASENAME}.c ;\ + fi;\ +- echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm;\ +- ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ++ echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS};\ ++ ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS} + + + # install: installs libeasel.a in ${libdir}/ diff --git a/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch new file mode 100644 index 000000000000..19d38c8e32ed --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch @@ -0,0 +1,132 @@ + easel/devkit/autodoc | 4 ++-- + easel/devkit/esl-dependencies | 4 ++-- + easel/devkit/sqc | 7 +++---- + easel/testsuite/coverage_report.pl | 4 ++-- + easel/testsuite/driver_report.pl | 4 ++-- + easel/testsuite/valgrind_report.pl | 4 ++-- + profmark/rocplot.pl | 4 ++-- + 7 files changed, 15 insertions(+), 16 deletions(-) + +diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc +index 16bda4d..f5c5efc 100755 +--- a/easel/devkit/autodoc ++++ b/easel/devkit/autodoc +@@ -49,8 +49,8 @@ + # + # SRE, Tue Nov 30 19:43:47 2004 + +-require "getopts.pl"; +-&Getopts('n:t'); ++use Getopt::Std; ++getopts('n:t'); + $cfile = shift; + + if ($opt_t) { $show_api_table = 1; } +diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies +index a4dc126..b61fa7a 100755 +--- a/easel/devkit/esl-dependencies ++++ b/easel/devkit/esl-dependencies +@@ -13,8 +13,8 @@ + # SRE, Mon Jun 11 11:15:31 2007 + # SVN $Id$ + +-require "getopts.pl" +-&Getopts('1afr'); ++use Getopt::Std; ++getopts('1afr'); + + if ($opt_1) { $show_summary_table = 1; } + if ($opt_a) { $list_augfiles = 1; } +diff --git a/easel/devkit/sqc b/easel/devkit/sqc +index af3adf6..0cdb458 100755 +--- a/easel/devkit/sqc ++++ b/easel/devkit/sqc +@@ -205,12 +205,11 @@ + # SRE, Tue Aug 6 11:16:39 2002 + # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $ + +-require "getopts.pl"; +-require "importenv.pl"; ++use Getopt::Std; + + # Parse our command line + # +-&Getopts('v'); ++getopts('v'); + if ($opt_v) { $verbose = 1; } + + +@@ -609,7 +608,7 @@ sub check_valgrind_status + # + sub tempname { + my ($dir, $name, $suffix); +- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} ++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} + + foreach $suffix ("aa".."zz") { + $name = "$dir"."esltmp".$suffix.$$; +diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl +old mode 100755 +new mode 100644 +index 9c77791..024ed34 +--- a/easel/testsuite/coverage_report.pl ++++ b/easel/testsuite/coverage_report.pl +@@ -16,9 +16,9 @@ + # + # SRE, Thu Mar 1 19:22:57 2007 (Janelia) + # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $ +-require "getopts.pl"; ++use Getopt::Std; + $have_sloccount = 1; +-&Getopts('cs'); ++getopts('cs'); + if ($opt_c) { $do_recompile = 1; } + if ($opt_s) { $have_sloccount = 0; } + +diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl +index 757854d..a9a8902 100755 +--- a/easel/testsuite/driver_report.pl ++++ b/easel/testsuite/driver_report.pl +@@ -25,8 +25,8 @@ + # SRE, Fri Mar 2 10:01:44 2007 (Janelia) + # SVN $Id: driver_report.pl 326 2009-02-28 15:49:07Z eddys $ + +-require "getopts.pl"; +-&Getopts('c'); ++use Getopt::Std; ++getopts('c'); + if ($opt_c) { $do_recompile = 1; } + + if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } +diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl +old mode 100755 +new mode 100644 +index 186a392..07026a0 +--- a/easel/testsuite/valgrind_report.pl ++++ b/easel/testsuite/valgrind_report.pl +@@ -10,8 +10,8 @@ + # + # SRE, Fri Mar 2 08:37:48 2007 [Janelia] + # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $ +-require "getopts.pl"; +-&Getopts('c'); ++use Getopt::Std; ++getopts('c'); + if ($opt_c) { $do_recompile = 1; } + + if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } +diff --git a/profmark/rocplot.pl b/profmark/rocplot.pl +index d4c0f67..4e8175a 100755 +--- a/profmark/rocplot.pl ++++ b/profmark/rocplot.pl +@@ -2,8 +2,8 @@ + + $nsearches = 1567; + +-require "getopts.pl"; +-&Getopts('n:X:x:'); ++use Getopt::Std ++getopts('n:X:x:'); + + if ($opt_n) { $nsearches = $opt_n; } + if ($opt_X) { diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild new file mode 100644 index 000000000000..7b1fbba5e075 --- /dev/null +++ b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +LICENSE="GPL-2" +HOMEPAGE="http://hmmer.janelia.org/" +SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz" + +SLOT="0" +IUSE="pvm threads" +KEYWORDS="~alpha amd64 ia64 ~ppc ~sparc x86" + +DEPEND="pvm? ( sys-cluster/pvm )" + +src_compile() { + ./configure \ + --host=${CHOST} \ + --prefix="${D}"/usr \ + --exec_prefix="${D}"/usr \ + --mandir="${D}"/usr/share/man \ + --enable-lfs \ + $(use_enable pvm) \ + $(use_enable threads) || die + emake || die +} + +src_install() { + einstall || die + + cd src + dolib libhmmer.a + insinto /usr/include/hmmer + doins *.h + + cd ../squid + dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate + dolib libsquid.a + insinto /usr/include/hmmer + doins *.h + + cd .. + dodoc NOTES + newdoc 00README README + insinto /usr/share/doc/${PF} + doins Userguide.pdf +} + +src_test() { + make check +} diff --git a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild new file mode 100644 index 000000000000..64fa50030079 --- /dev/null +++ b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +LICENSE="GPL-2" +HOMEPAGE="http://hmmer.janelia.org/" +SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz" + +SLOT="0" +IUSE="pvm threads" +KEYWORDS="~alpha amd64 ~ia64 ~ppc ppc64 ~sparc x86" + +DEPEND="pvm? ( sys-cluster/pvm )" + +src_compile() { + econf \ + --host=${CHOST} \ + --prefix="${D}"/usr \ + --exec_prefix="${D}"/usr \ + --mandir="${D}"/usr/share/man \ + --enable-lfs \ + $(use_enable pvm) \ + $(use_enable threads) || die + emake || die +} + +src_install() { + einstall || die + + cd src + dolib libhmmer.a + insinto /usr/include/hmmer + doins *.h + + cd ../squid + dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate + dolib libsquid.a + insinto /usr/include/hmmer + doins *.h + + cd .. + dodoc NOTES + newdoc 00README README + insinto /usr/share/doc/${PF} + doins Userguide.pdf +} + +src_test() { + make check +} diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild new file mode 100644 index 000000000000..86183e7f9d3a --- /dev/null +++ b/sci-biology/hmmer/hmmer-3.0.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +HOMEPAGE="http://hmmer.janelia.org/" +SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="+cpu_flags_x86_sse mpi +threads gsl static-libs" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos" + +DEPEND=" + mpi? ( virtual/mpi ) + gsl? ( >=sci-libs/gsl-1.12 )" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-fix_tests.patch \ + "${FILESDIR}"/${P}-perl-5.16-2.patch +} + +src_configure() { + econf \ + $(use_enable cpu_flags_x86_sse sse) \ + $(use_enable mpi) \ + $(use_enable threads) \ + $(use_with gsl) +} + +src_install() { + default + + use static-libs && dolib.a src/libhmmer.a easel/libeasel.a + + insinto /usr/share/${PN} + doins -r tutorial + dodoc Userguide.pdf +} diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml new file mode 100644 index 000000000000..66fa76626615 --- /dev/null +++ b/sci-biology/hmmer/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="pvm">Add support for parallel virtual machine + (<pkg>sys-cluster/pvm</pkg>)</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/iedera/Manifest b/sci-biology/iedera/Manifest new file mode 100644 index 000000000000..325eeedf3e8e --- /dev/null +++ b/sci-biology/iedera/Manifest @@ -0,0 +1 @@ +DIST iedera-1.04.tar.gz 123847 SHA256 39d60b052f40476aebead981020f53e6b801293c3f13c4aea3f65a230027f39b diff --git a/sci-biology/iedera/iedera-1.04.ebuild b/sci-biology/iedera/iedera-1.04.ebuild new file mode 100644 index 000000000000..ad1edbcdc4d6 --- /dev/null +++ b/sci-biology/iedera/iedera-1.04.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +DESCRIPTION="A subset seed design tool for DNA sequence alignment" +HOMEPAGE="http://bioinfo.lifl.fr/yass/iedera.php" +SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="" + +src_install() { + einstall || die + dodoc AUTHORS README NEWS +} diff --git a/sci-biology/iedera/metadata.xml b/sci-biology/iedera/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/iedera/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/infernal/Manifest b/sci-biology/infernal/Manifest new file mode 100644 index 000000000000..ab636b70040d --- /dev/null +++ b/sci-biology/infernal/Manifest @@ -0,0 +1 @@ +DIST infernal-1.0.2.tar.gz 15205421 SHA256 c4f89ac2e865c8b04a53a647703d88f96c31bb1d47d3e06f4b6090d7d15643ad SHA512 0399be14c17f053574e95d8c5b9eaf990545795a9268e20f0940e11a8e78fc49beb4b23994e9ea427764fbb29e9b39f6da9cb1d85eb4b56d354057b48515c4af WHIRLPOOL c4fa3326eb1b36252ce41ca1aeca68bed4373061ca6bc2bfc0af62c0805bfa1747272fbf223b8d47194853ae5cbe7af11d47493c258264503ea6aa7b142a6b60 diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch new file mode 100644 index 000000000000..5bc5bd008ff6 --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch @@ -0,0 +1,15 @@ +Respect LDFLAGS + +http://bugs.gentoo.org/show_bug.cgi?id=338177 + +--- src/Makefile.in ++++ src/Makefile.in +@@ -86,7 +86,7 @@ + all: $(PROGS) + + $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} +- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) + + + ################################################################# diff --git a/sci-biology/infernal/files/infernal-1.0.2-overflows.patch b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch new file mode 100644 index 000000000000..b9791fa1ca2e --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-overflows.patch @@ -0,0 +1,15 @@ +Fix buffer overflow + +http://bugs.gentoo.org/show_bug.cgi?id=338179 + +--- easel/esl_getopts.c ++++ easel/esl_getopts.c +@@ -1270,7 +1270,7 @@ + "Arg looks like option? Use %.24s%.24s if you really mean it.", + g->opt[opti].name, *ret_optarg); + } else +- ESL_FAIL(eslESYNTAX, "Option %.24s requires an argument", g->opt[opti].name); ++ ESL_FAIL(eslESYNTAX, g->errbuf, "Option %.24s requires an argument", g->opt[opti].name); + + g->optstring = NULL; /* An optchar that takes an arg must terminate an optstring. */ + } diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch new file mode 100644 index 000000000000..004742546f00 --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch @@ -0,0 +1,31 @@ +Fix parallel build + +http://bugs.gentoo.org/show_bug.cgi?id=311919 + +--- Makefile.in ++++ Makefile.in +@@ -82,9 +82,10 @@ + all: core + + core: +- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) +- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) +- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") ++ $(MAKE) -C easel ++ $(MAKE) -C src ++ $(MAKE) -C src module ++ $(MAKE) -C testsuite + + #.PHONY: $(RIGFILTERS) + #$(RIGFILTERS): core +--- easel/Makefile.in ++++ easel/Makefile.in +@@ -132,7 +132,7 @@ + esl_wuss.o + + all: libeasel.a +- (cd miniapps; make) ++ $(MAKE) -C miniapps + + .c.o: + ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< diff --git a/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch new file mode 100644 index 000000000000..c96dcae7b296 --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-perl-5.16-2.patch @@ -0,0 +1,147 @@ + benchmarks/cmsearch-rmark/sre.pl | 4 +--- + easel/devkit/autodoc | 4 ++-- + easel/devkit/esl-dependencies | 4 ++-- + easel/devkit/sqc | 7 +++---- + easel/testsuite/coverage_report.pl | 4 ++-- + easel/testsuite/driver_report.pl | 4 ++-- + easel/testsuite/valgrind_report.pl | 4 ++-- + 7 files changed, 14 insertions(+), 17 deletions(-) + +diff --git a/benchmarks/cmsearch-rmark/sre.pl b/benchmarks/cmsearch-rmark/sre.pl +index 9136717..e4df233 100644 +--- a/benchmarks/cmsearch-rmark/sre.pl ++++ b/benchmarks/cmsearch-rmark/sre.pl +@@ -6,8 +6,6 @@ + + package SRE_perlstuff; + +-require "importenv.pl"; +- + # Function: tempname + # + # Returns a unique temporary filename. +@@ -26,7 +24,7 @@ require "importenv.pl"; + # + sub main'tempname { + local ($dir, $name); +- if ($TMPDIR) { $dir = $TMPDIR; } else {$dir = "/tmp";} ++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}; } else {$dir = "/tmp";} + + foreach $suffix ("aa".."zz") { + $name = "$dir/sre$suffix$$"; +diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc +old mode 100755 +new mode 100644 +index 045ce36..22268f6 +--- a/easel/devkit/autodoc ++++ b/easel/devkit/autodoc +@@ -49,8 +49,8 @@ + # + # SRE, Tue Nov 30 19:43:47 2004 + +-require "getopts.pl"; +-&Getopts('n:t'); ++use Getopt::Std; ++getopts('n:t'); + $cfile = shift; + + if ($opt_t) { $show_api_table = 1; } +diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies +old mode 100755 +new mode 100644 +index a4dc126..b61fa7a +--- a/easel/devkit/esl-dependencies ++++ b/easel/devkit/esl-dependencies +@@ -13,8 +13,8 @@ + # SRE, Mon Jun 11 11:15:31 2007 + # SVN $Id$ + +-require "getopts.pl" +-&Getopts('1afr'); ++use Getopt::Std; ++getopts('1afr'); + + if ($opt_1) { $show_summary_table = 1; } + if ($opt_a) { $list_augfiles = 1; } +diff --git a/easel/devkit/sqc b/easel/devkit/sqc +old mode 100755 +new mode 100644 +index 81d03de..6201d3d +--- a/easel/devkit/sqc ++++ b/easel/devkit/sqc +@@ -176,12 +176,11 @@ + # SRE, Tue Aug 6 11:16:39 2002 + # SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $ + +-require "getopts.pl"; +-require "importenv.pl"; ++use Getopt::Std; + + # Parse our command line + # +-&Getopts('mp:r:v'); ++getopts('mp:r:v'); + if ($opt_m) { $do_memtest = 1; } + if ($opt_p) { push @prepdirs, $opt_p; } + if ($opt_r) { push @olddirs, $opt_r; } +@@ -510,7 +509,7 @@ check_ccmalloc_status + # + sub tempname { + my ($dir, $name, $suffix); +- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} ++ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} + + foreach $suffix ("aa".."zz") { + $name = "$dir"."esltmp".$suffix.$$; +diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl +old mode 100755 +new mode 100644 +index 9c77791..024ed34 +--- a/easel/testsuite/coverage_report.pl ++++ b/easel/testsuite/coverage_report.pl +@@ -16,9 +16,9 @@ + # + # SRE, Thu Mar 1 19:22:57 2007 (Janelia) + # SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $ +-require "getopts.pl"; ++use Getopt::Std; + $have_sloccount = 1; +-&Getopts('cs'); ++getopts('cs'); + if ($opt_c) { $do_recompile = 1; } + if ($opt_s) { $have_sloccount = 0; } + +diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl +old mode 100755 +new mode 100644 +index d1b4a9a..db4378f +--- a/easel/testsuite/driver_report.pl ++++ b/easel/testsuite/driver_report.pl +@@ -19,8 +19,8 @@ + # SRE, Fri Mar 2 10:01:44 2007 (Janelia) + # SVN $Id: driver_report.pl 231 2008-03-25 14:43:57Z eddys $ + +-require "getopts.pl"; +-&Getopts('c'); ++use Getopt::Std; ++getopts('c'); + if ($opt_c) { $do_recompile = 1; } + + if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } +diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl +old mode 100755 +new mode 100644 +index 186a392..07026a0 +--- a/easel/testsuite/valgrind_report.pl ++++ b/easel/testsuite/valgrind_report.pl +@@ -10,8 +10,8 @@ + # + # SRE, Fri Mar 2 08:37:48 2007 [Janelia] + # SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $ +-require "getopts.pl"; +-&Getopts('c'); ++use Getopt::Std; ++getopts('c'); + if ($opt_c) { $do_recompile = 1; } + + if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild new file mode 100644 index 000000000000..3c0ca9aa7b12 --- /dev/null +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils + +DESCRIPTION="Inference of RNA alignments" +HOMEPAGE="http://infernal.janelia.org/" +SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="mpi" +KEYWORDS="amd64 x86" + +DEPEND="mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-parallel-build.patch \ + "${FILESDIR}"/${P}-overflows.patch \ + "${FILESDIR}"/${P}-perl-5.16-2.patch \ + "${FILESDIR}"/${P}-ldflags.patch +} + +src_configure() { + econf \ + --prefix="${D}/usr" \ + $(use_enable mpi) +} + +src_install() { + default + + pushd documentation/manpages > /dev/null + for i in *; + do newman ${i} ${i/.man/.1} + done + popd > /dev/null + + insinto /usr/share/${PN} + doins -r benchmarks tutorial intro matrices + dodoc 00README* Userguide.pdf documentation/release-notes/* +} diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/infernal/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/iqpnni/Manifest b/sci-biology/iqpnni/Manifest new file mode 100644 index 000000000000..ec521a7104b3 --- /dev/null +++ b/sci-biology/iqpnni/Manifest @@ -0,0 +1,3 @@ +DIST iqpnni-3.2.tar.gz 638743 SHA256 0e97a03841e3460b9e0ddadbfa27393bf370ff82725a620c8d46a1ce85e4a20f +DIST iqpnni-3.3.1.tar.gz 650395 SHA256 bdc5873c5dd59b07b8f8c9547e86120b53fa3cd802ec7acdad61bacc4c3ac7d9 +DIST iqpnni-3.3.2.tar.gz 646603 SHA256 e4ffc783c7444bfadd40c9d55e9fb0275fcf7dca80aa3217768c9bf63c28567f diff --git a/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch b/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch new file mode 100644 index 000000000000..c4f49284abc1 --- /dev/null +++ b/sci-biology/iqpnni/files/iqpnni-3.3.1-gcc4.3.patch @@ -0,0 +1,13 @@ +diff -rc iqpnni-3.3.1-orig/src/constant.h iqpnni-3.3.1/src/constant.h +*** iqpnni-3.3.1-orig/src/constant.h 2009-01-04 19:33:35.000000000 -0500 +--- iqpnni-3.3.1/src/constant.h 2009-01-04 19:40:21.000000000 -0500 +*************** +*** 36,41 **** +--- 36,42 ---- + #include <stdio.h> + #include <math.h> + #include <string> ++ #include <string.h> + + using namespace std; + diff --git a/sci-biology/iqpnni/iqpnni-3.2.ebuild b/sci-biology/iqpnni/iqpnni-3.2.ebuild new file mode 100644 index 000000000000..070e962fb311 --- /dev/null +++ b/sci-biology/iqpnni/iqpnni-3.2.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Important Quartet Puzzling and NNI Operation" +HOMEPAGE="http://www.cibiv.at/software/iqpnni/" +SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_install() { + dobin src/iqpnni + + dodoc ChangeLog AUTHORS README NEWS TODO + if use doc ; then + dohtml manual/iqpnni-manual.html + insinto /usr/share/doc/${P} + doins manual/iqpnni-manual.pdf + fi +} diff --git a/sci-biology/iqpnni/iqpnni-3.3.1.ebuild b/sci-biology/iqpnni/iqpnni-3.3.1.ebuild new file mode 100644 index 000000000000..8916e7e51608 --- /dev/null +++ b/sci-biology/iqpnni/iqpnni-3.3.1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils + +DESCRIPTION="Important Quartet Puzzling and NNI Operation" +HOMEPAGE="http://www.cibiv.at/software/iqpnni/" +SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="doc" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-*.patch +} + +src_install() { + dobin src/iqpnni + + dodoc ChangeLog AUTHORS README NEWS TODO + if use doc ; then + dohtml manual/iqpnni-manual.html + insinto /usr/share/doc/${P} + doins manual/iqpnni-manual.pdf + fi +} diff --git a/sci-biology/iqpnni/iqpnni-3.3.2.ebuild b/sci-biology/iqpnni/iqpnni-3.3.2.ebuild new file mode 100644 index 000000000000..e9939ef0f506 --- /dev/null +++ b/sci-biology/iqpnni/iqpnni-3.3.2.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +DESCRIPTION="Important Quartet Puzzling and NNI Operation" +HOMEPAGE="http://www.cibiv.at/software/iqpnni/" +SRC_URI="http://www.cibiv.at/software/iqpnni/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_install() { + dobin src/iqpnni + + dodoc ChangeLog AUTHORS README NEWS TODO + if use doc ; then + dohtml manual/iqpnni-manual.html + insinto /usr/share/doc/${P} + doins manual/iqpnni-manual.pdf + fi +} diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/iqpnni/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest new file mode 100644 index 000000000000..6250f54bc17b --- /dev/null +++ b/sci-biology/kalign/Manifest @@ -0,0 +1 @@ +DIST kalign_2.03.orig.tar.gz 114022 SHA256 710318fea8e3091da6fdedd16d6f94b9de069846afa502f4fe00d5d6b07511c0 diff --git a/sci-biology/kalign/kalign-2.03-r1.ebuild b/sci-biology/kalign/kalign-2.03-r1.ebuild new file mode 100644 index 000000000000..4422bad730c0 --- /dev/null +++ b/sci-biology/kalign/kalign-2.03-r1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="Global and progressive multiple sequence alignment" +HOMEPAGE="http://msa.cgb.ki.se/" +SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +S="${WORKDIR}"/${PN} + +src_prepare() { + sed \ + -e "s/\$(CFLAGS) \$(OBJECTS)/\$(LDFLAGS) &/" \ + -i Makefile.in || die +} + +src_compile() { + emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" +} + +src_install() { + dobin ${PN} + dodoc README +} diff --git a/sci-biology/kalign/kalign-2.03.ebuild b/sci-biology/kalign/kalign-2.03.ebuild new file mode 100644 index 000000000000..3862e49eaf7f --- /dev/null +++ b/sci-biology/kalign/kalign-2.03.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Global and progressive multiple sequence alignment" +HOMEPAGE="http://msa.cgb.ki.se/" +SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/${PN}" + +src_unpack() { + unpack ${A} + sed -i 's/^CFLAGS.*= -O9/CFLAGS := ${CFLAGS} -O3/' "${S}"/Makefile.in +} + +src_install() { + dobin kalign + dodoc README +} diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/kalign/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/lagan/Manifest b/sci-biology/lagan/Manifest new file mode 100644 index 000000000000..fb04603869dd --- /dev/null +++ b/sci-biology/lagan/Manifest @@ -0,0 +1 @@ +DIST lagan20.tar.gz 589115 SHA256 a65e61ed4fd6608f4e5ad5b11a1b77f4fec1a207d822c5885b3e86727496e1fe diff --git a/sci-biology/lagan/files/lagan-2.0-flags.patch b/sci-biology/lagan/files/lagan-2.0-flags.patch new file mode 100644 index 000000000000..e324ef64c4c6 --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-flags.patch @@ -0,0 +1,107 @@ +diff --git a/Makefile b/Makefile +index fbbbe79..a1d449b 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,5 +1,5 @@ + all: +- (cd src; $(MAKE)) ++ $(MAKE) -C src + clean: + rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay + (cd src; $(MAKE) clean) +diff --git a/src/Makefile b/src/Makefile +index 7f6b6fd..dd6309b 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W + TRGT_DIR = .. + + all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay +- (cd glocal; $(MAKE)) ++ $(MAKE) -C glocal + clean: + rm -f *.o *~ utils/*~ mlagan.purify core + (cd glocal; $(MAKE) clean) + ../anchors: anchors.c skiplist.c +- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c + ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG + ../order: order.c diagmatrix.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c + ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c +- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG + ../utils/bin2mf: utils/bin2mf.c +- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c + ../utils/bin2bl: utils/bin2bl.c +- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c + ../utils/cextract: utils/cextract.c +- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c + ../utils/cstat: utils/cstat.c +- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c + ../utils/contigorder: utils/contigorder.c +- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c + ../utils/getbounds: utils/getbounds.c +- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c + ../utils/getcontigpos: utils/getcontigpos.c +- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c + ../utils/getlength: utils/getlength.c +- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c + ../utils/getoverlap: utils/getoverlap.c +- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c + ../utils/rc: utils/rc.c +- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c + ../utils/seqmerge: utils/seqmerge.c +- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c + ../utils/scorealign: utils/scorealign.c +- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm + ../utils/scorecontigs: utils/scorecontigs.c +- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm + ../utils/fa2xfa: utils/fa2xfa.c +- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c + ../utils/overlay: utils/overlay.c +- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c + ../utils/Glue: utils/Glue.cpp +- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp + ../utils/dotplot: utils/dotplot.cpp +- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp +diff --git a/src/glocal/Makefile b/src/glocal/Makefile +index ce1421a..b82507f 100755 +--- a/src/glocal/Makefile ++++ b/src/glocal/Makefile +@@ -10,10 +10,10 @@ TRGT = glocal + OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o + + .cpp.o: +- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp ++ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp + + $(TRGT): $(OBJECTS) +- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) ++ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB) + + clean : + rm -f *.o ./*~ *~ core diff --git a/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch new file mode 100644 index 000000000000..a4b1d6808e2f --- /dev/null +++ b/sci-biology/lagan/files/lagan-2.0-gcc4.3.patch @@ -0,0 +1,23 @@ +diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp +--- lagan20-orig/src/glocal/score.cpp 2009-02-04 15:25:57.698333297 +0000 ++++ lagan20/src/glocal/score.cpp 2009-02-04 15:27:23.894092890 +0000 +@@ -2,7 +2,7 @@ + #include<score.h> + #include<leftinfluence.h> + #include<rightinfluence.h> +-#include<fstream.h> ++#include<fstream> + + extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)]; + +diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp +--- lagan20-orig/src/utils/Glue.cpp 2009-02-04 15:25:57.702333182 +0000 ++++ lagan20/src/utils/Glue.cpp 2009-02-04 15:27:04.190822654 +0000 +@@ -1,6 +1,7 @@ + #include "MultiSequence.h" + #include "SafeVector.h" + #include "Output.h" ++#include <string.h> + #include <math.h> + #include <assert.h> + #include <fstream> diff --git a/sci-biology/lagan/lagan-2.0-r1.ebuild b/sci-biology/lagan/lagan-2.0-r1.ebuild new file mode 100644 index 000000000000..63b966e79ef0 --- /dev/null +++ b/sci-biology/lagan/lagan-2.0-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils + +MY_P="lagan20" + +DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA" +HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml" +SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i "/use Getopt::Long;/ i use lib \"/usr/share/${PN}/lib\";" "${S}/supermap.pl" || die + # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline + sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die + epatch "${FILESDIR}"/${P}-*.patch +} + +src_install() { + dobin lagan.pl slagan.pl mlagan + rm lagan.pl slagan.pl utils/Utils.pm + dodir /usr/share/${PN}/lib + insinto /usr/share/${PN}/lib + doins Utils.pm + exeinto /usr/share/${PN}/utils + doexe utils/* + exeinto /usr/share/${PN} + doexe *.pl anchors chaos glocal order prolagan + insinto /usr/share/${PN} + doins *.txt + dosym /usr/share/${PN}/supermap.pl /usr/bin/supermap + dosym /usr/bin/lagan.pl /usr/bin/lagan + dosym /usr/bin/slagan.pl /usr/bin/slagan + echo "LAGAN_DIR=\"/usr/share/${PN}\"" > ${S}/99${PN} + doenvd "${S}/99${PN}" + dodoc Readmes/README.* +} diff --git a/sci-biology/lagan/lagan-2.0-r2.ebuild b/sci-biology/lagan/lagan-2.0-r2.ebuild new file mode 100644 index 000000000000..a37a3736de08 --- /dev/null +++ b/sci-biology/lagan/lagan-2.0-r2.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils multilib toolchain-funcs + +MY_P="lagan20" + +DESCRIPTION="LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA" +HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml" +SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die + # NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h where libc getline is erroneously used instead of own getline + sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die + epatch "${FILESDIR}"/${P}-*.patch +} + +src_compile() { + emake \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CXXFLAGS="${CXXFLAGS}" \ + CFLAGS="${CFLAGS}" +} + +src_install() { + newbin lagan.pl lagan || die + newbin slagan.pl slagan || die + dobin mlagan || die + rm lagan.pl slagan.pl utils/Utils.pm + + insinto /usr/$(get_libdir)/${PN}/lib + doins Utils.pm || die + exeinto /usr/$(get_libdir)/${PN}/utils + doexe utils/* || die + exeinto /usr/$(get_libdir)/${PN} + doexe *.pl anchors chaos glocal order prolagan || die + insinto /usr/$(get_libdir)/${PN} + doins *.txt || die + dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap + echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > ${S}/99${PN} + doenvd "${S}/99${PN}" || die + dodoc Readmes/README.* || die +} diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/lagan/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest new file mode 100644 index 000000000000..0fad882975fa --- /dev/null +++ b/sci-biology/last/Manifest @@ -0,0 +1,2 @@ +DIST last-230.zip 418077 SHA256 8d55ee95e05a08afa72690df9086886e97142adcfbf750cf5cf6015b91215484 SHA512 46c858c2bd4a9aa00ac3b448ce78bdee6c1edd4f6569cff3c81ec8a7c661d89a9b5e7a888cbc6da190b243f0ec83c485b4574dadc6a58669d9b955eb70c329d1 WHIRLPOOL aaa0483a58821cca0fdd7875cb4e7c62493fd724729d957df1d51c7612e92e3acefae2727789f63a248f02c976a45c3209d6bac2c39f54d84f02d1106c2d0f85 +DIST last-299.zip 453159 SHA256 cc68e9c0b5220da67fd0239c9663dc0d1a05e63b337a6c98cfef6d5c38d0c54c SHA512 74e89129cc17482ec1a99e2d940ca62374c130fea2fa53ea7d2c3703b6ca5751f348110909d61562c4839d8fb1793619c2f41c25c8968b3ab53f0c7191f4a00b WHIRLPOOL 12e826c22c2d91845e89aa0c6e99af785973e8a276dec4f97ed292e144327c7c58024622d3f7285c6107bca7af1bf3c29a23ec9d22dc88ff5dc041a0df96f3ce diff --git a/sci-biology/last/files/162-gcc46.patch b/sci-biology/last/files/162-gcc46.patch new file mode 100644 index 000000000000..9c66c6d39f00 --- /dev/null +++ b/sci-biology/last/files/162-gcc46.patch @@ -0,0 +1,15 @@ + src/XdropAligner.hh | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/XdropAligner.hh b/src/XdropAligner.hh +index 9dea32e..3c0e35f 100644 +--- a/src/XdropAligner.hh ++++ b/src/XdropAligner.hh +@@ -12,6 +12,7 @@ + #include <vector> + #include <cassert> + #include <climits> // INT_MAX ++#include <cstddef> + + namespace cbrc{ + diff --git a/sci-biology/last/files/162-ldflags.patch b/sci-biology/last/files/162-ldflags.patch new file mode 100644 index 000000000000..e5dd3ee2234e --- /dev/null +++ b/sci-biology/last/files/162-ldflags.patch @@ -0,0 +1,16 @@ + src/makefile | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/src/makefile b/src/makefile +index e77ffa7..92e4575 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -51,7 +51,7 @@ lastal: $(ALSRC) $(ALINC) makefile $(OBJ) + $(CXX) $(STRICT) $(CXXFLAGS) -o $@ $(ALSRC) $(OBJ) + + lastex: $(EXSRC) $(EXINC) makefile +- $(CXX) -Igumbel_params $(CXXFLAGS) -o $@ $(EXSRC) ++ $(CXX) $(STRICT) -Igumbel_params $(CXXFLAGS) -o $@ $(EXSRC) + + $(OBJ): CA_code/*.c CA_code/*.h makefile + $(CC) $(CFLAGS) -c CA_code/lambda_calculator.c diff --git a/sci-biology/last/last-230.ebuild b/sci-biology/last/last-230.ebuild new file mode 100644 index 000000000000..51dc9ee0faf0 --- /dev/null +++ b/sci-biology/last/last-230.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Genome-scale comparison of biological sequences" +HOMEPAGE="http://last.cbrc.jp/" +SRC_URI="http://last.cbrc.jp/archive/${P}.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_prepare() { + sed \ + -e 's:-o $@:$(LDFLAGS) -o $@:g' \ + -i src/makefile || die +} + +src_compile() { + emake \ + -e -C src \ + CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + STRICT="" || die +} + +src_install() { + dobin src/last{al,db,ex} + exeinto /usr/share/${PN}/scripts + doexe scripts/* + dodoc doc/*.txt ChangeLog.txt README.txt +} diff --git a/sci-biology/last/last-299.ebuild b/sci-biology/last/last-299.ebuild new file mode 100644 index 000000000000..9d32fdf11c3c --- /dev/null +++ b/sci-biology/last/last-299.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils toolchain-funcs python-r1 + +DESCRIPTION="Genome-scale comparison of biological sequences" +HOMEPAGE="http://last.cbrc.jp/" +SRC_URI="http://last.cbrc.jp/${P}.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_prepare() { + sed \ + -e 's:-o $@:$(LDFLAGS) -o $@:g' \ + -i src/makefile || die +} + +src_compile() { + emake \ + -e -C src \ + CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + STRICT="" || die +} + +src_install() { + local i + + dobin src/last{al,db,ex} + + dodoc doc/*.txt ChangeLog.txt README.txt + dohtml doc/*html + + cd scripts || die + for i in *py; do + python_parallel_foreach_impl python_newscript ${i} ${i%.py} + done + dobin *sh +} diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/last/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest new file mode 100644 index 000000000000..0f4b923df331 --- /dev/null +++ b/sci-biology/mafft/Manifest @@ -0,0 +1,2 @@ +DIST mafft-7.050-without-extensions-src.tgz 380375 SHA256 29ddb276bfca24f5815acc41f1e640a705bb12c9d29b7c74902ebca68cece7bc SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e WHIRLPOOL d46d7d4dfe453bfb54b9e418308772fb063bffce1d6d45d92262bee45504301daff9a6e57ecde41912a6c11852bb64510fb5ba6df04c7e79dc671e7a31444d49 +DIST mafft-7.215-without-extensions-src.tgz 393239 SHA256 22099e42274ef0078302d7cb87180880ee5fd64ef15fdcafd8c95d0018191408 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada WHIRLPOOL de43ba4107e3c1149d5ce47085bacc996393a7ef73535777439b7024eea1dce5f28c1b3c7e518f644345b7b5ea5e70fccbcaba18f16ecb9a6f5f5c31a6b5dca4 diff --git a/sci-biology/mafft/files/6.811-respect.patch b/sci-biology/mafft/files/6.811-respect.patch new file mode 100644 index 000000000000..ebfb2c7be7b8 --- /dev/null +++ b/sci-biology/mafft/files/6.811-respect.patch @@ -0,0 +1,192 @@ +diff --git a/core/Makefile b/core/Makefile +index 8bb8baf..cf28559 100644 +--- a/core/Makefile ++++ b/core/Makefile +@@ -1,5 +1,5 @@ + PREFIX = /usr/local +-LIBDIR = $(PREFIX)/lib/mafft ++LIBDIR = $(PREFIX)/GENTOOLIBDIR/mafft + BINDIR = $(PREFIX)/bin + MANDIR = $(PREFIX)/man/man1 + +@@ -127,136 +127,136 @@ mltaln.h : functions.h + touch mltaln.h + + ord : $(OBJORD) +- $(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJORD) $(CFLAGS) $(LIBS) + + tbfast : $(OBJTBFAST) +- $(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS) + + tbfast2 : $(OBJTBFAST2) +- $(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS) + + disttbfast : $(OBJDISTTBFAST) +- $(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS) + + splittbfast : $(OBJSPLITTBFAST) +- $(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS) + + splitfromaln : $(OBJSPLITFROMALN) +- $(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS) + + splittbfast2 : $(OBJSPLITTBFAST2) +- $(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS) + + dummy : $(OBJDUMMY) +- $(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS) + + setcore : $(OBJSETCORE) +- $(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS) + + countlen : $(OBJCOUNTLEN) +- $(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS) + + seq2regtable : $(OBJSEQ2REGTABLE) +- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS) + + regtable2seq : $(OBJREGTABLE2SEQ) +- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS) + + f2cl : $(OBJF2CL) +- $(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS) + + mccaskillwrap : $(OBJMCCASKILLWRAP) +- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS) + + contrafoldwrap : $(OBJCONTRAFOLDWRAP) +- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS) + + pairlocalalign : $(OBJPAIRLOCALALIGN) +- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS) + + pairash : $(OBJPAIRASH) +- $(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS) + + rnatest : $(OBJRNATEST) +- $(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS) + + pair2hat3s : $(OBJPAIR2HAT3S) +- $(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS) + + multi2hat3s : $(OBJMULTI2HAT3S) +- $(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS) + + getlag : $(OBJGETLAG) +- $(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS) + + tditr : $(OBJTDITR) +- $(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS) + + dvtditr : $(OBJDVTDITR) +- $(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS) + + mafft-profile : $(OBJGALN) +- $(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS) + + gapfill : $(OBJGAPFILL) +- $(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS) + + dndfast4 : $(OBJDNDFAST4) +- $(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS) + + dndfast5 : $(OBJDNDFAST5) +- $(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS) + + dndfast6 : $(OBJDNDFAST6) +- $(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS) + + dndfast7 : $(OBJDNDFAST7) +- $(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS) + + dndblast : $(OBJDNDBLAST) +- $(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS) + + dndfast3 : $(OBJDNDFAST3) +- $(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS) + + triplet : $(OBJTRIPLET) +- $(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS) + + triplet3 : $(OBJTRIPLET3) +- $(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS) + + sextet3 : $(OBJSEXTET3) +- $(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS) + + sextet4 : $(OBJSEXTET4) +- $(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS) + + sextet5 : $(OBJSEXTET5) +- $(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS) + + mafft-distance : $(OBJDISTANCE) +- $(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS) + + triplet5 : $(OBJTRIPLET5) +- $(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS) + + triplet6 : $(OBJTRIPLET6) +- $(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS) + + octet4 : $(OBJOCTET4) +- $(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS) + + dndpre : $(OBJDNDPRE) +- $(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS) + + dndpre2 : $(OBJDNDPRESCORE) +- $(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS) + + score : $(OBJSCORE) +- $(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS) + + genMtx : $(OBJGENMTX) +- $(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS) + + gapfill.o : gapfill.c $(HEADER) + $(CC) $(CFLAGS) -c gapfill.c diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch new file mode 100644 index 000000000000..6fba7153622d --- /dev/null +++ b/sci-biology/mafft/files/mafft-7.037-respect.patch @@ -0,0 +1,217 @@ + core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- + 1 file changed, 50 insertions(+), 50 deletions(-) + +diff --git a/core/Makefile b/core/Makefile +index 9acebb3..3838a45 100644 +--- a/core/Makefile ++++ b/core/Makefile +@@ -145,151 +145,151 @@ mltaln.h : functions.h + touch mltaln.h + + version : version.c mltaln.h +- $(CC) -o $@ version.c $(MYCFLAGS) ++ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) + + tbfast : $(OBJTBFAST) +- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) + + addsingle : $(OBJADDSINGLE) +- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) + + tbfast2 : $(OBJTBFAST2) +- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) + + disttbfast : $(OBJDISTTBFAST) +- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) + + makedirectionlist : $(OBJMAKEDIRECTIONLIST) +- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) + + splittbfast : $(OBJSPLITTBFAST) +- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) + + splitfromaln : $(OBJSPLITFROMALN) +- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) + + splittbfast2 : $(OBJSPLITTBFAST2) +- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) + + dummy : $(OBJDUMMY) +- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) + + setcore : $(OBJSETCORE) +- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) + + countlen : $(OBJCOUNTLEN) +- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) + + seq2regtable : $(OBJSEQ2REGTABLE) +- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) + + regtable2seq : $(OBJREGTABLE2SEQ) +- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) + + setdirection : $(OBJSETDIRECTION) +- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) + + replaceu : $(OBJREPLACEU) +- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) + + restoreu : $(OBJRESTOREU) +- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) + + f2cl : $(OBJF2CL) +- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) + + mccaskillwrap : $(OBJMCCASKILLWRAP) +- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) + + contrafoldwrap : $(OBJCONTRAFOLDWRAP) +- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) + + pairlocalalign : $(OBJPAIRLOCALALIGN) +- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) + + pairash : $(OBJPAIRASH) +- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) + + rnatest : $(OBJRNATEST) +- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) + + pair2hat3s : $(OBJPAIR2HAT3S) +- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) + + multi2hat3s : $(OBJMULTI2HAT3S) +- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) + + getlag : $(OBJGETLAG) +- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) + + tditr : $(OBJTDITR) +- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) + + dvtditr : $(OBJDVTDITR) +- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) + + mafft-profile : $(OBJGALN) +- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) + + gapfill : $(OBJGAPFILL) +- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) + + dndfast4 : $(OBJDNDFAST4) +- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) + + dndfast5 : $(OBJDNDFAST5) +- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) + + dndfast6 : $(OBJDNDFAST6) +- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) + + dndfast7 : $(OBJDNDFAST7) +- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) + + dndblast : $(OBJDNDBLAST) +- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) + + dndfast3 : $(OBJDNDFAST3) +- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) + + triplet : $(OBJTRIPLET) +- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) + + triplet3 : $(OBJTRIPLET3) +- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) + + sextet3 : $(OBJSEXTET3) +- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) + + sextet4 : $(OBJSEXTET4) +- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) + + sextet5 : $(OBJSEXTET5) +- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) + + mafft-distance : $(OBJDISTANCE) +- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) + + triplet5 : $(OBJTRIPLET5) +- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) + + triplet6 : $(OBJTRIPLET6) +- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) + + octet4 : $(OBJOCTET4) +- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) + + dndpre : $(OBJDNDPRE) +- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) + + dndpre2 : $(OBJDNDPRESCORE) +- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) + + score : $(OBJSCORE) +- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) + + genMtx : $(OBJGENMTX) +- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) + + gapfill.o : gapfill.c $(HEADER) + $(CC) $(MYCFLAGS) -c gapfill.c +@@ -525,7 +525,7 @@ install : all + chmod 755 $(SCRIPTS) + $(INSTALL) $(SCRIPTS) $(BINDIR) + chmod 755 $(PROGS) +- $(INSTALL) -s $(PROGS) $(LIBDIR) ++ $(INSTALL) $(PROGS) $(LIBDIR) + $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) + + ( cd $(BINDIR); \ diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild new file mode 100644 index 000000000000..d064e73b8089 --- /dev/null +++ b/sci-biology/mafft/mafft-7.050.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-7.037-respect.patch + use threads && append-cppflags -Denablemultithread + sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" +} + +src_compile() { + pushd core > /dev/null || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" + popd > /dev/null || die +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die + bash ../core/mafft --globalpair sample > test.gins1 || die + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die + bash ../core/mafft --localpair sample > test.lins1 || die + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die + + diff test.fftns2 sample.fftns2 || die + diff test.fftnsi sample.fftnsi || die + diff test.gins1 sample.gins1 || die + diff test.ginsi sample.ginsi || die + diff test.lins1 sample.lins1 || die +} + +src_install() { + pushd core + emake PREFIX="${ED}usr" install + popd + dodoc readme +} diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild new file mode 100644 index 000000000000..b76c0e60839a --- /dev/null +++ b/sci-biology/mafft/mafft-7.215.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { +# epatch "${FILESDIR}"/${PN}-7.037-respect.patch + use threads && append-cppflags -Denablemultithread +# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" + sed \ + -e 's:$(LDFLAGS)::g' \ + -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ + -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ + -e '/INSTALL/s: -s : :g' \ + -i core/Makefile || die +} + +src_compile() { + cd core || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -Wno-unused-result" +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die + bash ../core/mafft --globalpair sample > test.gins1 || die + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die + bash ../core/mafft --localpair sample > test.lins1 || die + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die + + diff test.fftns2 sample.fftns2 || die + diff test.fftnsi sample.fftnsi || die + diff test.gins1 sample.gins1 || die + diff test.ginsi sample.ginsi || die + diff test.lins1 sample.lins1 || die +} + +src_install() { + dodoc readme + cd core || die + emake PREFIX="${ED}usr" install +} diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/mafft/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/mammoth/Manifest b/sci-biology/mammoth/Manifest new file mode 100644 index 000000000000..584405eb5350 --- /dev/null +++ b/sci-biology/mammoth/Manifest @@ -0,0 +1 @@ +DIST mammoth-1.0-src.tgz 319617 SHA256 7a21bc47db4a47cc5ebeeb4c46761a79eece0a802104a3d6189f388a03e59de2 diff --git a/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch new file mode 100644 index 000000000000..63bf9f246750 --- /dev/null +++ b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch @@ -0,0 +1,21 @@ +http://gcc.gnu.org/onlinedocs/gcc-4.2.2/gfortran/SYSTEM.html#SYSTEM + +This intrinsic is provided in both subroutine and function forms; +however, only one form can be used in any given program unit. + +--- src/6apply_rot_tras.f.orig 2007-12-10 00:51:35.000000000 -0800 ++++ src/6apply_rot_tras.f 2007-12-10 00:55:07.000000000 -0800 +@@ -47,11 +47,11 @@ + endif + + +- call system ('echo $PWD > junk1') ++ i = system ('echo $PWD > junk1') + open(unit=21,file='junk1') + read(21,'(a340)', end=7) path + 7 close(21) +- call system ('rm -f junk1') ++ i = system ('rm -f junk1') + + c write(6,*)'my path is ', path + c write(6,*)tras1,tras2,tras3, diff --git a/sci-biology/mammoth/mammoth-1.0-r1.ebuild b/sci-biology/mammoth/mammoth-1.0-r1.ebuild new file mode 100644 index 000000000000..750d95dd894b --- /dev/null +++ b/sci-biology/mammoth/mammoth-1.0-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools eutils fortran-2 flag-o-matic toolchain-funcs + +MY_P="${P}-src" + +DESCRIPTION="MAtching Molecular Models Obtained from THeory" +HOMEPAGE="http://ub.cbm.uam.es/software.php" +SRC_URI="${MY_P}.tgz" + +LICENSE="mammoth" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RESTRICT="fetch" + +S=${WORKDIR}/${MY_P} + +pkg_nofetch() { + einfo "Download the source code for MAMMOTH from" + einfo "${HOMEPAGE}" + einfo "and place it in ${DISTDIR}" +} + +src_prepare() { + # Broken with gfortran without this patch + epatch "${FILESDIR}"/${PV}-consistent-system-intrinsic.patch + + case $(tc-getFC) in + g77) append-fflags -ffixed-line-length-none ;; + gfortran) append-fflags -ffixed-line-length-none ;; + esac + + # It comes with a custom-modified configure for some reason, + # which forces you to pass in the Fortran compiler as a parameter. + # Let's do the standard stuff instead. + eautoreconf +} diff --git a/sci-biology/mammoth/metadata.xml b/sci-biology/mammoth/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/mammoth/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest new file mode 100644 index 000000000000..b5eb751fe292 --- /dev/null +++ b/sci-biology/maq/Manifest @@ -0,0 +1,2 @@ +DIST calib-36.dat.gz 196371 SHA256 d4480e04446eb273f1908add709dd5a24262c08a59a1647b9a2d053f4d30181b +DIST maq-0.7.1.tar.bz2 368645 SHA256 e1671e0408b0895f5ab943839ee8f28747cf5f55dc64032c7469b133202b6de2 diff --git a/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch new file mode 100644 index 000000000000..9f4247d441f5 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch @@ -0,0 +1,16 @@ + simulate.c | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/simulate.c b/simulate.c +index 788c440..67ba2ba 100644 +--- a/simulate.c ++++ b/simulate.c +@@ -383,7 +383,7 @@ static void simustat_core(gzFile fp, int Q_thres) + memset(wc_single, 0, 40); memset(tot_single, 0, 40); + memset(wc_pair, 0, 40); memset(tot_pair, 0, 40); + memset(abpair, 0, 4 * 256 * 10); +- memset(tc[2], 0, 4 * sizeof(int)); ++ memset(tc, 0, 4 * sizeof(int)); + while (maqmap_read1(fp, m1)) { + int is_correct; + bit32_t p1, p2; diff --git a/sci-biology/maq/files/maq-0.7.1-flags.patch b/sci-biology/maq/files/maq-0.7.1-flags.patch new file mode 100644 index 000000000000..721e53248b7a --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-flags.patch @@ -0,0 +1,24 @@ + configure.ac | 3 ++- + 1 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/configure.ac b/configure.ac +index ad2f1e6..4f9d7be 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -8,6 +8,7 @@ AC_PROG_CXX + + # set CFLAGS and CXXFLAGS + user_CFLAGS=${CFLAGS} ++user_CXXFLAGS=${CXXFLAGS} + generic_CFLAGS="-Wall" + ext_CFLAGS="" + case "${host_cpu}-${host_os}" in +@@ -37,7 +38,7 @@ AC_ARG_ENABLE(shortread, [ --enable-shortreads use shortread mode], + AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], + [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], []) + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS}" +-CXXFLAGS=$CFLAGS ++CXXFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CXXFLAGS}" + + AC_STDC_HEADERS + AC_CHECK_HEADER(zlib.h) diff --git a/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch new file mode 100644 index 000000000000..4b97da89be48 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-gcc-4.7.patch @@ -0,0 +1,34 @@ + stdhash.hh | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/stdhash.hh b/stdhash.hh +index eaf98af..16cd1a3 100644 +--- a/stdhash.hh ++++ b/stdhash.hh +@@ -412,7 +412,7 @@ public: + inline bool insert(const keytype_t &key) { + __lh3_hash_base_class<keytype_t>::rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } + else ++(this->n_size); // then ret == 2 +@@ -493,7 +493,7 @@ public: + inline bool insert(const keytype_t &key, const valtype_t &val) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + vals[i] = val; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } +@@ -503,7 +503,7 @@ public: + inline bool insert(const keytype_t &key, valtype_t **q) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + *q = vals + i; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } diff --git a/sci-biology/maq/maq-0.7.1-r1.ebuild b/sci-biology/maq/maq-0.7.1-r1.ebuild new file mode 100644 index 000000000000..645a2d65a620 --- /dev/null +++ b/sci-biology/maq/maq-0.7.1-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools eutils + +DESCRIPTION="Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences" +HOMEPAGE="http://maq.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${P}.tar.bz2 + mirror://sourceforge/${PN}/calib-36.dat.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" + +RDEPEND="sys-libs/zlib" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-flags.patch \ + "${FILESDIR}"/${P}-bfr-overfl.patch \ + "${FILESDIR}"/${P}-gcc-4.7.patch + sed \ + -e '/ext_CFLAGS/s:-m64::g' \ + -i configure* || die + eautoreconf +} + +src_install() { + default + insinto /usr/share/maq + doins "${WORKDIR}"/*.dat + doman maq.1 + dodoc ${PN}.pdf +} diff --git a/sci-biology/maq/maq-0.7.1.ebuild b/sci-biology/maq/maq-0.7.1.ebuild new file mode 100644 index 000000000000..1089eefbae04 --- /dev/null +++ b/sci-biology/maq/maq-0.7.1.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences" +HOMEPAGE="http://maq.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2 + mirror://sourceforge/${PN}/calib-36.dat.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="" + +src_install() { + emake DESTDIR="${D}" install || die + insinto /usr/share/maq + doins "${WORKDIR}"/*.dat || die + doman maq.1 + dodoc AUTHORS ChangeLog NEWS maq.pdf +} diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml new file mode 100644 index 000000000000..79ebcc09421b --- /dev/null +++ b/sci-biology/maq/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">maq</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest new file mode 100644 index 000000000000..f9ad87f8424e --- /dev/null +++ b/sci-biology/maqview/Manifest @@ -0,0 +1 @@ +DIST maqview-0.2.5.tar.gz 383410 SHA256 156794f114a00bb455a47ccefa50782441dc1b9668b6e7439ce0674060c085cb SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6 WHIRLPOOL 0ba5a15a1317b4bb78458b9e282348983be9e2c30980aef4e35a9f5dacfff57226eaa4403fb0b9d9d448ba033409d548db224ed544ad365226a8fb59be8b743e diff --git a/sci-biology/maqview/files/0.2.5-ldflags.patch b/sci-biology/maqview/files/0.2.5-ldflags.patch new file mode 100644 index 000000000000..92b9a3ed58ac --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-ldflags.patch @@ -0,0 +1,46 @@ + configure.ac | 18 +++--------------- + 1 files changed, 3 insertions(+), 15 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 90e612b..5a00d15 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -9,17 +9,10 @@ AC_PROG_INSTALL + AC_STDC_HEADERS + + is_static=0 +-case ${prefix} in +- NONE);; +- *) is_static=1 +- AC_MSG_WARN([Library libglut will be statically linked.]) +- LDFLAGS="-L${prefix}/lib" +- CPPFLAGS="-I${prefix}/include";; +-esac + + # set CFLAGS and LDFLAGS + +-true_CFLAGS="-g -O2 -Wall -W -DMAQ_LONGREADS" ++true_CFLAGS="-DMAQ_LONGREADS" + case "${host_os}" in + darwin*) + GLLIBS="-framework OpenGL -framework GLUT" +@@ -30,17 +23,12 @@ case "${host_os}" in + i?86) CPPFLAGS="$CPPFLAGS -D_FILE_OFFSET_BITS=64";; + esac + AC_CHECK_LIB([glut], [glutMouseWheelFunc], [CPPFLAGS="$CPPFLAGS -DHAVE_FREEGLUT"]) +- AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)], +- [is_static=1]) +- case $is_static in +- 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";; +- 0) GLLIBS="-lGL -lglut -lm";; +- esac ++ GLLIBS="-lGL -lglut -lm -lGLU" + AC_SUBST([GLLIBS]);; + # *) AC_MSG_ERROR([OS is not supported]);; + esac + AM_CONDITIONAL([HAVE_GL], [test "$isgl" = 1]) +-CFLAGS=$true_CFLAGS ++CFLAGS="${CFLAGS} $true_CFLAGS" + + AC_CONFIG_FILES([Makefile]) + AC_OUTPUT diff --git a/sci-biology/maqview/files/0.2.5-zlib.patch b/sci-biology/maqview/files/0.2.5-zlib.patch new file mode 100644 index 000000000000..cd35273de66b --- /dev/null +++ b/sci-biology/maqview/files/0.2.5-zlib.patch @@ -0,0 +1,33 @@ + Makefile.am | 6 +++--- + zrio.c | 2 +- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index dad515a..9617eb7 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,8 +1,8 @@ + bin_PROGRAMS = zrio maqindex maqview maqindex_socks +-zlib_src = adler32.c compress.c crc32.c deflate.c gzio.c inffast.c inflate.c \ +- infback.c inftrees.c trees.c uncompr.c zutil.c +-generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c $(zlib_src) ++generic_src = btree.c maqmap_index.c zrio.c stdhashc.h stdhashc.cc cns_cache.c const.c ++LIBS = -lz + zrio_SOURCES = zrio_main.c $(generic_src) ++zrio_LDADD = -lz + maqindex_SOURCES = maqmap_index_main.c $(generic_src) + maqview_SOURCES = read_cache.c view_goto.c view_panel.c gl_gui.c MainFrame.c \ + $(generic_src) +diff --git a/zrio.c b/zrio.c +index ffed00a..fe744df 100644 +--- a/zrio.c ++++ b/zrio.c +@@ -506,7 +506,7 @@ int build_index(int in, int64_t span, struct access **built, void (*notify)(void + totin += strm.avail_in; + totout += strm.avail_out; + tmp = strm.avail_out; +- ret = inflate_zr(&strm, Z_BLOCK); /* return at end of block */ ++ ret = inflate(&strm, Z_BLOCK); /* return at end of block */ + totin -= strm.avail_in; + totout -= strm.avail_out; + if(notify) notify(obj, window + WINSIZE - tmp, tmp - strm.avail_out, totout); diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch new file mode 100644 index 000000000000..043208bb79b5 --- /dev/null +++ b/sci-biology/maqview/files/maqview-0.2.5-gcc4.7.patch @@ -0,0 +1,16 @@ + stdhash.hh | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/stdhash.hh b/stdhash.hh +index eaf98af..f22c5a6 100644 +--- a/stdhash.hh ++++ b/stdhash.hh +@@ -493,7 +493,7 @@ public: + inline bool insert(const keytype_t &key, const valtype_t &val) { + rehash(); + hashint_t i; +- int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); ++ int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + vals[i] = val; + if (ret == 0) return true; + if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } diff --git a/sci-biology/maqview/maqview-0.2.5-r2.ebuild b/sci-biology/maqview/maqview-0.2.5-r2.ebuild new file mode 100644 index 000000000000..e549497830bd --- /dev/null +++ b/sci-biology/maqview/maqview-0.2.5-r2.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler" +HOMEPAGE="http://maq.sourceforge.net/" +SRC_URI="mirror://sourceforge/maq/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND=" + media-libs/freeglut + sys-libs/zlib" +RDEPEND="${DEPEND} + sci-biology/maq" + +S="${WORKDIR}/${PN}" + +PATCHES=( + "${FILESDIR}"/${PV}-ldflags.patch + "${FILESDIR}"/${PV}-zlib.patch + "${FILESDIR}"/${P}-gcc4.7.patch + ) diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml new file mode 100644 index 000000000000..79ebcc09421b --- /dev/null +++ b/sci-biology/maqview/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">maq</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mauve/mauve-9999.ebuild b/sci-biology/mauve/mauve-9999.ebuild new file mode 100644 index 000000000000..1c3446707e4d --- /dev/null +++ b/sci-biology/mauve/mauve-9999.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +ESVN_REPO_URI="https://mauve.svn.sourceforge.net/svnroot/mauve/mauve/trunk" + +WANT_ANT_TASKS="ant-nodeps" +EANT_GENTOO_CLASSPATH="biojava,zeus-jscl,dbus-java" +JAVA_ANT_REWRITE_CLASSPATH="true" +JAVA_PKG_BSFIX_NAME="build.xml" + +inherit subversion java-pkg-2 java-ant-2 eutils + +DESCRIPTION="Multiple genome alignment with large-scale evolutionary events (GUI component)" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="" + +LICENSE="GPL-2" +SLOT="0" +IUSE="doc" +KEYWORDS="" + +CDEPEND="~sci-biology/biojava-1.6 + >=dev-java/dbus-java-2.5.1 + ~dev-java/zeus-jscl-1.08 + dev-java/ant-nodeps" +RDEPEND=">=virtual/jre-1.5 + sci-biology/mauvealigner + ${CDEPEND}" +DEPEND=">=virtual/jdk-1.5 + media-gfx/icoutils + ${CDEPEND}" + +S="${WORKDIR}" + +java_prepare() { + find -name '*.jar' -not -name 'jarbundler*' -print -delete + perl -i -ne 'print unless /<dmg/ or /<taskdef.+name="dmg"/../<\/taskdef>/' build.xml + perl -i -ne 'print unless /<ssh/../<\/ssh/ or /<taskdef.+name="ssh"/../<\/taskdef>/' build.xml + perl -i -ne 'print unless /<retroweaver/ or /<taskdef.+name="retroweaver"/../<\/taskdef>/' build.xml +} + +src_install() { + java-pkg_dojar Mauve.jar + + java-pkg_dolauncher Mauve --main org.gel.mauve.gui.Mauve + + icotool -x win32/mauve.ico + insinto /usr/share/pixmaps + newins mauve_4_48x48x32.png Mauve.png + make_desktop_entry Mauve Mauve Mauve +} diff --git a/sci-biology/mauve/metadata.xml b/sci-biology/mauve/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/mauve/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/mauvealigner/mauvealigner-9999.ebuild b/sci-biology/mauvealigner/mauvealigner-9999.ebuild new file mode 100644 index 000000000000..cee185340513 --- /dev/null +++ b/sci-biology/mauvealigner/mauvealigner-9999.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +ESVN_REPO_URI="https://mauve.svn.sourceforge.net/svnroot/mauve/mauveAligner/trunk" + +inherit subversion autotools + +DESCRIPTION="Multiple genome alignment with large-scale evolutionary events (aligner component)" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="" + +LICENSE="GPL-2" +SLOT="0" +IUSE="doc" +KEYWORDS="" + +CDEPEND="sci-libs/libgenome + sci-libs/libmuscle + sci-libs/libmems" +DEPEND="${CDEPEND} + doc? ( app-doc/doxygen )" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}" + +src_prepare() { + eautoreconf +} + +src_install() { + emake install DESTDIR="${D}" || die +} diff --git a/sci-biology/mauvealigner/metadata.xml b/sci-biology/mauvealigner/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/mauvealigner/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest new file mode 100644 index 000000000000..88b4aef28107 --- /dev/null +++ b/sci-biology/mcl/Manifest @@ -0,0 +1,2 @@ +DIST mcl-08-312.tar.gz 2749006 SHA256 0061da0661e99f783d97e6ae10149fe5ce11fa332b24cc8a4a491a072867bb6e SHA512 9f89f81af398710ebb9135c93653d892fc9daef360d70f3b890a3133d8a17dddffe568b110d3370602cead895562bc0dc5a71020834b3b3e9b6d2abf4bf64b0b WHIRLPOOL 6d00665c545edb55605fb0438cc79a412150e68b9c63ffc51c93f8f8c33b9bcd6e4e5e435b3be89a64407a0a8f6f1b8e77567f653e45c08f1675dbf2b9e0b59e +DIST mcl-12-135.tar.gz 2970824 SHA256 3f5e0e7ad1074c7c4ef0139aa3318f92971fede7292dc3571eca2fd1da20a283 SHA512 97234e88f3430f223e1f303577b2b8853f40de6b204de415466719f691f529a795b17bf2fd48d4cc73d05900c87a10ba9afabbe54bce9367ee59215e7db0a8f5 WHIRLPOOL 1505643a460ba5bd6b834d070278a108fba57c9dc2a90a72a8e0726bd54a1b8fe3e4792a63397d58db62b036d22c325db2dd76f696a8692473987395c556a279 diff --git a/sci-biology/mcl/mcl-08.312.ebuild b/sci-biology/mcl/mcl-08.312.ebuild new file mode 100644 index 000000000000..9a2aafb0c037 --- /dev/null +++ b/sci-biology/mcl/mcl-08.312.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +MY_P="${PN}-${PV/./-}" + +DESCRIPTION="A Markov Cluster Algorithm implementation" +HOMEPAGE="http://micans.org/mcl/" +SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+blast" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + find \ + -name Makefile.am \ + -exec sed \ + -e '/docdir/d' \ + -e '/exampledir/s:doc::g' \ + -i '{}' + || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( $(use_enable blast) ) + autotools-utils_src_configure +} diff --git a/sci-biology/mcl/mcl-12.135.ebuild b/sci-biology/mcl/mcl-12.135.ebuild new file mode 100644 index 000000000000..9a2aafb0c037 --- /dev/null +++ b/sci-biology/mcl/mcl-12.135.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +MY_P="${PN}-${PV/./-}" + +DESCRIPTION="A Markov Cluster Algorithm implementation" +HOMEPAGE="http://micans.org/mcl/" +SRC_URI="http://micans.org/mcl/src/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+blast" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + find \ + -name Makefile.am \ + -exec sed \ + -e '/docdir/d' \ + -e '/exampledir/s:doc::g' \ + -i '{}' + || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( $(use_enable blast) ) + autotools-utils_src_configure +} diff --git a/sci-biology/mcl/metadata.xml b/sci-biology/mcl/metadata.xml new file mode 100644 index 000000000000..aa6527e1e839 --- /dev/null +++ b/sci-biology/mcl/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="blast"> + add support for NCBI BLAST data + </flag> + </use> +</pkgmetadata> diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest new file mode 100644 index 000000000000..3ed08610b06e --- /dev/null +++ b/sci-biology/meme/Manifest @@ -0,0 +1 @@ +DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e diff --git a/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch new file mode 100644 index 000000000000..1293de0ea080 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-Makefile.am.patch @@ -0,0 +1,17 @@ +--- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400 ++++ Makefile.am 2007-04-24 10:37:37.000000000 -0400 +@@ -57,11 +57,11 @@ + endif + + dbdir: +- mkdir -p $(MEME_DB) ++ mkdir -p $(DESTDIR)$(MEME_DB) + + install-data-local: +- mkdir -p $(MEME_LOGS) +- chmod a+w $(MEME_LOGS) ++ mkdir -p $(DESTDIR)$(MEME_LOGS) ++ chmod a+w $(DESTDIR)$(MEME_LOGS) + + distdir = $(PACKAGE)_$(VERSION) + diff --git a/sci-biology/meme/files/meme-3.5.4-patch1.patch b/sci-biology/meme/files/meme-3.5.4-patch1.patch new file mode 100644 index 000000000000..b072d7edc527 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-patch1.patch @@ -0,0 +1,198 @@ +--- meme_3.5.4/website/cgi-bin/process_request.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/process_request.pl 2007-05-30 01:35:02.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: process_request.pl 1339 2006-09-21 19:46:28Z tbailey $ ++## $Id: process_request.pl 1807 2007-05-30 01:34:31Z tbailey $ + ## + ## $Log: process_request.pl,v $ + ## Revision 1.6.6.1 2006/02/16 23:22:35 nadya +@@ -55,7 +55,8 @@ + $blocks_url = "http://blocks.fhcrc.org/blocks-bin/process_blocks.pl"; + # + # You can change this if you wish to use a different JASPAR server +-$jaspar_root = "http://mordor.cgb.ki.se"; ++#$jaspar_root = "http://mordor.cgb.ki.se"; ++$jaspar_root = "http://asp.ii.uib.no:8090"; + $jaspar_url = "$jaspar_root/cgi-bin/jaspar2005/jaspar_db.pl"; + # + # You can change this if you wish to use a different Meta-MEME server +@@ -221,7 +222,7 @@ + + $fasta = ""; # return value + @lines = split(/\n/, $block); # split block into lines +- for ($i = 1; $i<$#lines; $i++) { ++ for ($i = 2; $i<$#lines; $i++) { + last if $lines[$i] =~ /^\/\//; + @words = split(/\s+/, $lines[$i]); # split line into words + # get sequence line +@@ -239,7 +240,7 @@ + + $fasta = ""; # return value + @lines = split(/\n/, $block); # split block into lines +- for ($i = 1; $i<$#lines; $i++) { ++ for ($i = 2; $i<$#lines; $i++) { + last if $lines[$i] =~ /^\/\//; + @words = split(/\s+/, $lines[$i]); # split line into words + # get id line and sequence line +@@ -311,7 +312,8 @@ + $content = $request->content; + + # fix bug in JASPAR output; add database field to view buttons +- $content =~ s/rm=present/rm=present&db=$sub_db/g; ++ # remove fix: JASPAR fixed the bug ++ # $content =~ s/rm=present/rm=present&db=$sub_db/g; + + # display the page + print $content; +--- meme_3.5.4/src/ureadseq.c 2006-09-21 19:46:28.000000000 +0000 ++++ trunk/src/ureadseq.c 2007-05-18 08:18:05.000000000 +0000 +@@ -1,5 +1,5 @@ + /* +- * $Id: ureadseq.c 1339 2006-09-21 19:46:28Z tbailey $ ++ * $Id: ureadseq.c 1787 2007-05-18 08:17:28Z tbailey $ + * + * $Log$ + * Revision 1.2 2006/03/08 20:50:11 nadya +@@ -206,10 +206,9 @@ + + Local void addinfo(char *s, struct ReadSeqVars *V) + { +- char s2[256], *si; ++ char *si = (char *) malloc((strlen(s) + 40) * sizeof(char)); + boolean saveadd; + +- si = s2; + while (*s == ' ') s++; + sprintf(si, " %d) %s\n", V->nseq, s); + +@@ -217,6 +216,7 @@ + V->addit = true; + V->isseqchar = isAnyChar; + addseq( si, V); ++ free(si); + V->addit = saveadd; + V->isseqchar = isSeqChar; + } +@@ -966,7 +966,6 @@ + } while ((l == 0) && !feof(V->f)); + + if (feof(V->f)) V->err = eNoData; +- + else switch (format_) { + case kPlain : readPlain(V); break; + case kIG : readIG(V); break; +@@ -1181,7 +1180,7 @@ + int nlines= 0, k=0, splen= 0, otherlines= 0, aminolines= 0, dnalines= 0; + char sp[MAXLINE]; + long linestart=0; +- int maxlines2check=500; ++ int maxlines2check=5000; + + #define ReadOneLine(sp) \ + { done |= (feof(fseq)); \ +--- meme_3.5.4/src/include/ureadseq.h 2006-09-21 19:46:28.000000000 +0000 ++++ trunk/src/ureadseq.h 2007-05-18 08:18:05.000000000 +0000 +@@ -1,5 +1,5 @@ + /* +- * $Id: ureadseq.h 1339 2006-09-21 19:46:28Z tbailey $ ++ * $Id: ureadseq.h 1048 2006-07-06 20:07:44Z cegrant $ + * + * $Log$ + * Revision 1.1 2005/07/29 19:12:07 nadya +@@ -15,7 +15,7 @@ + #include "config.h" + #include "macros.h" + +-#define MAXLINE 1024 ++#define MAXLINE 10240 + + typedef char boolean; + #define NEWLINE '\n' +--- meme_3.5.4/src/read_seq_file.c 2006-09-21 19:46:28.000000000 +0000 ++++ ./read_seq_file.c 2007-05-18 06:51:06.000000000 +0000 +@@ -433,6 +433,7 @@ + name[i++] = c; /* non-blank: add to name */ + } + } ++ Resize(name, i+1, char); + name[i] = '\0'; + + /* read in description */ +--- meme_3.5.4/website/html/meme-install.html 2006-09-21 19:46:29.000000000 +0000 ++++ fred/meme-install.html 2007-05-30 02:00:56.000000000 +0000 +@@ -208,42 +208,39 @@ + <h2><a name="patch">Getting and installing the patches</a></h2> + <p>The distribution may have patches associated with it. They are available + from <a href="http://meme.nbcr.net/downloads/">http://meme.nbcr.net/downloads/</a>. +-The patch file name is <span class="command">filename.VERSION.patch</span>. In addition, a +-patched file is distributed as well and can be used as a drop-in substitute +-for the original file. The drop-in file is <span class="command">filename.VERSION</span>. +-It is necessary to download only one of the two files depending on the method used for +-patching. All patches for a specific version should be installed. The list +-below provides instructions for installation of availble patches for specific +-version. ++Patch files are located in a directory named ++<span class="command">VERSION.patches</span>, ++for example, <span class="command">meme_3.5.4.patches</span>. ++Patch file have names like: ++<span class="command">VERSION.patch_SERIAL_NO</span>, for example, <span class="command">meme_3.5.4.patch_3</span>. ++</p> <p> To install a patch, download the patch file from the URL given above. ++Then perform the following commands to install it: ++ <br><span class="command">$ cp PATCH_FILE VERSION </span> <br><span class="command">$ cd VERSION </span> ++ <br><span class="command">$ patch -p1 < PATCH_FILE </span> ++ <br><span class="command">$ make install </span> ++ <br><span class="command">$ make test </span> ++</p> ++<p> ++For example, to install the first patch to version meme_3.5.4, you would perform the following commands: ++ <br><span class="command">$ cp meme_3.5.4.patch_1 meme_3.5.4 </span> ++ <br><span class="command">$ cd meme_3.5.4 </span> ++ <br><span class="command">$ patch -p1 < meme_3.5.4.patch_1 </span> ++ <br><span class="command">$ make install </span> ++ <br><span class="command">$ make test </span> ++</p> ++<p> ++You must install all of the patches for a specific version in serial ++number order. For example, if you wish to install patch number 3, ++you must first have installed patches number 1 and 2 for that version. ++This is easy to do. Just download all the patches for your current ++version, copy them to your current versions's directory, and then ++install them in order by repeating the <span class="command">patch</span>, ++command above, with each patch file. You only need to run the ++<span class="command">install</span> and ++<span class="command">make test</span> commands once, after ++the last <span class="command">patch</patch> command. + </p> + +-<center> +-<table class="large" border=1 cellspacing=0> +-<tr> +- <th width=7% class="head">Version</th> +- <th width=25% class="head">Patch list</th> +- <th class="head">Installation</th> +-</tr> +-<tr> +- <td align=center>3.5.0</td> +- <td align=center>mast-client.txt</td> +- <td> +- <ol> +- <li>If downloaded a patch file <code>mast-client.txt.3.5.0.patch</code>: +- <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/</span> +- <br><span class="command"># cd meme_3.5.0/scripts/</span> +- <br><span class="command"># patch -p0 < mast-client.txt.3.5.0.patch </span> +- <br> +- </li> +- <li>If downloaded a patched file <code>mast-client.txt.3.5.0</code>: +- <br><span class="command"># cp mast-client.txt.3.5.0 meme_3.5.0/scripts/mast-client.txt</span> +- </li> +- </ol> +- </td> +-</tr> +-</table> +-</center> +- + <p> + <p>[<a href="#top"> Top </a>]</p> + diff --git a/sci-biology/meme/files/meme-3.5.4-patch2.patch b/sci-biology/meme/files/meme-3.5.4-patch2.patch new file mode 100644 index 000000000000..cc07a98307f2 --- /dev/null +++ b/sci-biology/meme/files/meme-3.5.4-patch2.patch @@ -0,0 +1,70 @@ +--- meme_3.5.4/website/cgi-bin/meme.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/meme.pl 2007-09-10 00:28:33.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: meme.pl 1339 2006-09-21 19:46:28Z tbailey $ ++## $Id: meme.pl 2054 2007-09-10 00:27:42Z tbailey $ + ## + ## $Log$ + ## Revision 1.12 2006/03/07 23:30:19 nadya +@@ -467,21 +467,21 @@ + + # check against allowed dna letters + $x = $_; +- $x =~ tr/ABCDGHKMNRSTUVWY//cd; ++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; + $new = length $x; + if ($old == $new) { + "dna"; + } else { + # check against allowed protein letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; + $new = length $x; + if ($old == $new) { + "protein"; + } else { + # get the unknown letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; + &whine(" + Your sequences contained the following unrecognized letters: $x. + <BR> +--- meme_3.5.4/website/cgi-bin/mast.pl 2006-09-21 19:46:29.000000000 +0000 ++++ trunk/website/cgi-bin/mast.pl 2007-09-10 00:38:14.000000000 +0000 +@@ -1,6 +1,6 @@ + #!@WHICHPERL@ + ## +-## $Id: mast.pl 1339 2006-09-21 19:46:28Z tbailey $ ++## $Id: mast.pl 2055 2007-09-10 00:37:11Z tbailey $ + ## + ## $Log$ + ## Revision 1.8 2006/03/07 23:30:19 nadya +@@ -479,21 +479,21 @@ + + # check against allowed nucleotide letters + $x = $_; +- $x =~ tr/ABCDGHKMNRSTUVWY//cd; ++ $x =~ tr/ABCDGHKMNRSTUVWY*-//cd; + $new = length $x; + if ($old == $new) { + return("DNA"); + } else { + # check against allowed protein letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//cd; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//cd; + $new = length $x; + if ($old == $new) { + return("PROTEIN"); + } else { + # get the unknown letters + $x = $_; +- $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ//d; ++ $x =~ tr/ABCDEFGHIKLMNPQRSTUVWXYZ*-//d; + &whine(" + Your sequences contained the following unrecognized letters: $x. + <BR> diff --git a/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch b/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch new file mode 100644 index 000000000000..1293de0ea080 --- /dev/null +++ b/sci-biology/meme/files/meme-4.0.0-Makefile.am.patch @@ -0,0 +1,17 @@ +--- Makefile.am.old 2007-04-24 10:36:50.000000000 -0400 ++++ Makefile.am 2007-04-24 10:37:37.000000000 -0400 +@@ -57,11 +57,11 @@ + endif + + dbdir: +- mkdir -p $(MEME_DB) ++ mkdir -p $(DESTDIR)$(MEME_DB) + + install-data-local: +- mkdir -p $(MEME_LOGS) +- chmod a+w $(MEME_LOGS) ++ mkdir -p $(DESTDIR)$(MEME_LOGS) ++ chmod a+w $(DESTDIR)$(MEME_LOGS) + + distdir = $(PACKAGE)_$(VERSION) + diff --git a/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch new file mode 100644 index 000000000000..e84006295735 --- /dev/null +++ b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch @@ -0,0 +1,134 @@ + Makefile.am | 6 +++--- + doc/Makefile.am | 2 +- + doc/examples/Makefile.am | 24 +++++++++++----------- + .../Makefile.am | 2 +- + doc/examples/sample_opal_scripts/Makefile.am | 2 +- + doc/images/Makefile.am | 2 +- + scripts/Makefile.am | 2 +- + 7 files changed, 20 insertions(+), 20 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 4a69e34..842e33f 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -18,11 +18,11 @@ ARCHIVE_REVISION: + install-data-hook: dbdir + + dbdir: +- mkdir -p $(MEME_DB) ++ mkdir -p $(DESTDIR)$(MEME_DB) + + install-data-local: +- mkdir -p $(MEME_LOGS) +- chmod a+w $(MEME_LOGS) ++ mkdir -p $(DESTDIR)$(MEME_LOGS) ++ chmod a+w $(DESTDIR)$(MEME_LOGS) + + distdir = $(PACKAGE)_$(VERSION) + +diff --git a/doc/Makefile.am b/doc/Makefile.am +index e0d6af9..e7bcb4f 100644 +--- a/doc/Makefile.am ++++ b/doc/Makefile.am +@@ -202,7 +202,7 @@ COMMON_DOC = \ + if WEBSITE + MEME_DOC_DIR = $(WEBDIR)/doc + else +-MEME_DOC_DIR = $(prefix)/doc ++MEME_DOC_DIR = $(docdir)/html + endif + + memedocdir = $(MEME_DOC_DIR) +diff --git a/doc/examples/Makefile.am b/doc/examples/Makefile.am +index 12970b5..633492c 100644 +--- a/doc/examples/Makefile.am ++++ b/doc/examples/Makefile.am +@@ -51,24 +51,24 @@ if WEBSITE + exdir = $(WEBDIR)/examples + other_exdir = $(WEBDIR)/doc/examples + else +-exdir = $(prefix)/doc/examples ++exdir = $(prefix)/share/meme/examples + other_exdir = $(exdir) + endif + + ex_DATA = $(EXAMPLES) + + install-data-hook: +- tar xzvf centrimo_example_output_files.tgz -C $(other_exdir) +- tar xzvf dreme_example_output_files.tgz -C $(other_exdir) +- tar xzvf fimo_example_output_files.tgz -C $(other_exdir) +- tar xzvf glam2_example_output_files.tgz -C $(other_exdir) +- tar xzvf glam2scan_example_output_files.tgz -C $(other_exdir) +- tar xzvf mast_example_output_files.tgz -C $(other_exdir) +- tar xzvf mcast_example_output_files.tgz -C $(other_exdir) +- tar xzvf meme_example_output_files.tgz -C $(other_exdir) +- tar xzvf memechip_example_output_files.tgz -C $(other_exdir) +- tar xzvf spamo_example_output_files.tgz -C $(other_exdir) +- tar xzvf tomtom_example_output_files.tgz -C $(other_exdir) ++ tar xzvf centrimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf dreme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf fimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf glam2_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf glam2scan_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf mast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf mcast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf meme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf memechip_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf spamo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) ++ tar xzvf tomtom_example_output_files.tgz -C $(DESTDIR)/$(other_exdir) + + # If .svnignore file doesn't exist + # create an empty one +diff --git a/doc/examples/compute_prior_dist_example_output_files/Makefile.am b/doc/examples/compute_prior_dist_example_output_files/Makefile.am +index 747028d..a358f58 100644 +--- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am ++++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am +@@ -22,7 +22,7 @@ EXAMPLES = \ + if WEBSITE + exdir = $(WEBDIR)/doc/examples/compute_prior_dist_example_output_files + else +-exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files ++exdir = $(prefix)/share/meme/examples/compute_prior_dist_example_output_files + endif + + ex_DATA = $(EXAMPLES) +diff --git a/doc/examples/sample_opal_scripts/Makefile.am b/doc/examples/sample_opal_scripts/Makefile.am +index 3a638b3..30925bb 100644 +--- a/doc/examples/sample_opal_scripts/Makefile.am ++++ b/doc/examples/sample_opal_scripts/Makefile.am +@@ -18,7 +18,7 @@ EXAMPLES = \ + if WEBSITE + exdir = $(WEBDIR)/doc/examples/sample_opal_scripts + else +-exdir = $(prefix)/doc/examples/sample_opal_scripts ++exdir = $(prefix)/share/meme/examples/sample_opal_scripts + endif + + ex_DATA = $(EXAMPLES) +diff --git a/doc/images/Makefile.am b/doc/images/Makefile.am +index c879621..a4696cd 100644 +--- a/doc/images/Makefile.am ++++ b/doc/images/Makefile.am +@@ -28,7 +28,7 @@ MEME_IMAGES = \ + if WEBSITE + memeimgdir = $(WEBDIR)/doc/images + else +-memeimgdir = $(prefix)/doc/images ++memeimgdir = $(docdir)/html/images + endif + + memeimg_DATA = $(MEME_IMAGES) +diff --git a/scripts/Makefile.am b/scripts/Makefile.am +index 4143e46..8a5c021 100644 +--- a/scripts/Makefile.am ++++ b/scripts/Makefile.am +@@ -8,7 +8,7 @@ + if WEBSITE + MEME_DOC_DIR = $(WEBDIR)/doc + else +-MEME_DOC_DIR = $(prefix)/doc ++MEME_DOC_DIR = $(docdir) + endif + + ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION) diff --git a/sci-biology/meme/meme-4.8.1-r2.ebuild b/sci-biology/meme/meme-4.8.1-r2.ebuild new file mode 100644 index 000000000000..8a1482c0b32d --- /dev/null +++ b/sci-biology/meme/meme-4.8.1-r2.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +PYTHON_DEPEND="2" + +inherit autotools eutils python + +DESCRIPTION="The MEME/MAST system - Motif discovery and search" +HOMEPAGE="http://meme.sdsc.edu/meme" +SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz" + +LICENSE="meme" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="debug examples mpi" + +DEPEND=" + app-shells/tcsh + dev-libs/libxml2:2 + dev-libs/libxslt + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${PN}_${PV}" + +#pkg_setup() { + # generate meme group to restrict logging to /var/log/meme +# enewgroup meme +# python_pkg_setup +# python_set_active_version 2 +#} + +src_prepare() { + use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am + sed \ + -e '/flags/s:-O3::g' \ + -e '/opt/s:-O::g' \ + -e '/debug/s:-ggdb::' \ + -e '/debug/s:-g::' \ + -e 's:CFLAGS=:CFLAGS+=:g' \ + -i configure.ac || die + epatch \ + "${FILESDIR}"/${P}-Makefile.am.patch + eautoreconf +} + +src_configure() { + MY_PREFIX="${ROOT}opt/meme" + USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi + econf \ + --sysconfdir="${EPREFIX}/etc/meme" \ + --with-logs="${ROOT}var/log/meme" \ + $(use_enable debug) \ + $USE_DISABLE_MPI +} + +src_test() { + # bug #297070 + emake -j1 test +} + +src_install() { + local i + default + + for i in "${ED}"/usr/bin/*; do + mv "${ED}"/usr/bin/{,meme-}$(basename ${i}) || die + done + + echo "PATH=/opt/${PN}/bin" > 99${PN} + doenvd 99${PN} + + # allow logging only for members of meme group + # diropts -m 0770 -g meme -o root + diropts -m ugo+rwxt -o root + keepdir /var/log/meme +} + +#pkg_postinst() { +# einfo 'Log files are produced in the "/var/log/meme" directory. Users' +# einfo 'need to be part of the meme group to use this facility.' +#} diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/meme/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/metadata.xml b/sci-biology/metadata.xml new file mode 100644 index 000000000000..7a808874b6e6 --- /dev/null +++ b/sci-biology/metadata.xml @@ -0,0 +1,46 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<catmetadata> + <longdescription lang="en"> + The sci-biology category contains software that can be used + in biological and related scientific environments. + </longdescription> + <longdescription lang="de"> + Die Kategorie sci-biology enthält Software, die in biologischen + und verwandten wissenschaftlichen Umgebungen genutzt werden kann. + </longdescription> + <longdescription lang="es"> + La categoría sci-biology contiene programas que pueden ser utilizados en + entornos relacionados con la biología. + </longdescription> + <longdescription lang="ja"> + sci-biologyカテゴリーには生物学の科学的な分野に利用される + ソフトウェアが含まれています。 + </longdescription> + <longdescription lang="nl"> + De sci-biology categorie bevat software, die in biologische en gerelateerde + wetenschappelijke omgevingen gebruikt kan worden. + </longdescription> + <longdescription lang="fr"> + La catégorie sci-biology contient des logiciels pour les sciences + biologiques et les disciplines connexes. + </longdescription> + <longdescription lang="vi"> + Nhóm sci-biology chứa các phần mềm sinh học và liên quan đến khoa học. + </longdescription> + <longdescription lang="sk"> + Kategória sci-biology obsahuje programy, ktoré sa používajú pri + biologickom výskume. + </longdescription> + <longdescription lang="it"> + La categoria sci-biology contiene programmi per la biologia. + </longdescription> + <longdescription lang="pt"> + A categoria sci-biology contém programas que podem ser usados + em ambientes relacionados a biologia. + </longdescription> + <longdescription lang="pl"> + Kategoria sci-biology zawiera programy naukowe związane z biologią. + </longdescription> +</catmetadata> + diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest new file mode 100644 index 000000000000..87d089e34446 --- /dev/null +++ b/sci-biology/mira/Manifest @@ -0,0 +1,2 @@ +DIST mira-4.0.2.tar.bz2 10368046 SHA256 a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80 SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e WHIRLPOOL d038472f9b129e97883f59c471df51f07315ee38eda5a9e804cdd2d33988306162b1bb1dde2cb7fd510c82be5734240dfd69364d39865a47af439762c7154747 +DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2 diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch new file mode 100644 index 000000000000..9bbd267cf4c8 --- /dev/null +++ b/sci-biology/mira/files/mira-3.0.0-asneeded.patch @@ -0,0 +1,56 @@ +http://bugs.gentoo.org/show_bug.cgi?id=305547 + +--- config/m4/ax_lib_expat.m4 ++++ config/m4/ax_lib_expat.m4 +@@ -96,6 +99,7 @@ + + EXPAT_CFLAGS="" + EXPAT_LDFLAGS="" ++ EXPAT_LIBS="" + EXPAT_VERSION="" + + dnl +@@ -105,7 +109,8 @@ + + if test -n "$expat_prefix"; then + expat_include_dir="$expat_prefix/include" +- expat_lib_flags="-L$expat_prefix/lib -lexpat" ++ expat_lib_flags="-L$expat_prefix/lib" ++ expat_libs="-lexpat" + run_expat_test="yes" + elif test "$expat_requested" = "yes"; then + if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then +@@ -126,6 +131,8 @@ + saved_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS $expat_lib_flags" + ++ saved_LIBS="$LIBS" ++ LIBS="$LIBS $expat_libs" + dnl + dnl Check Expat headers + dnl +@@ -171,7 +178,8 @@ + ]] + )], + [ + EXPAT_LDFLAGS="$expat_lib_flags" ++ EXPAT_LIBS="$expat_libs" + expat_lib_found="yes" + AC_MSG_RESULT([found]) + ], +@@ -185,6 +193,7 @@ + + CPPFLAGS="$saved_CPPFLAGS" + LDFLAGS="$saved_LDFLAGS" ++ LIBS="$saved_LIBS" + fi + + AC_MSG_CHECKING([for Expat XML Parser]) +@@ -194,6 +203,7 @@ + + AC_SUBST([EXPAT_CFLAGS]) + AC_SUBST([EXPAT_LDFLAGS]) ++ AC_SUBST([EXPAT_LIBS]) + + HAVE_EXPAT="yes" + else diff --git a/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch new file mode 100644 index 000000000000..27fb36467c8f --- /dev/null +++ b/sci-biology/mira/files/mira-3.2.1-boost-1.50.patch @@ -0,0 +1,52 @@ + config/m4/ax_boost_regex.m4 | 4 ++-- + src/examples_programming/Makefile.am | 2 +- + src/examples_programming/Makefile.in | 2 +- + 3 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4 +index 3c4a999..a3bb19b 100644 +--- a/config/m4/ax_boost_regex.m4 ++++ b/config/m4/ax_boost_regex.m4 +@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX], + for libextension in `ls $BOOSTLIBDIR/libboost_regex*.{so,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + if test "x$link_regex" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + fi +diff --git a/src/examples_programming/Makefile.am b/src/examples_programming/Makefile.am +index d77daaf..09c9965 100644 +--- a/src/examples_programming/Makefile.am ++++ b/src/examples_programming/Makefile.am +@@ -11,7 +11,7 @@ AM_LDFLAGS= -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L.. + + mira_101.C: + mira_101_SOURCES= mira_101.C +-mira_101_LDADD= -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) ++mira_101_LDADD= -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system + + read_101.C: + read_101_SOURCES= read_101.C +diff --git a/src/examples_programming/Makefile.in b/src/examples_programming/Makefile.in +index 27e6515..7dae4c4 100644 +--- a/src/examples_programming/Makefile.in ++++ b/src/examples_programming/Makefile.in +@@ -222,7 +222,7 @@ AM_CXXFLAGS = $(BOOST_CPPFLAGS) + INCLUDES = -I$(top_srcdir)/src $(all_includes) + AM_LDFLAGS = -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../examine/ -L../EdIt/ -L../caf/ -L../knn_abi373 -L../knn_alf $(BOOST_LDFLAGS) + mira_101_SOURCES = mira_101.C +-mira_101_LDADD = -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) ++mira_101_LDADD = -lmira -lmiraEdIt -lmiraExamine -lmirasupport -lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz $(BOOST_THREAD_LIB) $(BOOST_REGEX_LIB) $(BLOODYDARWINHACK) -lboost_system + read_101_SOURCES = read_101.C + read_101_LDADD = -lmirasupport -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio -lm -lz + readpool_101_SOURCES = readpool_101.C diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch new file mode 100644 index 000000000000..427192294c81 --- /dev/null +++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch @@ -0,0 +1,24 @@ + config/m4/ax_boost_regex.m4 | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4 +index 1ac06af..5b7be93 100644 +--- a/config/m4/ax_boost_regex.m4 ++++ b/config/m4/ax_boost_regex.m4 +@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX], + for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + if test "x$link_regex" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + fi diff --git a/sci-biology/mira/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch new file mode 100644 index 000000000000..14feb0284c9f --- /dev/null +++ b/sci-biology/mira/files/mira-4.0.2-cout.patch @@ -0,0 +1,16 @@ + src/progs/quirks.C | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/progs/quirks.C b/src/progs/quirks.C +index 47e5ee8..060b6f3 100644 +--- a/src/progs/quirks.C ++++ b/src/progs/quirks.C +@@ -25,6 +25,8 @@ + + #include <boost/filesystem.hpp> + ++#include <iostream> ++ + // make the "tcmalloc: large alloc" messages from TCMallom disappear + // by setting the reporting environment variable to a very large value + // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1 diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml new file mode 100644 index 000000000000..a2c7c1a0a6a7 --- /dev/null +++ b/sci-biology/mira/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">mira-assembler</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild new file mode 100644 index 000000000000..3fa476c026a2 --- /dev/null +++ b/sci-biology/mira/mira-4.0.2.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MIRA_3RDPARTY_PV="06-07-2012" +MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) + +inherit autotools eutils multilib + +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" +HOMEPAGE="http://www.chevreux.org/projects_mira.html" +SRC_URI=" + http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 + mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" +# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 +# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" + +S="${WORKDIR}"/"${PN}"-"${MY_PV}" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc" + +CDEPEND=" + dev-libs/boost + dev-util/google-perftools" +DEPEND="${CDEPEND} + app-editors/vim-core + dev-libs/expat" +RDEPEND="${CDEPEND}" + +#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED +# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) +DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) + +src_prepare() { + find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die + epatch \ + "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ + "${FILESDIR}"/${P}-cout.patch + + sed \ + -e "s:-O[23]::g" \ + -e "s:-funroll-loops::g" \ + -i configure.ac || die + + eautoreconf +} + +src_configure() { + econf \ + --with-boost="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ + --with-boost-thread=boost_thread-mt +} + +#src_compile() { +# base_src_compile +# # TODO: resolve docbook incompatibility for building docs +# if use doc; then emake -C doc clean docs || die; fi +#} + +src_install() { + default + dodoc ${DOCS[@]} + + dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} + dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} +} + +pkg_postinst() { + einfo "Documentation is no longer built, you can find it at:" + einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" +} diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest new file mode 100644 index 000000000000..c71420fd1e4c --- /dev/null +++ b/sci-biology/mosaik/Manifest @@ -0,0 +1,2 @@ +DIST Mosaik-1.0.1367-source.tar.bz2 8700231 SHA256 2a6ee1d25af835028b71f2518c6a00e929e64e7be6305183dfe0e242a015c750 +DIST Mosaik-1.0.1388-source.tar.bz2 8730164 SHA256 d6a8effa49adac617a388e2132aaf1a6b0679c783574d7df2cbd952a5f96e60c diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml new file mode 100644 index 000000000000..4dfd5b0bdafa --- /dev/null +++ b/sci-biology/mosaik/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="google-code">mosaik-aligner</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mosaik/mosaik-1.0.1367.ebuild b/sci-biology/mosaik/mosaik-1.0.1367.ebuild new file mode 100644 index 000000000000..f43c9b72ac37 --- /dev/null +++ b/sci-biology/mosaik/mosaik-1.0.1367.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies" +HOMEPAGE="http://code.google.com/p/mosaik-aligner/" +SRC_URI="http://mosaik-aligner.googlecode.com/files/Mosaik-${PV}-source.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/${PN}-source" + +src_compile() { + emake -C src || die +# emake -C MosaikTools/c++ || die +# emake -C MosaikTools/perl || die +} + +src_install() { + dobin bin/* || die + + insinto /usr/share/${PN} + doins -r MosaikTools || die + + dodoc README Mosaik-1.0-Documentation.pdf +} diff --git a/sci-biology/mosaik/mosaik-1.0.1388.ebuild b/sci-biology/mosaik/mosaik-1.0.1388.ebuild new file mode 100644 index 000000000000..4c9664caa80a --- /dev/null +++ b/sci-biology/mosaik/mosaik-1.0.1388.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies" +HOMEPAGE="http://code.google.com/p/mosaik-aligner/" +SRC_URI="http://mosaik-aligner.googlecode.com/files/Mosaik-${PV}-source.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/mosaik-aligner" + +src_prepare() { + sed -i 's/-static//' src/includes/linux.inc || die +} + +src_compile() { + emake -C src || die +# emake -C MosaikTools/c++ || die +# emake -C MosaikTools/perl || die +} + +src_install() { + dobin bin/* || die + + insinto /usr/share/${PN} + doins -r MosaikTools || die + + dodoc README Mosaik-1.0-Documentation.pdf +} diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest new file mode 100644 index 000000000000..e0cf36aefaf6 --- /dev/null +++ b/sci-biology/mothur/Manifest @@ -0,0 +1,2 @@ +DIST mothur-1.27.0.zip 7095054 SHA256 7521d0dfc849dc9ef707bf83032e471966914b9833247c49e5d30b8d9281a6c7 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 WHIRLPOOL 32e5c9c2be6e593b2dbc64be38c49b4dec3ea048cd3c972cf948136b394608a2dc168be58b7fb500a17fc6a152b7777fcd09b3f9fb3bf60c7dd92d043a4bf361 +DIST mothur-1.6.0.zip 465292 SHA256 75583a204d199ddcf9b845fc0adbaf240d7b1f08584fed5e6465982f68ffe121 SHA512 f775ff64991f00423108f295eca640f5c5d85a38e01b31af44ddf91f8897968e934f79899a21606dfd81fdc3e91751df277237e94d56d74f862e472e8da3386c WHIRLPOOL 31ca8decceb38ebd17f15c5f937df70b501833311cbf1aec794bb174d409a0c01e77abb399347781ad820c06411e56c566382a32818a0c57214aad2ad16cc132 diff --git a/sci-biology/mothur/files/mothur-1.27.0-makefile.patch b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch new file mode 100644 index 000000000000..52a02585df14 --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch @@ -0,0 +1,52 @@ + makefile | 14 ++++++-------- + 1 files changed, 6 insertions(+), 8 deletions(-) + +diff --git a/makefile b/makefile +index db7c904..109488f 100644 +--- a/makefile ++++ b/makefile +@@ -10,18 +10,18 @@ + # + + USEMPI ?= no +-64BIT_VERSION ?= yes ++64BIT_VERSION ?= no + USEREADLINE ?= yes + CYGWIN_BUILD ?= no + USECOMPRESSION ?= no + MOTHUR_FILES="\"Enter_your_default_path_here\"" + RELEASE_DATE = "\"8/8/2012\"" + VERSION = "\"1.27.0\"" +-FORTAN_COMPILER = gfortran +-FORTRAN_FLAGS = ++FORTAN_COMPILER = ${FC} ++FORTRAN_FLAGS = ${FCFLAGS} + + # Optimize to level 3: +-CXXFLAGS += -O3 ++#CXXFLAGS += -O3 + + ifeq ($(strip $(64BIT_VERSION)),yes) + #if you are using centos uncomment the following lines +@@ -69,7 +69,7 @@ endif + + + ifeq ($(strip $(USEMPI)),yes) +- CXX = mpic++ ++# CXX = mpic++ + CXXFLAGS += -DUSE_MPI + endif + +@@ -95,11 +95,9 @@ OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) + OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) + OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f)) + +-mothur : fortranSource $(OBJECTS) uchime ++mothur : fortranSource $(OBJECTS) + $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) + +- strip mothur +- + uchime: + cd uchime_src && ./mk && mv uchime .. && cd .. + diff --git a/sci-biology/mothur/files/mothur-1.27.0-overflows.patch b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch new file mode 100644 index 000000000000..0b612cf7b529 --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch @@ -0,0 +1,93 @@ + chimerauchimecommand.cpp | 2 +- + clearcutcommand.cpp | 32 ++++++++++++++++---------------- + 2 files changed, 17 insertions(+), 17 deletions(-) + +diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp +index bd31c19..2070840 100644 +--- a/chimerauchimecommand.cpp ++++ b/chimerauchimecommand.cpp +@@ -1264,7 +1264,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc + } + + if (ucl) { +- char* tempucl = new char[5]; ++ char* tempucl = new char[6]; + strcpy(tempucl, "--ucl"); + cPara.push_back(tempucl); + } +diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp +index 6a0eb25..2e8164e 100644 +--- a/clearcutcommand.cpp ++++ b/clearcutcommand.cpp +@@ -269,35 +269,35 @@ int ClearcutCommand::execute() { + + vector<char*> cPara; + +- char* tempClearcut = new char[8]; ++ char* tempClearcut = new char[16]; + strcpy(tempClearcut, "clearcut"); + cPara.push_back(tempClearcut); + + //you gave us a distance matrix +- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); } ++ if (phylipfile != "") { char* temp = new char[16]; strcpy(temp, "--distance"); cPara.push_back(temp); } + + //you gave us a fastafile +- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); } ++ if (fastafile != "") { char* temp = new char[16]; strcpy(temp, "--alignment"); cPara.push_back(temp); } + +- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); } +- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); } +- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); } ++ if (version) { char* temp = new char[16]; strcpy(temp, "--version"); cPara.push_back(temp); } ++ if (verbose) { char* temp = new char[16]; strcpy(temp, "--verbose"); cPara.push_back(temp); } ++ if (quiet) { char* temp = new char[16]; strcpy(temp, "--quiet"); cPara.push_back(temp); } + if (seed != "*") { + string tempSeed = "--seed=" + seed; + char* temp = new char[tempSeed.length()]; + strcpy(temp, tempSeed.c_str()); + cPara.push_back(temp); + } +- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); } +- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } +- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } ++ if (norandom) { char* temp = new char[16]; strcpy(temp, "--norandom"); cPara.push_back(temp); } ++ if (shuffle) { char* temp = new char[16]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } ++ if (neighbor) { char* temp = new char[16]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } + + string tempIn = "--in=" + inputFile; + char* tempI = new char[tempIn.length()]; + strcpy(tempI, tempIn.c_str()); + cPara.push_back(tempI); + +- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); } ++ if (stdoutWanted) { char* temp = new char[16]; strcpy(temp, "--stdout"); cPara.push_back(temp); } + else{ + string tempOut = "--out=" + outputName; + +@@ -306,10 +306,10 @@ int ClearcutCommand::execute() { + cPara.push_back(temp); + } + +- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); } +- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); } +- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); } +- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); } ++ if (DNA) { char* temp = new char[16]; strcpy(temp, "--DNA"); cPara.push_back(temp); } ++ if (protein) { char* temp = new char[16]; strcpy(temp, "--protein"); cPara.push_back(temp); } ++ if (jukes) { char* temp = new char[16]; strcpy(temp, "--jukes"); cPara.push_back(temp); } ++ if (kimura) { char* temp = new char[16]; strcpy(temp, "--kimura"); cPara.push_back(temp); } + if (matrixout != "") { + string tempMatrix = "--matrixout=" + outputDir + matrixout; + char* temp = new char[tempMatrix.length()]; +@@ -326,8 +326,8 @@ int ClearcutCommand::execute() { + cPara.push_back(temp); + } + +- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); } +- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); } ++ if (expblen) { char* temp = new char[16]; strcpy(temp, "--expblen"); cPara.push_back(temp); } ++ if (expdist) { char* temp = new char[16]; strcpy(temp, "--expdist"); cPara.push_back(temp); } + + char** clearcutParameters; + clearcutParameters = new char*[cPara.size()]; diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/mothur/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild new file mode 100644 index 000000000000..3de23de65d51 --- /dev/null +++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 toolchain-funcs + +DESCRIPTION="A suite of algorithms for ecological bioinformatics" +HOMEPAGE="http://www.mothur.org/" +SRC_URI="http://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="mpi +readline" +KEYWORDS="amd64 ~x86" + +RDEPEND=" + sci-biology/uchime + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + app-arch/unzip" + +S=${WORKDIR}/Mothur.source + +pkg_setup() { + fortran-2_pkg_setup + use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX) + use amd64 && append-cppflags -DBIT_VERSION +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-overflows.patch +} + +src_compile() { + emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline) +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/mothur/mothur-1.6.0.ebuild b/sci-biology/mothur/mothur-1.6.0.ebuild new file mode 100644 index 000000000000..034f6fae1a65 --- /dev/null +++ b/sci-biology/mothur/mothur-1.6.0.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="A suite of algorithms for ecological bioinformatics" +HOMEPAGE="http://www.mothur.org/" +SRC_URI="mirror://gentoo/${P}.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="app-arch/unzip" +RDEPEND="" + +S="${WORKDIR}/mothur-v.${PV}" + +src_prepare() { + sed \ + -e 's/CC_OPTIONS =.*$/CC_OPTIONS = ${CXXFLAGS} /' \ + -e 's|CC = g++|CC = '$(tc-getCXX)'|' \ + -e '/^LNK_OPTIONS/s:$:${LDFLAGS}:g' \ + -i makefile || die +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest new file mode 100644 index 000000000000..d932da527753 --- /dev/null +++ b/sci-biology/mrbayes/Manifest @@ -0,0 +1 @@ +DIST mrbayes-3.1.2.tar.gz 545968 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 WHIRLPOOL 45c9750a1e3e3ac85a1085bcaf8fc5c108b730a3dfa2f9e8d81cea8720bd6f02815c3145c19ee6c369a43f4565c2b234ec81cd5721672abded17186264de2e3f diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch new file mode 100644 index 000000000000..2f8bab1e7665 --- /dev/null +++ b/sci-biology/mrbayes/files/mb_readline_312.patch @@ -0,0 +1,37 @@ +Index: Makefile +=================================================================== +RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v +retrieving revision 3.23 +retrieving revision 3.24 +diff -U2 -r3.23 -r3.24 +--- Makefile 22 Dec 2005 16:13:06 -0000 3.23 ++++ Makefile 3 Jan 2006 16:43:13 -0000 3.24 +@@ -50,4 +50,5 @@ + ifeq ($(strip $(USEREADLINE)),yes) + CFLAGS += -DUSE_READLINE ++# CFLAGS += -DCOMPLETIONMATCHES + LIBS += -lncurses -lreadline + endif +Index: bayes.c +=================================================================== +RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v +retrieving revision 3.39 +retrieving revision 3.40 +diff -U2 -r3.39 -r3.40 +--- bayes.c 23 Dec 2005 16:26:28 -0000 3.39 ++++ bayes.c 3 Jan 2006 16:43:13 -0000 3.40 +@@ -382,9 +382,11 @@ + char **readline_completion(const char *text, int start, int stop) { + char **matches = (char **) NULL; +- ++ ++#ifdef COMPLETIONMATCHES + if(start == 0) +- matches = rl_completion_matches (text, command_generator); ++ matches = rl_completion_matches (text, command_generator); ++#endif + +- return (matches); ++ return (matches); + } + #endif diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml new file mode 100644 index 000000000000..8a6a5b986dc7 --- /dev/null +++ b/sci-biology/mrbayes/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> +MrBayes is a program for the Bayesian estimation of phylogeny. +Bayesian inference of phylogeny is based upon a quantity called the +posterior probability distribution of trees, which is the probability of a +tree conditioned on the observations. The conditioning is accomplished using +Bayes's theorem. The posterior probability distribution of trees is +impossible to calculate analytically; instead, MrBayes uses a simulation +technique called Markov chain Monte Carlo (or MCMC) to approximate the +posterior probabilities of trees. +</longdescription> + <upstream> + <remote-id type="sourceforge">mrbayes</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild new file mode 100644 index 000000000000..b4303b8f90b3 --- /dev/null +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Bayesian Inference of Phylogeny" +HOMEPAGE="http://mrbayes.csit.fsu.edu/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="debug mpi readline" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND=" + sys-libs/ncurses + mpi? ( virtual/mpi ) + readline? ( sys-libs/readline:0 )" +RDEPEND="${DEPEND}" + +src_prepare() { + use readline && epatch "${FILESDIR}"/mb_readline_312.patch + sed -e 's:-ggdb::g' -i Makefile || die +} + +src_compile() { + local myconf mycc + + if use mpi; then + mycc=mpicc + else + mycc=$(tc-getCC) + fi + + use mpi && myconf="MPI=yes" + use readline || myconf="${myconf} USEREADLINE=no" + use debug && myconf="${myconf} DEBUG=yes" + emake \ + OPTFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + CC=${mycc} \ + ${myconf} +} + +src_install() { + dobin mb + insinto /usr/share/${PN} + doins *.nex +} diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild new file mode 100644 index 000000000000..0c5a5015ecc7 --- /dev/null +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Bayesian Inference of Phylogeny" +HOMEPAGE="http://mrbayes.csit.fsu.edu/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="debug mpi readline" + +DEPEND=" + sys-libs/ncurses + mpi? ( virtual/mpi ) + readline? ( sys-libs/readline:0= )" +RDEPEND="${DEPEND}" + +src_prepare() { + if use mpi; then + sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support." + fi + if ! use readline; then + sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \ + -i Makefile || die "Patching readline support." + else + # Only needed for OSX with an old (4.x) version of + # libreadline, but it doesn't hurt for other distributions. + epatch "${FILESDIR}"/mb_readline_312.patch + fi + sed -e 's:-ggdb::g' -i Makefile || die +} + +src_compile() { + local myconf mycc + + if use mpi; then + mycc=mpicc + else + mycc=$(tc-getCC) + fi + + use mpi && myconf="MPI=yes" + use readline || myconf="${myconf} USEREADLINE=no" + use debug && myconf="${myconf} DEBUG=yes" + emake \ + OPTFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + CC=${mycc} \ + ${myconf} +} + +src_install() { + dobin mb + insinto /usr/share/${PN} + doins *.nex +} diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest new file mode 100644 index 000000000000..bae1ccf2f14c --- /dev/null +++ b/sci-biology/mummer/Manifest @@ -0,0 +1,3 @@ +DIST MUMmer3.20.tar.gz 3155446 SHA256 9c7880b4ce25ef3c6bed9ccdc26f1c4d7e74eb0ef1ce403907790c0f96c0f260 +DIST MUMmer3.21.tar.gz 3155965 SHA256 7fb1456c8c21eab4913a522e4b79bc5c84b7373feb54614a7003b16d47dc23b8 +DIST MUMmer3.22.tar.gz 3156338 SHA256 429022a8c6a7ae55fb1dd94dbdac1b21f662d6278668f5531c735911d9fc77da diff --git a/sci-biology/mummer/files/3.22-ldflags.patch b/sci-biology/mummer/files/3.22-ldflags.patch new file mode 100644 index 000000000000..d3c4a60a1adb --- /dev/null +++ b/sci-biology/mummer/files/3.22-ldflags.patch @@ -0,0 +1,16 @@ +diff --git a/src/tigr/Makefile b/src/tigr/Makefile +index cf6b9ca..5b28d1e 100644 +--- a/src/tigr/Makefile ++++ b/src/tigr/Makefile +@@ -9,9 +9,9 @@ AUX_BIN_DIR := $(CURDIR) + endif + + OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@ +-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \ ++BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \ + chmod 755 $(BIN_DIR)/$@ +-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \ ++AUX_BIN_RULE = $(CXX) $(LDFLAGS) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \ + chmod 755 $(AUX_BIN_DIR)/$@ + VPATH := $(AUX_BIN_DIR):$(BIN_DIR) + diff --git a/sci-biology/mummer/files/3.22-prll.patch b/sci-biology/mummer/files/3.22-prll.patch new file mode 100644 index 000000000000..3b24ee40214a --- /dev/null +++ b/sci-biology/mummer/files/3.22-prll.patch @@ -0,0 +1,56 @@ +diff --git a/Makefile b/Makefile +index 4db4977..bbd00ed 100644 +--- a/Makefile ++++ b/Makefile +@@ -114,15 +114,15 @@ install: all + + + kurtz: +- cd $(KURTZ_SRC_DIR); $(MAKE) mummer ++ $(MAKE) -C $(KURTZ_SRC_DIR) mummer + + + scripts: +- cd $(SCRIPT_DIR); $(MAKE) all ++ $(MAKE) -C $(SCRIPT_DIR) all + + + tigr: +- cd $(TIGR_SRC_DIR); $(MAKE) all ++ $(MAKE) -C $(TIGR_SRC_DIR) all + + + uninstall: clean +diff --git a/src/kurtz/Makefile b/src/kurtz/Makefile +index 85dfc16..5bff793 100644 +--- a/src/kurtz/Makefile ++++ b/src/kurtz/Makefile +@@ -1,7 +1,7 @@ + all: +- cd libbasedir; $(MAKE) all +- cd streesrc; $(MAKE) all +- cd mm3src; $(MAKE) all ++ $(MAKE) -C libbasedir all ++ $(MAKE) -C streesrc all ++ $(MAKE) -C mm3src all + + clean: + rm -f *~ +@@ -10,11 +10,11 @@ clean: + cd mm3src; $(MAKE) clean + + mummer: +- cd libbasedir; $(MAKE) libbase.a +- cd streesrc; $(MAKE) libstree.a +- cd mm3src; $(MAKE) mummer ++ $(MAKE) -C libbasedir libbase.a ++ $(MAKE) -C streesrc libstree.a ++ $(MAKE) -C mm3src mummer + + splintall: +- cd libbasedir; ${MAKE} splintall +- cd streesrc; ${MAKE} splintall +- cd mm3src; ${MAKE} splintall ++ $(MAKE) -C libbasedir splintall ++ $(MAKE) -C streesrc splintall ++ $(MAKE) -C mm3src splintall diff --git a/sci-biology/mummer/files/mummer-3.20-gcc43.patch b/sci-biology/mummer/files/mummer-3.20-gcc43.patch new file mode 100644 index 000000000000..4d3edb41e46a --- /dev/null +++ b/sci-biology/mummer/files/mummer-3.20-gcc43.patch @@ -0,0 +1,12 @@ +--- src/tigr/show-diff.cc.orig 2008-06-16 17:55:34.000000000 +0000 ++++ src/tigr/show-diff.cc 2008-06-16 17:56:25.000000000 +0000 +@@ -14,6 +14,8 @@ + #include <cstdlib> + #include <cassert> + #include <climits> ++#include <algorithm> ++ + using namespace std; + + + diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml new file mode 100644 index 000000000000..f82b462e1f95 --- /dev/null +++ b/sci-biology/mummer/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">mummer</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/mummer/mummer-3.20.ebuild b/sci-biology/mummer/mummer-3.20.ebuild new file mode 100644 index 000000000000..2f566667ceca --- /dev/null +++ b/sci-biology/mummer/mummer-3.20.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils + +MY_P="MUMmer${PV}" +DESCRIPTION="A rapid whole genome aligner" +HOMEPAGE="http://mummer.sourceforge.net/" +SRC_URI="mirror://sourceforge/mummer/${MY_P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="doc" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="app-shells/tcsh" + +S="${WORKDIR}/${MY_P}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-gcc43.patch + # Warning: package uses CPPFLAGS on c in addition to cpp, despite the name + sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \ + -e 's/LDFLAGS =$//' "${S}/Makefile" +} + +src_compile() { + emake || die "emake failed" + + sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \ + -e 's|\(set bindir = \).*|\1/usr/bin|' \ + -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \ + -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \ + scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die "Failed to replace paths" + sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh +} + +src_install() { + dobin nucmer2xfig show-coords mapview show-snps run-mummer{1,3} \ + exact-tandems promer repeat-match show-aligns gaps mummer \ + show-tiling mgaps nucmer mummerplot delta-filter combineMUMs aux_bin/* || die + newbin annotate mummer-annotate || die + + insinto /usr/share/${PN}/scripts + doins scripts/{*.awk,*.csh,*.pl} + insinto /usr/share/${PN}/lib + doins scripts/Foundation.pm || die + + dodoc ACKNOWLEDGEMENTS ChangeLog README + insinto /usr/share/doc/${PF} + use doc && doins -r docs +} diff --git a/sci-biology/mummer/mummer-3.21.ebuild b/sci-biology/mummer/mummer-3.21.ebuild new file mode 100644 index 000000000000..64eaf1b3646a --- /dev/null +++ b/sci-biology/mummer/mummer-3.21.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit eutils + +DESCRIPTION="A rapid whole genome aligner" +HOMEPAGE="http://mummer.sourceforge.net/" +SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="doc" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="app-shells/tcsh" + +S="${WORKDIR}/MUMmer${PV}" + +src_unpack() { + unpack ${A} + # Warning: package uses CPPFLAGS on c as well as cpp, despite the name + sed -i -e 's/CPPFLAGS =/CPPFLAGS = ${CFLAGS} /' \ + -e 's/LDFLAGS =$//' "${S}/Makefile" || die +} + +src_compile() { + emake || die + + sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \ + -e 's|\(set bindir = \).*|\1/usr/bin|' \ + -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \ + -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \ + scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die + mv annotate mummer-annotate || die + sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die +} + +src_install() { + dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die + + insinto /usr/share/${PN}/scripts + doins scripts/{*.awk,*.csh,*.pl} || die + insinto /usr/share/${PN}/lib + doins scripts/Foundation.pm || die + + dodoc ACKNOWLEDGEMENTS ChangeLog README + insinto /usr/share/doc/${PF} + use doc && doins -r docs +} diff --git a/sci-biology/mummer/mummer-3.22-r1.ebuild b/sci-biology/mummer/mummer-3.22-r1.ebuild new file mode 100644 index 000000000000..ad60acce35a4 --- /dev/null +++ b/sci-biology/mummer/mummer-3.22-r1.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit eutils flag-o-matic + +DESCRIPTION="A rapid whole genome aligner" +HOMEPAGE="http://mummer.sourceforge.net/" +SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="doc" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="app-shells/tcsh" + +S="${WORKDIR}/MUMmer${PV}" + +src_prepare() { + use amd64 && append-flags -DSIXTYFOURBITS + + epatch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-ldflags.patch + + sed \ + -e '/^CFLAGS/d' \ + -e '/^CXXFLAGS/d' \ + -e '/^LDFLAGS/d' \ + -i Makefile || die +} + +src_compile() { + emake || die + + sed -i -e 's|\($AUX_BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($BIN_DIR = "\).*"|\1/usr/bin"|' \ + -e 's|\($SCRIPT_DIR = "\).*"|\1/usr/share/'${PN}'/lib"|' \ + -e 's|\(set bindir = \).*|\1/usr/bin|' \ + -e 's|\(set scriptdir = \).*|\1/usr/share/'${PN}'/scripts|' \ + -e 's|\(use lib "\).*"|\1/usr/share/'${PN}'/lib"|' \ + scripts/* exact-tandems mapview mummerplot nucmer promer run-mummer{1,3} || die + mv annotate mummer-annotate || die + sed -i 's|$bindir/annotate|$bindir/mummer-annotate|' run-mummer1 scripts/run-mummer1.csh || die +} + +src_install() { + dobin $(find . -maxdepth 1 -type f -executable) aux_bin/* || die + + insinto /usr/share/${PN}/scripts + doins scripts/{*.awk,*.csh,*.pl} || die + insinto /usr/share/${PN}/lib + doins scripts/Foundation.pm || die + + dodoc ACKNOWLEDGEMENTS ChangeLog README || die + insinto /usr/share/doc/${PF} + if use doc; then + doins -r docs || die + fi +} diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest new file mode 100644 index 000000000000..2dbd476bb5b4 --- /dev/null +++ b/sci-biology/muscle/Manifest @@ -0,0 +1 @@ +DIST muscle3.8.31_src.tar.gz 515267 SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad SHA512 2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce WHIRLPOOL daea88aaeaaacf5a2da68484010091ae46c69713659f92f45e5e2096af9e7d8c645d14e5b6c4c8e73e4df35a086dee823fcab6d442cd3881b773fb0113ce897d diff --git a/sci-biology/muscle/files/3.7-bufferoverflow.patch b/sci-biology/muscle/files/3.7-bufferoverflow.patch new file mode 100644 index 000000000000..670ad64959cb --- /dev/null +++ b/sci-biology/muscle/files/3.7-bufferoverflow.patch @@ -0,0 +1,26 @@ +diff --git a/globalslinux.cpp b/globalslinux.cpp +index 63baaa1..b1cfcb0 100644 +--- a/globalslinux.cpp ++++ b/globalslinux.cpp +@@ -156,7 +156,7 @@ double GetRAMSizeMB() + } + return DEFAULT_RAM; + } +- int Bytes = atoi(pMem+9)*1000; ++ long Bytes = atol(pMem+9)*1000; + return ((double) Bytes)/1e6; + } + +diff --git a/progress.cpp b/progress.cpp +index a0e91bb..f9b093e 100644 +--- a/progress.cpp ++++ b/progress.cpp +@@ -41,7 +41,7 @@ const char *MemToStr(double MB) + if (MB < 0) + return ""; + +- static char Str[9]; ++ static char Str[16]; + static double MaxMB = 0; + static double RAMMB = 0; + diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch new file mode 100644 index 000000000000..7c0e7308df54 --- /dev/null +++ b/sci-biology/muscle/files/3.8.31-make.patch @@ -0,0 +1,26 @@ +diff --git a/src/mk b/src/mk +index 475d25a..d4b7e83 100755 +--- a/src/mk ++++ b/src/mk +@@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln + rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt + for CPPName in $CPPNames + do +- echo $CPPName >> /dev/tty +- g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt ++ echo "${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o" ++ ${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o + done + + LINK_OPTS= + if [ `uname -s` == Linux ] ; then + LINK_OPTS=-static + fi +-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt +-tail muscle.make.stderr.txt + +-strip muscle +-ls -lh muscle +-sum muscle ++echo "${CXX} ${LDFLAGS} -o muscle $ObjNames" ++${CXX} ${LDFLAGS} -o muscle $ObjNames diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/muscle/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild new file mode 100644 index 000000000000..555419da883f --- /dev/null +++ b/sci-biology/muscle/muscle-3.8.31.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_P="${PN}${PV}_src" + +DESCRIPTION="Multiple sequence comparison by log-expectation" +HOMEPAGE="http://www.drive5.com/muscle/" +SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="" + +RDEPEND="!sci-libs/libmuscle" +DEPEND="" + +S="${WORKDIR}"/${PN}${PV}/src + +src_prepare() { + epatch "${FILESDIR}"/${PV}-make.patch + tc-export CXX +} + +src_install() { + dobin "${PN}" + dodoc *.txt +} diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest new file mode 100644 index 000000000000..b4e27e229585 --- /dev/null +++ b/sci-biology/ncbi-tools/Manifest @@ -0,0 +1 @@ +DIST ncbi-tools-2.2.26.tar.gz 68691452 SHA256 d8fffac25efc8ca894c707c840a4797a8a949ae6fd983d2f91c9972f788efb7d SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 WHIRLPOOL 6f390a4487b7ebf9d5ca31018f3b33602a695e4b0a4b090952fec9c7e8c3956edc197e75ffd32588f9431cc04b4262a2ca2e3b0ba50dd622ed73a4da6655a956 diff --git a/sci-biology/ncbi-tools/files/21ncbi-r1 b/sci-biology/ncbi-tools/files/21ncbi-r1 new file mode 100644 index 000000000000..d4de68e6081a --- /dev/null +++ b/sci-biology/ncbi-tools/files/21ncbi-r1 @@ -0,0 +1,6 @@ +# Location of the formatdb data sets +BLASTDB="/usr/share/ncbi/formatdb" +# Location of the BLAST matrixes. +BLASTMAT="/usr/share/ncbi/data" +# Location of the ".ncbi.rc" file which sets the default path for shared data. +NCBI=/etc/ncbi diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch new file mode 100644 index 000000000000..bbc4623609c8 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch @@ -0,0 +1,81 @@ + corelib/ncbilcl.beos | 2 +- + corelib/ncbilcl.hlx | 2 +- + corelib/ncbilcl.lnx | 4 ++-- + corelib/ncbilcl.plx | 2 +- + corelib/ncbilcl.qnx | 2 +- + 5 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/corelib/ncbilcl.beos b/corelib/ncbilcl.beos +index f720567..fe6346f 100644 +--- a/corelib/ncbilcl.beos ++++ b/corelib/ncbilcl.beos +@@ -77,7 +77,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.hlx b/corelib/ncbilcl.hlx +index 1492f93..0e98fb6 100644 +--- a/corelib/ncbilcl.hlx ++++ b/corelib/ncbilcl.hlx +@@ -67,7 +67,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-/*#define _SVID_SOURCE 1 */ ++/*#define _DEFAULT_SOURCE 1 */ + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.lnx b/corelib/ncbilcl.lnx +index 46e2978..b3256b3 100644 +--- a/corelib/ncbilcl.lnx ++++ b/corelib/ncbilcl.lnx +@@ -65,7 +65,7 @@ + * fixes for new RedHat6.2 + * + * Revision 6.3 2000/02/10 16:36:32 vakatov +-* Added _SVID_SOURCE ++* Added _DEFAULT_SOURCE + * + * Revision 6.2 1999/07/12 05:50:49 vakatov + * Avoid redefinition of #_REENTRANT +@@ -141,7 +141,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + #define _GNU_SOURCE 1 + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.plx b/corelib/ncbilcl.plx +index bf5824c..f2b53e1 100644 +--- a/corelib/ncbilcl.plx ++++ b/corelib/ncbilcl.plx +@@ -68,7 +68,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-/*#define _SVID_SOURCE 1 */ ++/*#define _DEFAULT_SOURCE 1 */ + + + /*----------------------------------------------------------------------*/ +diff --git a/corelib/ncbilcl.qnx b/corelib/ncbilcl.qnx +index c3d1f0a..4b27bd1 100644 +--- a/corelib/ncbilcl.qnx ++++ b/corelib/ncbilcl.qnx +@@ -72,7 +72,7 @@ + #endif + + /* good for the EGCS C/C++ compiler on Linux(e.g. putenv(), tempnam() proto) */ +-#define _SVID_SOURCE 1 ++#define _DEFAULT_SOURCE 1 + + + diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch new file mode 100644 index 000000000000..e6763214a6e5 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-bfr-overflow.patch @@ -0,0 +1,103 @@ + cdromlib/cdnewlib.c | 6 +++--- + corelib/ncbierr.c | 2 +- + corelib/ncbisgml.c | 8 ++++---- + demo/errhdr.c | 2 +- + 4 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c +index 461292c..be4a2d6 100644 +--- a/cdromlib/cdnewlib.c ++++ b/cdromlib/cdnewlib.c +@@ -2676,7 +2676,7 @@ static int CdDevice_FileBuildPath (CdDevice *cddev, char *fpath, const char *fdi + char volname[16]; + volname[0] = '\0'; + if (cddev->volume != NULL) +- strncat(volname,cddev->volume->volume_name,sizeof volname); ++ strncat(volname,cddev->volume->volume_name,sizeof volname - 1); + else + sprintf(volname,"entrez%d",cddev->hint); + if (!FileBuildPath(fpath,volname,NULL)) +@@ -2748,7 +2748,7 @@ static int CdDevice_Init (CdDevice *cddev) + memset((void*)&info,0,sizeof info); + fpath[0] = '\0'; + if (cddev->inf.root !=NULL) +- strncat(fpath,cddev->inf.root,sizeof fpath); ++ strncat(fpath,cddev->inf.root,sizeof fpath - 1); + + if (cddev->ins_volname) + { +@@ -2766,7 +2766,7 @@ static int CdDevice_Init (CdDevice *cddev) + { + fpath[0] = '\0'; + if (cddev->inf.root !=NULL) +- strncat(fpath,cddev->inf.root,sizeof fpath); ++ strncat(fpath,cddev->inf.root,sizeof fpath - 1); + sprintf(volname,"entrez%d",j+1); + FileBuildPath(fpath,volname,NULL); + if (CdTestPath(fpath,&info)) +diff --git a/corelib/ncbierr.c b/corelib/ncbierr.c +index 0429d86..7b96a2e 100644 +--- a/corelib/ncbierr.c ++++ b/corelib/ncbierr.c +@@ -952,7 +952,7 @@ static FILE * ErrMsgRoot_fopen (ErrMsgRoot *ctx) + if (FileLength(file)==0 || (fd = FileOpen(file,s_msg_mode)) == NULL) + { + strcpy(path,info->msgpath); +- strncat(path,file,sizeof(path)); ++ strncat(path,file,sizeof(path) - 1); + fd = FileOpen(path,s_msg_mode); + } + +diff --git a/corelib/ncbisgml.c b/corelib/ncbisgml.c +index 99412be..a653aef 100644 +--- a/corelib/ncbisgml.c ++++ b/corelib/ncbisgml.c +@@ -260,7 +260,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t + } + if (i >= num_sgml_entity) + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); +@@ -279,7 +279,7 @@ NLM_EXTERN char * LIBCALL Nlm_Sgml2Ascii (const char *sgml, char *ascii, size_t + from++; + if (*from == '\0') + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,2, "Unbalanced <> in SGML [%s]",bad); +@@ -335,7 +335,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) + } + if (i >= num_sgml_entity) + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,3,"Unrecognized SGML entity &%s in [%s]",tbuf,bad); +@@ -349,7 +349,7 @@ NLM_EXTERN size_t LIBCALL Nlm_Sgml2AsciiLen (const char *sgml) + from++; + if (*from == '\0') + { +- char bad[SGML_ERROR_MSG_LIM]; ++ char bad[SGML_ERROR_MSG_LIM + 2]; + bad[0] = '\0'; + strncat(bad,sgml,SGML_ERROR_MSG_LIM); + ErrPostEx(SEV_ERROR,E_SGML,2,"Unbalanced <> in SGML [%s]",bad); +diff --git a/demo/errhdr.c b/demo/errhdr.c +index 01cd955..5081489 100644 +--- a/demo/errhdr.c ++++ b/demo/errhdr.c +@@ -41,7 +41,7 @@ int main (int argc, char **argv) + else if (mod[0] == '\0') + { + char *p; +- strncat(mod,argv[i],sizeof mod); ++ strncat(mod,argv[i],sizeof mod - 1); + if ((p = strstr(argv[i],".msg")) != NULL) + *p = '\0'; + } diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch new file mode 100644 index 000000000000..c12feff51af1 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-2.2.26-format-security.patch @@ -0,0 +1,124 @@ + api/alignmgr2.c | 2 +- + api/pgppop.c | 2 +- + api/txalign.c | 10 +++++----- + desktop/seqpanel.c | 4 ++-- + tools/spidey.c | 4 ++-- + 5 files changed, 11 insertions(+), 11 deletions(-) + +diff --git a/api/alignmgr2.c b/api/alignmgr2.c +index 5b43ef3..4b9007e 100644 +--- a/api/alignmgr2.c ++++ b/api/alignmgr2.c +@@ -5616,7 +5616,7 @@ NLM_EXTERN void AlnMgr2PrintSeqAlign(SeqAlignPtr sap, Int4 linesize, Boolean isn + spp = SeqPortNew(bsp, amp->from_row, amp->to_row, amp->strand, seqcode); + ctr = SeqPortRead(spp, (Uint1Ptr)buf, amp->to_row-amp->from_row+1); + buf[ctr] = '\0'; +- fprintf(ofp, buf); ++ fprintf(ofp, "%s", buf); + SeqPortFree(spp); + } + } +diff --git a/api/pgppop.c b/api/pgppop.c +index d16d79d..b359378 100644 +--- a/api/pgppop.c ++++ b/api/pgppop.c +@@ -2994,7 +2994,7 @@ Char DefLine[255]; + if (szSeq){ + if (!DDV_GetSequenceFromParaG(pgp,&szSeq,bspLength,IsAA,NULL, + NULL,NULL)) continue; +- fprintf(fp,szSeq); ++ fprintf(fp, "%s", szSeq); + fprintf(fp,"\n"); + MemFree(szSeq); + } +diff --git a/api/txalign.c b/api/txalign.c +index 5877f9c..cb35fbc 100644 +--- a/api/txalign.c ++++ b/api/txalign.c +@@ -1767,13 +1767,13 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ + Char checkboxBuf[200]; + sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqGi\" value=\"%ld\" onClick=\"synchronizeCheck(this.value, 'getSeqAlignment%ld', 'getSeqGi', this.checked)\">", sip->data.intvalue, query_number_glb); +- sprintf(docbuf+pos,checkboxBuf); ++ sprintf(docbuf+pos,"%s", checkboxBuf); + + pos += StringLen(checkboxBuf); + } + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, +@@ -1790,7 +1790,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + sprintf(HTML_buffer, "<a name = THC%ld></a><a href=\"http://www.tigr.org/docs/tigr-scripts/hgi_scripts/thc_report.spl?est=THC%ld&report_type=n\">", (long) oip->id, (long) oip->id); + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, + tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); +@@ -1799,7 +1799,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + sprintf(HTML_buffer, "<a name = TI%ld></a><a href=\"http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&dopt=fasta&val=%ld\">", (long) oip->id, (long) oip->id); + + html_len = StringLen(HTML_buffer); +- sprintf(docbuf+pos, HTML_buffer); ++ sprintf(docbuf+pos, "%s", HTML_buffer); + pos += html_len; + pos += print_label_to_buffer_all_ex(docbuf+pos, tdp->label, tdp->pos, + tdp->strand, FALSE, TRUE, label_size, num_size, show_strand, strip_semicolon); +@@ -1816,7 +1816,7 @@ static CharPtr DrawTextToBuffer(ValNodePtr tdp_list, CharPtr PNTR m_buf, Boolean + if(options&TXALIGN_HTML&&options&TXALIGN_MASTER&&DbHasGi&&(options&TXALIGN_GET_SEQUENCE)){ + Char checkboxBuf[200]; + sprintf(checkboxBuf, "<input type=\"checkbox\" name=\"getSeqMaster\" value=\"\" onClick=\"uncheckable('getSeqAlignment%ld', 'getSeqMaster')\">", query_number_glb); +- sprintf(docbuf+pos,checkboxBuf); ++ sprintf(docbuf+pos,"%s",checkboxBuf); + + pos += StringLen(checkboxBuf); + } +diff --git a/desktop/seqpanel.c b/desktop/seqpanel.c +index 2e78e13..c7538aa 100644 +--- a/desktop/seqpanel.c ++++ b/desktop/seqpanel.c +@@ -8661,7 +8661,7 @@ WriteAlignmentInterleaveToFileEx + seqbuf, alnbuf, &alnbuf_len, + show_substitutions); + MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len); +- fprintf (fp, printed_line); ++ fprintf (fp, "%s", printed_line); + } + fprintf (fp, "\n"); + start = stop + 1; +@@ -8757,7 +8757,7 @@ extern void WriteAlignmentContiguousToFile + seqbuf, alnbuf, &alnbuf_len, + show_substitutions); + MemCpy (printed_line, alnbuf, alnbuf_len); +- fprintf (fp, printed_line); ++ fprintf (fp, "%s", printed_line); + start = stop + 1; + stop += seq_chars_per_row; + } +diff --git a/tools/spidey.c b/tools/spidey.c +index d6ce62d..ac9f59a 100644 +--- a/tools/spidey.c ++++ b/tools/spidey.c +@@ -2088,7 +2088,7 @@ static void SPI_PrintResult(FILE *ofp, FILE *ofp2, SPI_RegionInfoPtr srip, Biose + fprintf(ofp2, " "); + ctr++; + } +- fprintf(ofp2, buf); ++ fprintf(ofp2, "%s", buf); + if (spp){ + SeqPortFree(spp); + } +@@ -2417,7 +2417,7 @@ static void SPI_PrintHerdResult(FILE *ofp, FILE *ofp2, SPI_mRNAToHerdPtr herd, S + ctr = SeqPortRead(spp, (Uint1Ptr)buf, 10); + if (ctr > 0) + buf[ctr] = '\0'; +- fprintf(ofp2, buf); ++ fprintf(ofp2, "%s", buf); + SeqPortFree(spp); + } + done = TRUE; diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch new file mode 100644 index 000000000000..1cd7976af599 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch @@ -0,0 +1,27 @@ +--- ncbi-20050605/make/makedis.csh 2005-05-13 05:42:12.000000000 +0200 ++++ ncbi/make/makedis.csh 2005-09-20 22:02:38.000000000 +0200 +@@ -472,6 +472,24 @@ + + set net_stat = $status + ++if ("$?NCBI_MT_OTHERLIBS" == "1") then ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ THREAD_OBJ=$NCBI_THREAD_OBJ \ ++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all' ++else ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all' ++endif ++eval echo $CMD ++eval echo $CMD | sh ++ + if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then + echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat + cat <<EOF diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch new file mode 100644 index 000000000000..cb7d1adf9208 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-extra_vib.patch @@ -0,0 +1,37 @@ +--- ncbi-20061015/make/makedis.csh 2006-09-14 17:37:03.000000000 +0200 ++++ ncbi/make/makedis.csh 2007-03-07 21:00:36.090836460 +0100 +@@ -485,6 +485,34 @@ + + set net_stat = $status + ++if ( $net_stat == 0 ) then ++ # Compile additional tools, usually hidden ++ if ( ! $?EXTRA_VIB ) then ++ set EXTRA_VIB = ( asn2all ) ++ endif ++ ++ if ("$?NCBI_MT_OTHERLIBS" == "1") then ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ THREAD_OBJ=$NCBI_THREAD_OBJ \ ++ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' ++ else ++ set CMD='make $MFLG -f makenet.unx \ ++ CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \ ++ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ ++ AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ ++ NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB $EXTRA_VIB' ++ endif ++ eval echo $CMD ++ eval echo $CMD | sh ++ ++ set net_stat = $status ++ ++endif ++ + if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then + echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat + cat <<EOF diff --git a/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch new file mode 100644 index 000000000000..867b203aecb1 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbi-tools-lop.patch @@ -0,0 +1,15 @@ +--- platform/linux-power.ncbi.mk.bak 2005-08-04 22:45:13.000000000 -0500 ++++ platform/linux-power.ncbi.mk 2005-08-04 22:45:35.000000000 -0500 +@@ -9,10 +9,10 @@ + #it appears the flags above do not work anymore with newer libc, + #the new flags should work. Dima. 08/23/01 + NCBI_AR=ar +-NCBI_CC = xlc_r -w -qcpluscmt -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE ++NCBI_CC = gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE + NCBI_CFLAGS1 = -c + NCBI_LDFLAGS1 = -O3 -D_LARGE_FILES +-NCBI_OPTFLAG = -O3 -qmaxmem=-1 -D_LARGE_FILE ++NCBI_OPTFLAG = -O3 -D_LARGE_FILE + NCBI_BIN_MASTER = /vol/stcfs/rchen/LoP/ncbi/bin + NCBI_BIN_COPY = /vol/stcfs/rchen/LoP/ncbi/bin + NCBI_INCDIR = /vol/stcfs/rchen/LoP/ncbi/include diff --git a/sci-biology/ncbi-tools/files/ncbirc b/sci-biology/ncbi-tools/files/ncbirc new file mode 100644 index 000000000000..dd77b452fe74 --- /dev/null +++ b/sci-biology/ncbi-tools/files/ncbirc @@ -0,0 +1,2 @@ +[NCBI] +Data=@GENTOO_PORTAGE_EPREFIX@/usr/share/ncbi/data diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/ncbi-tools/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild new file mode 100644 index 000000000000..5542dd5f67b2 --- /dev/null +++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic prefix toolchain-funcs + +DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/" +SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc static-libs X" + +RDEPEND=" + app-shells/tcsh + dev-lang/perl + media-libs/libpng:0= + X? ( + media-libs/fontconfig + x11-libs/motif:0= + x11-libs/libICE + x11-libs/libX11 + x11-libs/libXft + x11-libs/libXmu + x11-libs/libXt + )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/ncbi" + +EXTRA_VIB="asn2all asn2asn" + +pkg_setup() { + echo + ewarn 'Please note that the NCBI toolkit (and especially the X' + ewarn 'applications) are known to have compilation and run-time' + ewarn 'problems when compiled with agressive compilation flags. The' + ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' + ewarn 'X support is enabled.' + echo +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-extra_vib.patch \ + "${FILESDIR}"/${P}-bfr-overflow.patch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch + + if use ppc || use ppc64; then + epatch "${FILESDIR}"/${PN}-lop.patch + fi + + if ! use X; then + sed \ + -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ + -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ + -i "${S}"/make/makedis.csh || die + else + # X applications segfault on startup on x86 with -O3. + use x86 || replace-flags '-O3' '-O2' + fi + + # Apply user C flags... + cd "${S}"/platform + sed \ + -e "s:-O[s0-9]\?::g" \ + -e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \ + -e 's:-x[A-Z]*::g' \ + -e 's:-pipe::g' \ + -e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \ + -e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \ + -e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \ + -e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \ + -e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \ + -e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \ + -e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \ + -i * || die + + # We use dynamic libraries + sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die + + sed \ + -re "s:/usr(/bin/.*sh):\1:g" \ + -e "s:(/bin/.*sh):${EPREFIX}\1:g" \ + -i $(find "${S}" -type f) || die +} + +src_compile() { + export EXTRA_VIB + cd "${WORKDIR}" + csh ncbi/make/makedis.csh || die + mkdir "${S}"/cgi "${S}"/real || die + mv "${S}"/bin/*.cgi "${S}"/cgi || die + mv "${S}"/bin/*.REAL "${S}"/real || die + cd "${S}"/demo + emake \ + -f ../make/makenet.unx \ + CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ + LDFLAGS="${LDFLAGS}" \ + spidey + cp spidey ../bin/ || die +} + +src_install() { + #sci-geosciences/cdat-lite + mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die + + dobin "${S}"/bin/* + + for i in ${EXTRA_VIB}; do + dobin "${S}"/build/${i} || die "Failed to install binaries." + done + use static-libs && dolib.a "${S}"/lib/*.a + mkdir -p "${ED}"/usr/include/ncbi + cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ + die "Failed to install headers." + + # TODO: wwwblast with webapps + #insinto /usr/share/ncbi/lib/cgi + #doins ${S}/cgi/* + #insinto /usr/share/ncbi/lib/real + #doins ${S}/real/* + + # Basic documentation + dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} + newdoc "${S}"/doc/fa2htgs/README README.fa2htgs + newdoc "${S}"/config/README README.config + newdoc "${S}"/network/encrypt/README README.encrypt + newdoc "${S}"/network/nsclilib/readme README.nsclilib + newdoc "${S}"/sequin/README README.sequin + mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die + doman "${S}"/doc/man/* + + # Hypertext user documentation + dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} + insinto /usr/share/doc/${PF}/html + doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install + + # Developer documentation + if use doc; then + # Demo programs + mkdir "${ED}"/usr/share/ncbi + mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die + fi + + # Shared data (similarity matrices and such) and database directory. + insinto /usr/share/ncbi + doins -r "${S}"/data + dodir /usr/share/ncbi/formatdb + + # Default config file to set the path for shared data. + insinto /etc/ncbi + newins "${FILESDIR}"/ncbirc .ncbirc + eprefixify "${ED}"/etc/ncbi/.ncbirc + + # Env file to set the location of the config file and BLAST databases. + newenvd "${FILESDIR}"/21ncbi-r1 21ncbi +} diff --git a/sci-biology/newick-utils/Manifest b/sci-biology/newick-utils/Manifest new file mode 100644 index 000000000000..fa2d5255b412 --- /dev/null +++ b/sci-biology/newick-utils/Manifest @@ -0,0 +1,2 @@ +DIST newick-utils-1.3.0.tar.gz 6872730 SHA256 2c4d364a6b74d484b795681a08f648e1c89c373e6aa29c2b84bf690530bc54ee +DIST newick-utils-1.5.0.tar.gz 7400423 SHA256 b5508ff31228c8d9fc9fb2e9b70aa24192248998c4e315dd82135323c05e1f67 diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/newick-utils/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/newick-utils/newick-utils-1.3.0.ebuild b/sci-biology/newick-utils/newick-utils-1.3.0.ebuild new file mode 100644 index 000000000000..94c51c218310 --- /dev/null +++ b/sci-biology/newick-utils/newick-utils-1.3.0.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +DESCRIPTION="Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing)" +HOMEPAGE="http://cegg.unige.ch/newick_utils" +SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="!dev-games/libnw" + +src_install() { + einstall || die +} + +src_test() { + emake -C tests check-TESTS || die +} diff --git a/sci-biology/newick-utils/newick-utils-1.5.0.ebuild b/sci-biology/newick-utils/newick-utils-1.5.0.ebuild new file mode 100644 index 000000000000..6bf8d108ca81 --- /dev/null +++ b/sci-biology/newick-utils/newick-utils-1.5.0.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +DESCRIPTION="Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing)" +HOMEPAGE="http://cegg.unige.ch/newick_utils" +SRC_URI="http://cegg.unige.ch/pub/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="!dev-games/libnw" + +src_install() { + einstall || die +} + +src_test() { + emake -C tests check-TESTS || die +} diff --git a/sci-biology/njplot/Manifest b/sci-biology/njplot/Manifest new file mode 100644 index 000000000000..17c26994a8c4 --- /dev/null +++ b/sci-biology/njplot/Manifest @@ -0,0 +1 @@ +DIST njplot-2.3.tar.gz 83641 SHA256 c62a8293511469ba1246c415e7f1974113d520c8a11b04c2ad4a886267c2de1f SHA512 51e7d48187f88c4afb36d55cf8de98dad3cd4cd541137262885fe84bedff9db83224cdfa3c6a14518cd8170a06139b798518afe9fbadd89162986ed788355059 WHIRLPOOL e3e9d9bd844b7d663c7724ea06027641a9948cda133baed8d311b2fb00a6ecf31553a259db67a84478ae04878716f91dd2a9f9df5e2b21254ec9e75958851eca diff --git a/sci-biology/njplot/files/njplot-2.3-buildsystem.patch b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch new file mode 100644 index 000000000000..61f8b95ea160 --- /dev/null +++ b/sci-biology/njplot/files/njplot-2.3-buildsystem.patch @@ -0,0 +1,59 @@ + makefile | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/makefile b/makefile +index ccb7dc2..9488c2a 100644 +--- a/makefile ++++ b/makefile +@@ -7,10 +7,10 @@ NO_PDF = -DNO_PDF + #PDFLIB = -L$(PDF) -lpdf + + # c compiler and linker +-CC = gcc ++CC ?= gcc + + # Vibrant top directory +-VIBRANT = /banques0/ncbiJun04 ++VIBRANT = /usr/include/ncbi + + + # X11 include directory +@@ -24,15 +24,15 @@ OBJECTS = njplot-vib.o + OBJUNROOTED = unrooted-vib.o preptree.o + + +-CFLAGS = -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ ++CFLAGS += -c -DWIN_MOTIF -Dunix -I$(VIBRANT)/include -I$(VIBRANT)/vibrant -I$(VIBRANT)/corelib \ + -I$(VIBRANT) -I$(PDF) -I$(X11INCL) -I$(MOTIFINCL) $(HELPFILENAME) $(NO_PDF) \ +- -Wimplicit-function-declaration -g ++ -Wimplicit-function-declaration + + all: njplot unrooted newicktops newicktotxt + + + njplot : $(OBJECTS) +- $(CC) -g -o njplot $(OBJECTS) \ ++ $(CC) $(LDFLAGS) -o njplot $(OBJECTS) \ + -L$(VIBRANT)/lib \ + -lvibrant -lncbi \ + $(PDFLIB) \ +@@ -40,16 +40,16 @@ njplot : $(OBJECTS) + -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm + + unrooted : $(OBJUNROOTED) +- $(CC) -g -o unrooted $(OBJUNROOTED) \ ++ $(CC) $(LDFLAGS) -o unrooted $(OBJUNROOTED) \ + -L$(VIBRANT)/lib -lvibrant -lncbi \ + -L$(MOTIFLIB) -lXm \ + -L/usr/X11R6/lib -lXmu -lXt -lX11 -lm + + newicktops: njplot-vib.c +- $(CC) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm ++ $(CC) $(LDFLAGS) $(CFLAGS) -DNO_GUI -DNO_PDF -o $@ njplot-vib.c -lm + + newicktotxt: njplot-vib.c +- $(CC) -DTTY -o $@ njplot-vib.c -lm ++ $(CC) -DTTY $(LDFLAGS) $(CFLAGS) -o $@ njplot-vib.c -lm + + + .c.o : diff --git a/sci-biology/njplot/files/njplot-2.3-format-security.patch b/sci-biology/njplot/files/njplot-2.3-format-security.patch new file mode 100644 index 000000000000..686b8475e9ed --- /dev/null +++ b/sci-biology/njplot/files/njplot-2.3-format-security.patch @@ -0,0 +1,16 @@ + njplot-vib.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/njplot-vib.c b/njplot-vib.c +index fe55609..63fd3b6 100644 +--- a/njplot-vib.c ++++ b/njplot-vib.c +@@ -1976,7 +1976,7 @@ PDFONLY" no window interface, just write the PDF/PostScript tree plot\n" + #else + fprintf(stderr, + #endif +- message); ++ "%s", message); + exit(0); + } + } diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml new file mode 100644 index 000000000000..31592430880f --- /dev/null +++ b/sci-biology/njplot/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + NJplot is a tree drawing program able to draw any phylogenetic tree + expressed in the Newick phylogenetic tree format (e.g., the format used + by the PHYLIP package). NJplot is especially convenient for rooting the + unrooted trees obtained from parsimony, distance or maximum likelihood + tree-building methods. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/njplot/njplot-2.3-r1.ebuild b/sci-biology/njplot/njplot-2.3-r1.ebuild new file mode 100644 index 000000000000..f766af55ea96 --- /dev/null +++ b/sci-biology/njplot/njplot-2.3-r1.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-biology/ncbi-tools[X,static-libs] + x11-libs/libXmu" +DEPEND="${RDEPEND}" + +src_prepare() { + sed -i -e "s%njplot.help%${EPREFIX}/usr/share/doc/${PF}/njplot.help%" njplot-vib.c || die + epatch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-buildsystem.patch + tc-export CC +} + +src_install() { + dobin newicktops newicktotxt njplot unrooted + doman *.1 + dodoc README njplot.help +} diff --git a/sci-biology/njplot/njplot-2.3.ebuild b/sci-biology/njplot/njplot-2.3.ebuild new file mode 100644 index 000000000000..03bcad009906 --- /dev/null +++ b/sci-biology/njplot/njplot-2.3.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit toolchain-funcs + +DESCRIPTION="A phylogenetic tree drawing program which supports tree rooting" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/njplot.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/njplot/archive/njplot-${PV}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="amd64 x86" +IUSE="" + +RDEPEND=" + sci-biology/ncbi-tools[X,static-libs] + x11-libs/libXmu" +DEPEND="${RDEPEND}" + +src_prepare() { + sed -i -e 's|/banques0/ncbiJun04|/usr/include/ncbi|' \ + -e 's/CC = gcc/CC='$(tc-getCC)'/' -e 's/CFLAGS =/CFLAGS +=/' \ + makefile || die + sed -i -e "s%njplot.help%/usr/share/doc/${PF}/njplot.help%" njplot-vib.c || die +} + +src_install() { + dobin newicktops newicktotxt njplot unrooted || die + doman *.1 || die + dodoc README njplot.help +} diff --git a/sci-biology/pals/Manifest b/sci-biology/pals/Manifest new file mode 100644 index 000000000000..b024eadc948a --- /dev/null +++ b/sci-biology/pals/Manifest @@ -0,0 +1 @@ +DIST pals-1.0.tar.gz 24895 SHA256 2768adfdd93f56f859744ff9bbbabcc4571b38fa8ea247d505599beee3a962c2 diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/pals/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/pals/pals-1.0.ebuild b/sci-biology/pals/pals-1.0.ebuild new file mode 100644 index 000000000000..283bf5d6dfca --- /dev/null +++ b/sci-biology/pals/pals-1.0.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit toolchain-funcs + +DESCRIPTION="Pairwise Aligner for Long Sequences" +HOMEPAGE="http://www.drive5.com/pals/" +#SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +src_compile() { + emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die +} + +src_install() { + dobin pals || die +} diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest new file mode 100644 index 000000000000..f4ddf21f97d9 --- /dev/null +++ b/sci-biology/paml/Manifest @@ -0,0 +1 @@ +DIST paml4.4c.tar.gz 2891715 SHA256 08aad25b6b06a359d4f2f12a60ea601c95694864d5f29f7028f67b80890974d6 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a WHIRLPOOL 44ae42dd6088039be1041cdce70ce9ee907b8f85d4e25f9d556df4738ea3ea91f700f96f627f20a13d226038132fd23aecbc5b452bfb6716b9499c8d2be491e4 diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/paml/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild new file mode 100644 index 000000000000..7868859871b9 --- /dev/null +++ b/sci-biology/paml/paml-4.4c-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs versionator + +MY_P=$(version_format_string '${PN}$1$2') + +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html" +SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + # Notice send by mail to prof. Ziheng Yang + sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608 +} + +src_compile() { + emake -C src \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -Wno-unused-result" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + dodoc README.txt doc/* + + insinto /usr/share/${PN}/control + doins *.ctl + + insinto /usr/share/${PN}/dat + doins stewart* *.dat dat/* + + insinto /usr/share/${PN} + doins -r examples/ + + cd src || die + dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 +} diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest new file mode 100644 index 000000000000..1275fda8b314 --- /dev/null +++ b/sci-biology/phrap/Manifest @@ -0,0 +1 @@ +DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052 diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/phrap/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/phrap/phrap-1.080812-r1.ebuild b/sci-biology/phrap/phrap-1.080812-r1.ebuild new file mode 100644 index 000000000000..d6864dc373cb --- /dev/null +++ b/sci-biology/phrap/phrap-1.080812-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Shotgun assembly and alignment utilities" +HOMEPAGE="http://www.phrap.org/" +SRC_URI="phrap-${PV}-distrib.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + dev-lang/perl + dev-perl/perl-tk" + +S="${WORKDIR}" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file" + einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\"" + einfo "and put it in ${DISTDIR}" +} + +src_prepare() { + sed -i 's/CFLAGS=/#CFLAGS=/' makefile || die + sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview || die +} + +src_install() { + dobin cross_match loco phrap phrapview swat + newbin cluster cluster_phrap + for i in {general,phrap,swat}.doc ; do + newdoc ${i} ${i}.txt + done +} diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest new file mode 100644 index 000000000000..92cfe6ce81b8 --- /dev/null +++ b/sci-biology/phred/Manifest @@ -0,0 +1 @@ +DIST phred-dist-071220.b-acd.tar.gz 357767 SHA256 364b0b54c29717ba4c8acc48a128eaf25ba1d7f06acab7565975f6879764a975 diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/phred/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/phred/phred-071220.ebuild b/sci-biology/phred/phred-071220.ebuild new file mode 100644 index 000000000000..22600ba92c50 --- /dev/null +++ b/sci-biology/phred/phred-071220.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A base caller for Sanger DNA sequencing" +HOMEPAGE="http://phrap.org/phredphrapconsed.html" +SRC_URI="phred-dist-071220.b-acd.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Please visit ${HOMEPAGE} and obtain the file" + elog "${SRC_URI}, then place it in ${DISTDIR}" +} + +src_compile() { + sed -i -e 's/CFLAGS=/CFLAGS += /' Makefile + emake daev || die + emake || die +} + +src_install() { + dobin phred daev || die + insinto /usr/share/${PN} + doins phredpar.dat || die + echo "PHRED_PARAMETER_FILE=/usr/share/${PN}/phredpar.dat" > 99phred + doenvd 99phred || die + newdoc DAEV.DOC DAEV.DOC.txt + newdoc PHRED.DOC PHRED.DOC.txt +} diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest new file mode 100644 index 000000000000..5971f2782bbb --- /dev/null +++ b/sci-biology/phylip/Manifest @@ -0,0 +1,2 @@ +DIST phylip-3.69.tar.gz 1511935 SHA256 27947ce8dab4416e4823db38b3d1b0bf17bc545b6907cf09dcf6177df94c1a8f SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d WHIRLPOOL 25c45ac2a96278eaef9a62aecc367aa32a894df0cd5aff9b626abd013ecbe52f9d4bdaf7805ba5c5d8699f9a74d3d26cfe6e1c1b22960c03061171625d16415f +DIST phylip-3.696.tar.gz 3955721 SHA256 cd0a452ca51922142ad06d585e2ef98565536a227cbd2bd47a2243af72c84a06 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be WHIRLPOOL 7d4d4bd703ecd84b7570c937484c15f52643221ca178fb494f81b18991149fc2f8d1c8c5b99b57e20ada0bef7e93dcb15c55410f8f1012b1656419fab19b3cab diff --git a/sci-biology/phylip/files/README.Gentoo b/sci-biology/phylip/files/README.Gentoo new file mode 100644 index 000000000000..3b2062003996 --- /dev/null +++ b/sci-biology/phylip/files/README.Gentoo @@ -0,0 +1,15 @@ +Using the PHYlogeny Inference Package on Gentoo systems + +Location of the factor program + +On Gentoo systems, the PHYLIP program "factor" is named "factor-phylip", in +order to avoid a file collision with the program of the same name provided by +the "sys-apps/coreutils" package. + +Location of the font files + +PHYLIP programs will find font files only if they are in a directory +referenced by the "PATH" variable or if they are in the current working +directory. When working with PHYLIP programs that need these files, either +copy or symlink the fonts you need to your working directory, or add +"/usr/share/phylip/fonts/" to your "PATH" variable. diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/phylip/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild new file mode 100644 index 000000000000..ecc44200ac57 --- /dev/null +++ b/sci-biology/phylip/phylip-3.69-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION=" The PHYLogeny Inference Package" +HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" +SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" + +SLOT="0" +LICENSE="freedist" +IUSE="" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" + +RDEPEND="x11-libs/libXaw" +DEPEND="${RDEPEND} + x11-proto/xproto" + +S="${WORKDIR}/${P}/src" + +src_prepare() { + sed \ + -e "s/CFLAGS = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \ + -e "s/CC = cc/CC = $(tc-getCC)/" \ + -e "s/DC = cc/DC = $(tc-getCC)/" \ + -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ + -i Makefile || die "Patching Makefile failed." + mkdir ../fonts || die +} + +src_compile() { + emake -j1 all put +} + +src_install() { + cd "${WORKDIR}/${P}" || die + + mv exe/font* fonts || die "Font move failed." + mv exe/factor exe/factor-${PN} || die "Renaming factor failed." + + dobin exe/* + + dodoc "${FILESDIR}"/README.Gentoo + + dohtml -r phylip.html doc + + insinto /usr/share/${PN}/ + doins -r fonts +} diff --git a/sci-biology/phylip/phylip-3.696.ebuild b/sci-biology/phylip/phylip-3.696.ebuild new file mode 100644 index 000000000000..d5960bb62bb7 --- /dev/null +++ b/sci-biology/phylip/phylip-3.696.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION=" The PHYLogeny Inference Package" +HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" +SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD-2" +IUSE="" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" + +RDEPEND="x11-libs/libXaw" +DEPEND="${RDEPEND} + x11-proto/xproto" + +S="${WORKDIR}/${P}/src" + +src_prepare() { + mv Makefile.unx Makefile || die + sed \ + -e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \ + -i Makefile || die "Patching Makefile failed." + mkdir ../fonts || die +} + +src_compile() { + emake -j1 \ + CC="$(tc-getCC)" \ + DC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -Wno-unused-result" \ + all put +} + +src_install() { + cd "${WORKDIR}/${P}" || die + + mv exe/font* fonts || die "Font move failed." + mv exe/factor exe/factor-${PN} || die "Renaming factor failed." + + dobin exe/* + + dodoc "${FILESDIR}"/README.Gentoo + + dohtml -r phylip.html doc + + insinto /usr/share/${PN}/ + doins -r fonts +} diff --git a/sci-biology/phyml/Manifest b/sci-biology/phyml/Manifest new file mode 100644 index 000000000000..d285799277e1 --- /dev/null +++ b/sci-biology/phyml/Manifest @@ -0,0 +1 @@ +DIST phyml_v2.4.5.tar.gz 92143 SHA256 e8a1d3980137f8e528d0e59472aff37dbac615860a7d3ee4cdb64f30dfea296e SHA512 119716290eca0de4da05b0bacbec96139f4c89f6a033b861d1cb2655a620766bd0bea0675c4d7722a31d888652a28bf3544a643f39f11682982ede80dc5928c3 WHIRLPOOL e9c0e36ea871c61fc617ed0a10d306bdb66d84da0b9a08107fb9e1f6370e10676c5ad8a0a5e5404ccad6ae2f62551d566614a173cfdd4a0a523f727fc7924ce0 diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml new file mode 100644 index 000000000000..d0355f85e406 --- /dev/null +++ b/sci-biology/phyml/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription lang="en"> + Phyml is a simple, fast, and accurate algorithm to estimate large + phylogenies by maximum likelihood. Given input sequence files, it + estimates phylogenies using maximum likelihood, and is capable of + processing large amounts of phylogenetic data. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/phyml/phyml-2.4.5-r2.ebuild b/sci-biology/phyml/phyml-2.4.5-r2.ebuild new file mode 100644 index 000000000000..7d9815baa78b --- /dev/null +++ b/sci-biology/phyml/phyml-2.4.5-r2.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 + +inherit toolchain-funcs + +MY_P=${PN}_v${PV} + +DESCRIPTION="Estimation of large phylogenies by maximum likelihood" +HOMEPAGE="http://atgc.lirmm.fr/phyml/" +SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -e 's/^hello !!!//' \ + -e 's/$(CC) -o/$(CC) $(LDFLAGS) -o/' \ + -i Makefile || die +} + +src_compile() { + emake -e CC="$(tc-getCC)" || die +} + +src_install() { + dobin phyml || die +} diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest new file mode 100644 index 000000000000..814765877966 --- /dev/null +++ b/sci-biology/picard/Manifest @@ -0,0 +1 @@ +DIST picard-1.103.tar.bz2 15037887 SHA256 777af2a0aadd97a2b909160774e6e0ad99cef6de7763096f10660ccbe2baca63 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca WHIRLPOOL de5a0341473174bfc7a1f1b8d1b3b6122b212a1d964dda534912347595a3da9fe2a86692959df7375896292e3f3657a9c27c2f1694fca60d48ff23192b93b098 diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch new file mode 100644 index 000000000000..00e89b95056a --- /dev/null +++ b/sci-biology/picard/files/1.103-gentoo.patch @@ -0,0 +1,131 @@ +diff --git a/build.xml b/build.xml +index fca2271..11f4fbd 100755 +--- a/build.xml ++++ b/build.xml +@@ -52,9 +52,6 @@ + <property name="testng.verbosity" value="2"/> + <property name="test.debug.port" value="5005" /> <!-- override on the command line if desired --> + +- <property environment="env"/> +- <property name="java6.home" value="${env.JAVA6_HOME}"/> +- + <condition property="isUnix"> + <os family="unix"/> + </condition> +@@ -78,9 +75,6 @@ + <pathelement location="${classes}"/> + </path> + +- <path id="java6.lib.ref"> +- <fileset dir="${java6.home}/lib" includes="*.jar"/> +- </path> + </target> + + <!-- CLEAN --> +@@ -94,10 +88,6 @@ + </target> + + <!-- COMPILE --> +- <target name="compile" depends="compile-src, compile-tests" +- description="Compile files without cleaning"> +- </target> +- + <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/> + + <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning"> +@@ -138,7 +128,7 @@ + </target> + + <!-- TEST --> +- <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests"> ++ <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests"> + <taskdef resource="testngtasks" classpathref="classpath"/> + <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}" + failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}" +@@ -151,6 +141,8 @@ + <classfileset dir="${classes.test}"> + <include name="**/Test*.class"/> + <include name="**/*Test.class"/> ++ <exclude name="**/ValidateSamFileTest.class" /> ++ <exclude name="**/VCFWriterUnitTest.class" /> + </classfileset> + <jvmarg value="-Xmx2G"/> + </testng> +@@ -165,7 +157,7 @@ + </target> + + <target name="single-test" +- depends="compile, compile-tests" ++ depends="compile-tests" + description="Compile and run a single test."> + <taskdef resource="testngtasks" classpathref="classpath"/> + <fail unless="name" message="Please provide input test: -Dname=..." /> +@@ -200,13 +192,12 @@ + </jar> + </target> + +- <target name="picard-jar" depends="compile" ++ <target name="picard-jar" depends="compile-src" + description="Builds picard-${picard-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/picard-${picard-version}.jar" compress="no"> + <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/> + <fileset dir="${src.scripts}" includes="**/*.R"/> +- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/> + <manifest> + <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/> + <attribute name="Implementation-Vendor" value="Broad Institute"/> +@@ -214,7 +205,7 @@ + </jar> + </target> + +- <target name="tribble-jar" depends="compile" ++ <target name="tribble-jar" depends="compile-src" + description="Builds tribble-${tribble-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no"> +@@ -225,7 +216,7 @@ + </copy> + </target> + +- <target name="variant-jar" depends="compile" ++ <target name="variant-jar" depends="compile-src" + description="Builds variant-${variant-version}.jar for inclusion in other projects"> + <mkdir dir="${dist}"/> + <jar destfile="${dist}/variant-${variant-version}.jar" compress="no"> +@@ -262,7 +253,7 @@ + </javadoc> + </target> + +- <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar"> ++ <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar"> + <delete dir="${command_tmp}"/> + + <mkdir dir="${command_tmp}"/> +@@ -344,7 +335,7 @@ + </target> + + <!-- ALL --> +- <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> ++ <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> + <zip zipfile="${dist}/picard-tools-${picard-version}.zip"> + <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/> + <zipfileset dir="${lib}" includes="snappy*.jar"/> +@@ -468,8 +459,6 @@ + target="${javac.target}"> + <classpath refid="@{compile.classpath}"/> + <compilerarg line="@{compiler.args}" /> +- <!-- ensure that Java 6 bootclasspath is used --> +- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> + </javac> + </sequential> + </macrodef> +@@ -494,8 +483,6 @@ + <pathelement location="${classes}"/> + </classpath> + <compilerarg line="@{compiler.args}"/> +- <!-- ensure that Java 6 bootclasspath is used --> +- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> + </javac> + </sequential> + </macrodef> diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml new file mode 100644 index 000000000000..265affea91d0 --- /dev/null +++ b/sci-biology/picard/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>ercpe@gentoo.org</email> + <name>Johann Schmitz (ercpe)</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild new file mode 100644 index 000000000000..16e71f41f2b0 --- /dev/null +++ b/sci-biology/picard/picard-1.103.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +JAVA_PKG_IUSE="doc source test" +WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java-based command-line utilities that manipulate SAM files" +HOMEPAGE="http://picard.sourceforge.net/" +SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-java/snappy:1.0 + dev-java/cofoja:0 + dev-java/commons-jexl:2 + dev-java/ant-core:0" + +DEPEND=">=virtual/jdk-1.6 + dev-java/ant-apache-bcel:0 + test? ( + dev-java/testng:0 + dev-lang/R + ) + ${CDEPEND}" +RDEPEND=">=virtual/jre-1.6 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_TEST_TARGET="test" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" +EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" + +java_prepare() { + mkdir "${S}"/lib || die + + epatch "${FILESDIR}"/${PV}-gentoo.patch + + mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die +} + +src_install() { + cd dist || die + + for i in *-${PV}.jar; do + java-pkg_newjar $i ${i/-${PV}/} + rm $i || die + done + + java-pkg_dojar *.jar + for i in *.jar; do + java-pkg_dolauncher ${i/.jar/} --jar $i; + done + + use source && java-pkg_dosrc "${S}"/src/java/* + use doc && java-pkg_dojavadoc "${S}"/javadoc +} + +src_test() { + java-pkg-2_src_test +} diff --git a/sci-biology/piler/Manifest b/sci-biology/piler/Manifest new file mode 100644 index 000000000000..a63f193ecb5b --- /dev/null +++ b/sci-biology/piler/Manifest @@ -0,0 +1 @@ +DIST piler-1.0.tar.gz 35220 SHA256 2940530c0afd7e49ca6e9cd8a1e3fd9890d87c71f9c19a42b1e468add83ccc69 diff --git a/sci-biology/piler/files/piler-1.0-glibc-2.10.patch b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch new file mode 100644 index 000000000000..4c7f124c5e3d --- /dev/null +++ b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch @@ -0,0 +1,12 @@ +diff -ur piler.orig/gff.cpp piler/gff.cpp +--- piler.orig/gff.cpp 2004-12-18 01:25:29.000000000 +0200 ++++ piler/gff.cpp 2009-08-09 17:22:33.000000000 +0300 +@@ -70,7 +70,7 @@ + const char *Attrs = Fields[8];
+
+ // Truncate attrs if comment found
+- char *Pound = strchr(Attrs, '#');
++ char *Pound = const_cast <char*> (strchr(Attrs, '#'));
+ if (0 != Pound)
+ *Pound = 0;
+
diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/piler/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/piler/piler-1.0.ebuild b/sci-biology/piler/piler-1.0.ebuild new file mode 100644 index 000000000000..139f92cda50f --- /dev/null +++ b/sci-biology/piler/piler-1.0.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils toolchain-funcs + +DESCRIPTION="Analysis of repetitive DNA found in genome sequences" +HOMEPAGE="http://www.drive5.com/piler/" +#SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND="" +RDEPEND="|| ( sci-biology/muscle + sci-libs/libmuscle ) + sci-biology/pals" + +S=${WORKDIR} + +src_prepare() { + epatch "${FILESDIR}"/${P}-glibc-2.10.patch +} + +src_compile() { + emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die +} + +src_install() { + dobin piler +} diff --git a/sci-biology/pilercr/Manifest b/sci-biology/pilercr/Manifest new file mode 100644 index 000000000000..b810410070ad --- /dev/null +++ b/sci-biology/pilercr/Manifest @@ -0,0 +1 @@ +DIST pilercr-1.0.tar.gz 1709144 SHA256 75f58d58567c478e271c4c554071a7d6d642e6daef8981ee2618daa7b53fa923 diff --git a/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch new file mode 100644 index 000000000000..7b49df872e27 --- /dev/null +++ b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch @@ -0,0 +1,33 @@ +diff -dur work/multaln.h work-orig/multaln.h +--- work/multaln.h 2007-04-17 19:02:18.000000000 +0000 ++++ work-orig/multaln.h 2009-02-18 21:25:26.166333299 +0000 +@@ -6,6 +6,7 @@ + #define _CRT_SECURE_NO_DEPRECATE 1
+ #endif
+
++#include <cstring>
+ #include <vector>
+ #include <limits.h>
+ #include <ctype.h>
+diff -dur work/seqvect.h work-orig/seqvect.h +--- work/seqvect.h 2006-04-06 23:36:18.000000000 +0000 ++++ work-orig/seqvect.h 2009-02-18 21:25:26.171090246 +0000 +@@ -1,6 +1,7 @@ + #ifndef SeqVect_h
+ #define SeqVect_h
+
++#include <stdio.h>
+ #include <vector>
+ #include "seq.h"
+
+diff -dur work/tree.h work-orig/tree.h +--- work/tree.h 2006-04-05 23:52:42.000000000 +0000 ++++ work-orig/tree.h 2009-02-18 21:25:26.171090246 +0000 +@@ -1,6 +1,7 @@ + #ifndef tree_h
+ #define tree_h
+
++#include <stdlib.h>
+ #include <limits.h>
+
+ class Clust;
diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/pilercr/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/pilercr/pilercr-1.0.ebuild b/sci-biology/pilercr/pilercr-1.0.ebuild new file mode 100644 index 000000000000..3241d42a863c --- /dev/null +++ b/sci-biology/pilercr/pilercr-1.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)" +HOMEPAGE="http://www.drive5.com/pilercr/" +#SRC_URI="http://www.drive5.com/pilercr/pilercr.tar.gz" +SRC_URI="mirror://gentoo/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S="${WORKDIR}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc43.patch +} + +src_compile() { + emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest new file mode 100644 index 000000000000..1bd3f237d4c8 --- /dev/null +++ b/sci-biology/plink/Manifest @@ -0,0 +1,2 @@ +DIST plink-1.07-src.zip 2257297 SHA256 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b SHA512 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3 WHIRLPOOL 01e69f605e1b52c6087dd75b506a7705d3bdb8e7dfdd0158e125f4fc4d962fad70c4ec430a139029b3b4ae91b822eb10123fab062c6552b946ec96ca7caf37da +DIST plink-1.90_pre140514.zip 822157 SHA256 c6f93153d079b4b7f9ae4a51a3b4dcc7bc5ed60b408d39fce6234b98570b8ea7 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4 WHIRLPOOL ebcccc1dc0461afd973aa63313237bfd5d904543785115fa71f3af1925d8bb21da15bd0baf60e38f4da534c8c554202a7af6c642b274ca9a458fc0035c2758d2 diff --git a/sci-biology/plink/files/1.07-flags.patch b/sci-biology/plink/files/1.07-flags.patch new file mode 100644 index 000000000000..aa130f29beb2 --- /dev/null +++ b/sci-biology/plink/files/1.07-flags.patch @@ -0,0 +1,44 @@ +diff --git a/Makefile b/Makefile +index 172c795..466f09f 100644 +--- a/Makefile ++++ b/Makefile +@@ -26,25 +26,25 @@ WITH_R_PLUGINS = 1 + WITH_WEBCHECK = 1 + FORCE_32BIT = + WITH_ZLIB = 1 +-WITH_LAPACK = +-FORCE_DYNAMIC = ++WITH_LAPACK = 1 ++FORCE_DYNAMIC = 1 + + # Put C++ compiler here; Windows has it's own specific version + CXX_UNIX = g++ + CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe + + # Any other compiler flags here ( -Wall, -g, etc) +-CXXFLAGS = ++CXXFLAGS ?= -O2 + + # Misc +-LIB_LAPACK = /usr/lib/liblapack.so.3 ++LIB_LAPACK = `$(PKG_CONFIG) --libs lapack` + + + # -------------------------------------------------------------------- + # Do not edit below this line + # -------------------------------------------------------------------- + +-CXXFLAGS += -O3 -I. ++CXXFLAGS += -I. + OUTPUT = plink + + # Some system specific flags +@@ -151,7 +151,7 @@ OBJ = $(SRC:.cpp=.o) + all : $(OUTPUT) + + $(OUTPUT) : +- $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) + + $(OBJ) : $(HDR) + diff --git a/sci-biology/plink/files/plink-1.07-gcc47.patch b/sci-biology/plink/files/plink-1.07-gcc47.patch new file mode 100644 index 000000000000..6c289edae153 --- /dev/null +++ b/sci-biology/plink/files/plink-1.07-gcc47.patch @@ -0,0 +1,64 @@ + elf.cpp | 6 +++--- + idhelp.cpp | 8 ++++---- + sets.cpp | 8 ++++---- + 3 files changed, 11 insertions(+), 11 deletions(-) + +diff --git a/elf.cpp b/elf.cpp +index ec2ed3d..a57665f 100644 +--- a/elf.cpp ++++ b/elf.cpp +@@ -1175,10 +1175,10 @@ void Plink::elfBaseline() + << setw(8) << gcnt << " " + << setw(8) << (double)cnt / (double)gcnt << "\n"; + +- map<int,int>::iterator i = chr_cnt.begin(); +- while ( i != chr_cnt.end() ) ++ map<int,int>::iterator j = chr_cnt.begin(); ++ while ( j != chr_cnt.end() ) + { +- int c = i->first; ++ int c = j->first; + int x = chr_cnt.find( c )->second; + int y = chr_gcnt.find( c )->second; + +diff --git a/idhelp.cpp b/idhelp.cpp +index a9244fa..8882097 100644 +--- a/idhelp.cpp ++++ b/idhelp.cpp +@@ -772,12 +772,12 @@ void IDHelper::idHelp() + for (int j = 0 ; j < jointField.size(); j++ ) + { + set<IDField*> & jf = jointField[j]; +- set<IDField*>::iterator j = jf.begin(); ++ set<IDField*>::iterator k = jf.begin(); + PP->printLOG(" { "); +- while ( j != jf.end() ) ++ while ( k != jf.end() ) + { +- PP->printLOG( (*j)->name + " " ); +- ++j; ++ PP->printLOG( (*k)->name + " " ); ++ ++k; + } + PP->printLOG(" }"); + } +diff --git a/sets.cpp b/sets.cpp +index 3a8f92f..66787e8 100644 +--- a/sets.cpp ++++ b/sets.cpp +@@ -768,11 +768,11 @@ vector_t Set::profileTestScore() + ////////////////////////////////////////////// + // Reset original missing status + +- vector<Individual*>::iterator i = PP->sample.begin(); +- while ( i != PP->sample.end() ) ++ vector<Individual*>::iterator j = PP->sample.begin(); ++ while ( j != PP->sample.end() ) + { +- (*i)->missing = (*i)->flag; +- ++i; ++ (*j)->missing = (*j)->flag; ++ ++j; + } + + //////////////////////////////////////////////// diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml new file mode 100644 index 000000000000..80af0e1d0365 --- /dev/null +++ b/sci-biology/plink/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="webcheck"> + add support for online update checking every time the program starts + </flag> + <flag name="R"> + add support R language + </flag> + </use> +</pkgmetadata> diff --git a/sci-biology/plink/plink-1.07-r1.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild new file mode 100644 index 000000000000..ca32ecf62a18 --- /dev/null +++ b/sci-biology/plink/plink-1.07-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Whole genome association analysis toolset" +HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/" +SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip" + +LICENSE="GPL-2" +SLOT="0" +IUSE="lapack -webcheck R" +KEYWORDS="amd64 x86" + +DEPEND=" + app-arch/unzip + lapack? ( virtual/pkgconfig )" +RDEPEND=" + sys-libs/zlib + lapack? ( virtual/lapack )" + +S="${WORKDIR}/${P}-src" + +# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian. +# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream. + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-flags.patch \ + "${FILESDIR}"/${P}-gcc47.patch + use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die + use R || sed -i '/WITH_R_PLUGINS =/ s/^/#/' "${S}/Makefile" || die + use lapack || sed -i '/WITH_LAPACK =/ s/^/#/' "${S}/Makefile" || die + tc-export PKG_CONFIG +} + +src_compile() { + emake \ + CXX_UNIX=$(tc-getCXX) +} + +src_install() { + newbin plink p-link + dodoc README.txt +} diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild new file mode 100644 index 000000000000..45b80be23c36 --- /dev/null +++ b/sci-biology/plink/plink-1.90_pre140514.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Whole genome association analysis toolset" +HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/" +SRC_URI="http://pngu.mgh.harvard.edu/~purcell/static/bin/plink140514/plink_src.zip -> ${P}.zip" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + app-arch/unzip + virtual/pkgconfig" +RDEPEND=" + sys-libs/zlib + virtual/cblas + virtual/lapack + " + +S="${WORKDIR}/" + +# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian. +# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream. + +src_prepare() { + sed \ + -e 's:zlib-1.2.8/zlib.h:zlib.h:g' \ + -i *.{c,h} || die + + sed \ + -e 's:g++:$(CXX):g' \ + -e 's:gcc:$(CC):g' \ + -e 's:gfortran:$(FC):g' \ + -i Makefile || die + tc-export PKG_CONFIG +} + +src_compile() { + emake \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \ + BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)" +} + +src_install() { + newbin plink p-link +} diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest new file mode 100644 index 000000000000..5a988dfac24d --- /dev/null +++ b/sci-biology/poa/Manifest @@ -0,0 +1 @@ +DIST poaV2.tar.gz 62612 SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2 diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/2-respect-flags.patch new file mode 100644 index 000000000000..bdd638cf64b7 --- /dev/null +++ b/sci-biology/poa/files/2-respect-flags.patch @@ -0,0 +1,26 @@ +diff --git a/Makefile b/Makefile +index a65bed0..713a7ab 100644 +--- a/Makefile ++++ b/Makefile +@@ -26,9 +26,10 @@ LIBOBJECTS= \ + stringptr.o + + +-CC = gcc ++CC ?= gcc + #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. +-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. ++OPT_CFLAGS = -g ++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. + # -I$(HOME)/lib/include + # -DREPORT_MAX_ALLOC + +@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS) + + # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!! + poa: $(OBJECTS) liblpo.a +- $(CC) -o $@ $(OBJECTS) -lm liblpo.a ++ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a + + what: + @echo poa: partial-order based sequence alignment program diff --git a/sci-biology/poa/files/respect-cflags.patch b/sci-biology/poa/files/respect-cflags.patch new file mode 100644 index 000000000000..2ae08db4ff4d --- /dev/null +++ b/sci-biology/poa/files/respect-cflags.patch @@ -0,0 +1,13 @@ +diff -urN poaV2.orig/Makefile poaV2/Makefile +--- poaV2.orig/Makefile 2004-03-11 21:33:30.000000000 -0800 ++++ poaV2/Makefile 2006-03-09 20:09:27.000000000 -0800 +@@ -28,7 +28,8 @@ + + CC = gcc + #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. +-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. ++OPT_CFLAGS = -g ++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. + # -I$(HOME)/lib/include + # -DREPORT_MAX_ALLOC + diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml new file mode 100644 index 000000000000..65027f64ec24 --- /dev/null +++ b/sci-biology/poa/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">poamsa</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild new file mode 100644 index 000000000000..8a1a23ca4902 --- /dev/null +++ b/sci-biology/poa/poa-2-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +MY_P="${PN}V${PV}" + +DESCRIPTION="Fast multiple sequence alignments using partial-order graphs" +HOMEPAGE="http://bioinfo.mbi.ucla.edu/poa/" +SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz" + +# According to SF project page +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="static-libs" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-respect-flags.patch +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + OPT_CFLAGS="${CFLAGS}" \ + poa +} + +src_install() { + dobin "${S}"/poa "${S}"/make_pscores.pl + use static-libs && dolib.a "${S}"/liblpo.a + dodoc "${S}"/README "${S}"/multidom.* + insinto /usr/share/poa + doins "${S}"/*.mat +} + +pkg_postinst() { + elog "poa requires a score matrix as the first argument." + elog "This package installs two examples to ${EROOT}usr/share/poa/." +} diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest new file mode 100644 index 000000000000..96826545f7c3 --- /dev/null +++ b/sci-biology/prank/Manifest @@ -0,0 +1,3 @@ +DIST prank.source.140603.tgz 150346 SHA256 9a48064132c01b6dba1eec90279172bf6c13d96b3f1b8dd18297b1a53d17dec6 SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7 WHIRLPOOL 5884563e6035b7e5a06b064035980e9fcee1cafcf559d86c8b9c8fc23628c7e9d1ba3e153a06f7322bb536120adcc6c8d169381f95d0a491b57836ada35a0de6 +DIST prank.src.100701.tgz 115444 SHA256 2ba63fc8f998a86e6fc688170b03f831eeb8d8deda95cbf0986e8a3a3b09ec79 +DIST prank.src.111130.tgz 133330 SHA256 61473a6b7b199f2d05e35a31adf813a2813decc9aa1429de118b62a51d7aac14 SHA512 94f382bd71d6a58fe9b87b436bdec97ed297ebf88f3074d8e2971a24dcdc4509e737161aa057be0ac15783c1cfe7ca6d0a09ad80d0247b92426134097d4b400c WHIRLPOOL 37b96f3dc0e53f7d0b70ddfc5664dc65eff4dbec322788d391c32f5d74103663b547825dcc58fe5da3b5b44086c36fcf00a3a2253e696d6212baa3958d13fc5b diff --git a/sci-biology/prank/files/prank-111130-gcc-4.7.patch b/sci-biology/prank/files/prank-111130-gcc-4.7.patch new file mode 100644 index 000000000000..d7defbcadfec --- /dev/null +++ b/sci-biology/prank/files/prank-111130-gcc-4.7.patch @@ -0,0 +1,15 @@ + src/check_version.cpp | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/check_version.cpp b/src/check_version.cpp +index e968a05..6dfa062 100644 +--- a/src/check_version.cpp ++++ b/src/check_version.cpp +@@ -8,6 +8,7 @@ + #include <string> + #include <sstream> + #include <iostream> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml new file mode 100644 index 000000000000..2cd3c04eeca0 --- /dev/null +++ b/sci-biology/prank/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="google-code">prank-msa</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/prank/prank-100701.ebuild b/sci-biology/prank/prank-100701.ebuild new file mode 100644 index 000000000000..913ff56ee71b --- /dev/null +++ b/sci-biology/prank/prank-100701.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="Probabilistic Alignment Kit" +HOMEPAGE="http://wasabiapp.org/software/prank/" +SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.${PV}.tgz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S=${WORKDIR}/${PN} + +src_prepare() { + sed -i -e "s/\$(LINK)/& \$(LDFLAGS)/" Makefile || die +} + +src_compile() { + emake \ + LINK="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" +} + +src_install() { + dobin prank +} diff --git a/sci-biology/prank/prank-111130.ebuild b/sci-biology/prank/prank-111130.ebuild new file mode 100644 index 000000000000..4d4f6e912495 --- /dev/null +++ b/sci-biology/prank/prank-111130.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="Probabilistic Alignment Kit" +HOMEPAGE="http://wasabiapp.org/software/prank/" +SRC_URI="http://prank-msa.googlecode.com/files/prank.src.${PV}.tgz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/prank-msa/src" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc-4.7.patch + sed \ + -e "s/\$(LINK)/& \$(LDFLAGS)/" \ + -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \ + -i Makefile || die +} + +src_compile() { + emake \ + LINK="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" +} + +src_install() { + dobin prank +} diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild new file mode 100644 index 000000000000..a18b7ab9d553 --- /dev/null +++ b/sci-biology/prank/prank-140603.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="Probabilistic Alignment Kit" +HOMEPAGE="http://wasabiapp.org/software/prank/" +SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/${PN}-msa/src" + +src_prepare() { + sed \ + -e "s/\$(LINK)/& \$(LDFLAGS)/" \ + -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \ + -i Makefile || die +} + +src_compile() { + emake \ + LINK="$(tc-getCXX)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest new file mode 100644 index 000000000000..19da14fe3f93 --- /dev/null +++ b/sci-biology/primer3/Manifest @@ -0,0 +1,2 @@ +DIST primer3-2.3.5.tar.gz 1655871 SHA256 e0c06a36dc384f656835a8d5ecb4b5069493b7dd98775b38a233863ab591c54b SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec WHIRLPOOL 321069f568fad409b31f2fd4caa36f1128523383f5b294dffc68d57a67489ee2ac17d53bedd8e36df9b688c43c06c91f47bdaf81b4fda6597d916ea06643e666 +DIST primer3-src-2.3.6.tar.gz 1667573 SHA256 2ff54faf957f0d7e4c79d9536fa1027b028bc5e4c6005f142df42ef85562ecd4 SHA512 671b420f3bc9b6b9972e19a757925ada170e5f8c0e3e8a90630a48e6cde44abc0e1e09b9ea90129f94b58f835e30440f3d91c14fb4b796fd94eb478b2ca28ead WHIRLPOOL 61bbc676c38b1b96806c9ac54d130aae936a5406213759613a3be76016cdd4ebf76c5a54d1ceffc7bd2634829d9aef9d64f87cc85289793b40ab031e01a5917f diff --git a/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch new file mode 100644 index 000000000000..66a5a52d4e8e --- /dev/null +++ b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch @@ -0,0 +1,25 @@ +Respect LDFLAGS + +http://bugs.gentoo.org/show_bug.cgi?id=335225 + +--- src/Makefile ++++ src/Makefile +@@ -103,10 +103,10 @@ + $(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+
+ oligotm: oligotm_main.c oligotm.h $(OLIGOTM_LIB)
+- $(CC) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)
+
+ long_seq_tm_test: long_seq_tm_test_main.c oligotm.o
+- $(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+
+ boulder_input.o: boulder_input.c boulder_input.h primer3.h primer3_release.h dpal.h
+ $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ boulder_input.c
+@@ -136,4 +136,4 @@ + primer_test: test
+
+ test: $(PRIMER_EXE) ntdpal
+- cd ../test; make test
++ $(MAKE) -C ../test test
diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch new file mode 100644 index 000000000000..cf47b35af502 --- /dev/null +++ b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch @@ -0,0 +1,148 @@ + src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------ + 1 file changed, 31 insertions(+), 30 deletions(-) + +diff --git a/src/Makefile b/src/Makefile +index 607ab45..a88adf4 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -52,15 +52,16 @@ TESTOPTS= + WINMAKE=mingw32-make + + LDLIBS = -lm +-AR = ar +-CC = gcc +-CPP = g++ +-O_OPTS = -O2 +-CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__ +-P_DEFINES = ++AR ?= ar ++CC ?= gcc ++CXX ?= g++ ++O_OPTS ?= ++CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__ ++P_DEFINES ?= + +-CFLAGS = $(CC_OPTS) $(O_OPTS) +-LDFLAGS = -g ++CFLAGS += $(CC_OPTS) $(O_OPTS) ++CXXFLAGS += $(CC_OPTS) $(O_OPTS) ++LDFLAGS += + # Note, for profiling, use + # make O_OPTS='-pg -O0' LDFLAGS='-g -pg' + +@@ -92,7 +93,7 @@ LIBPRIMER3 = libprimer3.a + LIBPRIMER3_DYN = libprimer3.so.1.0.0 + LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) + DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN) +-RANLIB = ranlib ++RANLIB ?= ranlib + + PRIMER_OBJECTS1=primer3_boulder_main.o\ + format_output.o\ +@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o + $(RANLIB) $@ + + $(LIBOLIGOTM_LIB): oligotm.o +- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o + + $(LIBDPAL): dpal_primer.o + $(AR) rv $@ dpal_primer.o + $(RANLIB) $@ + + $(LIBDPAL_DYN): dpal_primer.o +- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o + + $(LIBTHAL): thal_primer.o + $(AR) rv $@ thal_primer.o + $(RANLIB) $@ + + $(LIBTHAL_DYN): thal_primer.o +- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o + + $(LIBPRIMER3): libprimer3.o p3_seq_lib.o + $(AR) rv $@ libprimer3.o p3_seq_lib.o + $(RANLIB) $@ + + $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o +- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o + + $(PRIMER_EXE): $(PRIMER_OBJECTS) +- $(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) + + libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h +- $(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c ++ $(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c + + $(NTDPAL_EXE): ntdpal_main.o dpal.o +- $(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o ++ $(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o + + $(NTTHAL_EXE): thal_main.o thal.o +- $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) + + $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM) +- $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) + + $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o +- $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) + + read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c + + print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c + + dpal.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) -o $@ dpal.c + + # We use '-ffloat-store' on windows to prevent undesirable + # precision which may lead to differences in floating point results. + thal.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c + + p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h +- $(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c ++ $(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c + + dpal_primer.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c + + thal_primer.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c + + format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c + + ntdpal_main.o: ntdpal_main.c dpal.h +- $(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c + + thal_main.o: thal_main.c thal.h +- $(CPP) -c $(CFLAGS) -o $@ thal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ thal_main.c + # We use CC_OPTS above rather than CFLAGS because + # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2 + + oligotm.o: oligotm.c oligotm.h + + primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c + + primer_test: test + diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml new file mode 100644 index 000000000000..1fbadfaf3b77 --- /dev/null +++ b/sci-biology/primer3/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + Primer3 picks primers for PCR reactions, considering: oligonucleotide + melting temperature, size, GC content, and primer-dimer possibilities; + PCR product size; positional constraints within the source sequence; + and miscellaneous other constraints. All of these criteria are + user-specifiable as constraints, and some are specifiable as terms in + an objective function that characterizes an optimal primer pair. + </longdescription> + <upstream> + <remote-id type="sourceforge">primer3</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/primer3/primer3-2.3.5.ebuild b/sci-biology/primer3/primer3-2.3.5.ebuild new file mode 100644 index 000000000000..4135610c2524 --- /dev/null +++ b/sci-biology/primer3/primer3-2.3.5.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Primer Design for PCR reactions" +HOMEPAGE="http://primer3.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="" +KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="dev-lang/perl" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch + + if [[ ${CHOST} == *-darwin* ]]; then + sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die + fi + + tc-export CC CXX AR RANLIB +} + +src_compile() { + emake -C src +} + +src_test () { + emake -C test | tee "${T}"/test.log + grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" +} + +src_install () { + dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} + dodoc src/release_notes.txt example + insinto /opt/primer3_config + doins -r src/primer3_config/* primer3*settings.txt + dohtml primer3_manual.htm +} diff --git a/sci-biology/primer3/primer3-2.3.6.ebuild b/sci-biology/primer3/primer3-2.3.6.ebuild new file mode 100644 index 000000000000..9ba9ff0796c3 --- /dev/null +++ b/sci-biology/primer3/primer3-2.3.6.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Primer Design for PCR reactions" +HOMEPAGE="http://primer3.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${PV}/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="" +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="dev-lang/perl" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch + + if [[ ${CHOST} == *-darwin* ]]; then + sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die + fi + + tc-export CC CXX AR RANLIB +} + +src_compile() { + emake -C src +} + +src_test () { + emake -C test | tee "${T}"/test.log + grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" +} + +src_install () { + dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} + dodoc src/release_notes.txt example + insinto /opt/primer3_config + doins -r src/primer3_config/* primer3*settings.txt + dohtml primer3_manual.htm +} diff --git a/sci-biology/prints/Manifest b/sci-biology/prints/Manifest new file mode 100644 index 000000000000..17763180d42d --- /dev/null +++ b/sci-biology/prints/Manifest @@ -0,0 +1 @@ +DIST prints-39.0.tar.bz2 26277011 RMD160 15e50aadf48f55ea77eed159ac4892509b31e2d5 SHA1 27ebc398d2e2911aa50493cc4fb3354d1d258312 SHA256 671f870230424014d4b104b24adb13ad5a30f1d947d9565de4943f77dccb5187 diff --git a/sci-biology/prints/metadata.xml b/sci-biology/prints/metadata.xml new file mode 100644 index 000000000000..7d2927f1d2fb --- /dev/null +++ b/sci-biology/prints/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + A protein motif fingerprint database maintained at the University of + Manchester. A fingerprint is a group of conserved motifs used to + characterise a protein family; its diagnostic power is refined by + iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs + do not overlap, but are separated along a sequence, though they may be + contiguous in 3D-space. Fingerprints can encode protein folds and + functionalities more flexibly and powerfully than can single motifs, + full diagnostic potency deriving from the mutual context provided by + motif neighbours. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/prints/prints-39.0.ebuild b/sci-biology/prints/prints-39.0.ebuild new file mode 100644 index 000000000000..c6dc22372252 --- /dev/null +++ b/sci-biology/prints/prints-39.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +MY_PV="${PV/./_}" + +DESCRIPTION="A protein motif fingerprint database" +HOMEPAGE="http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="public-domain" +IUSE="emboss minimal" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir PRINTS || die + echo + einfo "Indexing PRINTS for usage with EMBOSS." + EMBOSS_DATA="." printsextract -auto -infile prints${MY_PV}.dat || die \ + "Indexing PRINTS failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins newpr.lis ${PN}${MY_PV}.{all.fasta,dat,kdat,lis,nam,vsn} || die \ + "Installing raw database failed." + fi + if use emboss; then + insinto /usr/share/EMBOSS/data/PRINTS + doins PRINTS/* || die "Installing EMBOSS data files failed." + fi + dodoc README || die "Documentation installation failed." +} diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest new file mode 100644 index 000000000000..1d0739662628 --- /dev/null +++ b/sci-biology/probcons/Manifest @@ -0,0 +1 @@ +DIST probcons_v1_12.tar.gz 43200 SHA256 ecf3f9ab9ad47e14787c76d1c64aeea5533d4038c4be0236c00cdd79104cf383 diff --git a/sci-biology/probcons/files/gcc-4.3.patch b/sci-biology/probcons/files/gcc-4.3.patch new file mode 100644 index 000000000000..37c45c03a98f --- /dev/null +++ b/sci-biology/probcons/files/gcc-4.3.patch @@ -0,0 +1,44 @@ +diff -u probcons.orig/CompareToRef.cc probcons/CompareToRef.cc +--- probcons.orig/CompareToRef.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/CompareToRef.cc 2008-04-08 16:39:41.000000000 -0700 +@@ -16,6 +16,7 @@ + #include <limits> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + +diff -u probcons.orig/FixRef.cc probcons/FixRef.cc +--- probcons.orig/FixRef.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/FixRef.cc 2008-04-08 16:39:33.000000000 -0700 +@@ -17,6 +17,7 @@ + #include <algorithm> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + +diff -u probcons.orig/Main.cc probcons/Main.cc +--- probcons.orig/Main.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/Main.cc 2008-04-08 16:39:14.000000000 -0700 +@@ -21,6 +21,7 @@ + #include <climits> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + +diff -u probcons.orig/ProjectPairwise.cc probcons/ProjectPairwise.cc +--- probcons.orig/ProjectPairwise.cc 2008-04-08 16:38:46.000000000 -0700 ++++ probcons/ProjectPairwise.cc 2008-04-08 16:39:25.000000000 -0700 +@@ -16,6 +16,7 @@ + #include <limits> + #include <cstdio> + #include <cstdlib> ++#include <cstring> + #include <cerrno> + #include <iomanip> + diff --git a/sci-biology/probcons/files/probcons-1.12-cxxflags.patch b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch new file mode 100644 index 000000000000..e07ebe1a613f --- /dev/null +++ b/sci-biology/probcons/files/probcons-1.12-cxxflags.patch @@ -0,0 +1,47 @@ +diff --git a/Makefile b/Makefile +index 75fc47a..4a19140 100644 +--- a/Makefile ++++ b/Makefile +@@ -15,6 +15,8 @@ CXX = g++ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12" + + # debug mode +@@ -25,7 +27,7 @@ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12" + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + + ################################################################################ + # 3) Dependencies +@@ -37,19 +39,19 @@ TARGETS = probcons compare project makegnuplot + all : $(TARGETS) + + probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc +- $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o probcons Main.cc -lm + + compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc +- $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o compare CompareToRef.cc + + fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc +- $(CXX) $(CXXFLAGS) -o fixref FixRef.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o fixref FixRef.cc + + project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc +- $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o project ProjectPairwise.cc + + makegnuplot : MakeGnuPlot.cc +- $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc + + .PHONY : clean + clean: diff --git a/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch new file mode 100644 index 000000000000..1596f3b31916 --- /dev/null +++ b/sci-biology/probcons/files/probcons-1.12-gcc-4.6.patch @@ -0,0 +1,15 @@ + SafeVector.h | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/SafeVector.h b/SafeVector.h +index abf4b64..9c3292e 100644 +--- a/SafeVector.h ++++ b/SafeVector.h +@@ -8,6 +8,7 @@ + #ifndef SAFEVECTOR_H + #define SAFEVECTOR_H + ++#include <cstddef> + #include <cassert> + #include <vector> + diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/probcons/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild new file mode 100644 index 000000000000..1b3e76cd92ba --- /dev/null +++ b/sci-biology/probcons/probcons-1.12-r1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_P="${PN}_v${PV/./_}" + +DESCRIPTION="Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences" +HOMEPAGE="http://probcons.stanford.edu/" +SRC_URI="http://probcons.stanford.edu/${MY_P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +# Gnuplot is explicitly runtime-only, it's run using system() +RDEPEND=" + !sci-geosciences/gmt + sci-visualization/gnuplot" +DEPEND="" + +S="${WORKDIR}/${PN}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-cxxflags.patch \ + "${FILESDIR}"/gcc-4.3.patch \ + "${FILESDIR}"/${P}-gcc-4.6.patch +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + OPT_CXXFLAGS="${CXXFLAGS}" +} + +src_install() { + dobin probcons project makegnuplot + # Overlap with imagemagick + newbin compare compare-probcons + dodoc README +} + +pkg_postinst() { + ewarn "The 'compare' binary is installed as 'compare-probcons'" + ewarn "to avoid overlap with other packages." + einfo "You may also want to download the user manual" + einfo "from http://probcons.stanford.edu/manual.pdf" +} diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest new file mode 100644 index 000000000000..c7ebb5b77b50 --- /dev/null +++ b/sci-biology/prodigal/Manifest @@ -0,0 +1,2 @@ +DIST prodigal.v2_50.tar.gz 496654 RMD160 335ef065f1b03c6e063172c1c7eb6343402ee8de SHA1 ca7f7a9fa8d2bf1b5a0965cde25385704c96bc4e SHA256 0220dcc740c49941f9c2536b3aa81d3193f885bfd05c694f805d90d2cefbc421 +DIST prodigal.v2_60.tar.gz 615326 RMD160 bcc876588dfc6fddd9e7c0a433347f8604d7db67 SHA1 23a45dafedd98c04f9a4edbe82b037120644eaa2 SHA256 f18b093e0ac3b9ba40fc4d7bb76c2e20f2edb6d265451c82e3396138c9aac331 diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml new file mode 100644 index 000000000000..6e8b2ee66e66 --- /dev/null +++ b/sci-biology/prodigal/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="google-code">prodigal</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/prodigal/prodigal-2.50.ebuild b/sci-biology/prodigal/prodigal-2.50.ebuild new file mode 100644 index 000000000000..8e28c0a24196 --- /dev/null +++ b/sci-biology/prodigal/prodigal-2.50.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +MY_PV=${PV//./_} + +DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" +HOMEPAGE="http://prodigal.ornl.gov/ http://code.google.com/p/prodigal/" +SRC_URI="http://prodigal.googlecode.com/files/prodigal.v${MY_PV}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/prodigal.v${MY_PV}" + +src_prepare() { + sed -i -e 's/CFLAGS=/CFLAGS+=/' -e 's/LDFLAGS=/LDFLAGS+=/' Makefile || die +} + +src_install() { + dobin prodigal + dodoc README CHANGES +} diff --git a/sci-biology/prodigal/prodigal-2.60.ebuild b/sci-biology/prodigal/prodigal-2.60.ebuild new file mode 100644 index 000000000000..21c788eaccff --- /dev/null +++ b/sci-biology/prodigal/prodigal-2.60.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +MY_PV=${PV//./_} + +DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" +HOMEPAGE="http://prodigal.ornl.gov/ http://code.google.com/p/prodigal/" +SRC_URI="http://prodigal.googlecode.com/files/prodigal.v${MY_PV}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/prodigal.v${MY_PV}" + +src_prepare() { + sed -i -e 's/CFLAGS=/CFLAGS+=/' -e 's/LDFLAGS=/LDFLAGS+=/' Makefile || die +} + +src_install() { + dobin prodigal + dodoc README CHANGES +} diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest new file mode 100644 index 000000000000..386263860516 --- /dev/null +++ b/sci-biology/profphd/Manifest @@ -0,0 +1,2 @@ +DIST profphd-1.0.39.tar.xz 4406776 SHA256 4ff67e7b4dcb5748ee5115f1e7b9de7de6ca1c5a7982971a7147fe4ee5a5d288 SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b WHIRLPOOL 7e149f3e724ae5e727810ace6a1063708c35bb957861e4873c0763e48af5362ea50757d94c592052fec9d6e63767d036a39104a72ba6deb981c1f6023f19464e +DIST profphd-1.0.40.tar.xz 4491592 SHA256 50c85da552993758df191e3e06910fb221a156a8eaba94badf5a716b04648c5c SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3 WHIRLPOOL 4d7ac3cf32607cefc983116fa8fe8e795e92e89590bd612a2180e9fd59ec5c60220b065a2fddf3552aa81a3d02f852a36e08086d0867ac28ded2faf0d31a38ad diff --git a/sci-biology/profphd/files/profphd-1.0.39-perl.patch b/sci-biology/profphd/files/profphd-1.0.39-perl.patch new file mode 100644 index 000000000000..10682271601c --- /dev/null +++ b/sci-biology/profphd/files/profphd-1.0.39-perl.patch @@ -0,0 +1,16 @@ + src/prof/prof | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/prof/prof b/src/prof/prof +index 4f26024..356442d 100755 +--- a/src/prof/prof ++++ b/src/prof/prof +@@ -238,7 +238,7 @@ See each keyword for more help. Most of these are likely to be broken. + + alternative connectivity patterns (default=3) + +-=item 3 ++=item C<3> + + predict sec + acc + htm + diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/profphd/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild new file mode 100644 index 000000000000..8deb4f87abae --- /dev/null +++ b/sci-biology/profphd/profphd-1.0.39.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Secondary structure and solvent accessibility predictor" +HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" +SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="dev-lang/perl" +RDEPEND="${DEPEND} + dev-perl/librg-utils-perl + sci-libs/profnet + sci-libs/profphd-utils +" + +src_prepare() { + sed \ + -e '/ln -s/s:prof$:profphd:g' \ + -i src/prof/Makefile || die + epatch "${FILESDIR}"/${P}-perl.patch +} + +src_compile() { + emake prefix="${EPREFIX}/usr" +} + +src_install() { + emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install +} diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild new file mode 100644 index 000000000000..518ab5f1e473 --- /dev/null +++ b/sci-biology/profphd/profphd-1.0.40.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Secondary structure and solvent accessibility predictor" +HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction" +SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="dev-lang/perl" +RDEPEND="${DEPEND} + dev-perl/librg-utils-perl + sci-libs/profnet + sci-libs/profphd-utils +" + +src_prepare() { + sed \ + -e '/ln -s/s:prof$:profphd:g' \ + -i src/prof/Makefile || die + epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch +} + +src_compile() { + emake prefix="${EPREFIX}/usr" +} + +src_install() { + emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install +} diff --git a/sci-biology/prosite/Manifest b/sci-biology/prosite/Manifest new file mode 100644 index 000000000000..abbafda0a493 --- /dev/null +++ b/sci-biology/prosite/Manifest @@ -0,0 +1,4 @@ +DIST prosite-19.36.tar.bz2 4462981 RMD160 4d80651193b4c34bfdf42b770d4ec07927666057 SHA1 52acc49f0452b344a20b52983cbd896b6dd3b79b SHA256 6f923d4794f50c8e68d030d01cb6675579007cc04c197d811886dfb4ae853607 +DIST prosite-20.36.tar.bz2 5953220 RMD160 51f2da1efc886616e78ebced1a32c3a916bdef8f SHA1 328518c8e936d8960846bdefa8164a6f78a73503 SHA256 05593ff424d4145e19a7f394dab5a64fe0c5c6a640091fe03451f52bd31bfd25 +DIST prosite-20.52.tar.bz2 7038156 RMD160 506a64a15ea1145eadb8138b192718436282a2c1 SHA1 39abf5053c21f3d03ce0bb0bfc1fb3fb82284fb6 SHA256 89e5fc11e2ed18b1f16cc78e5271cccf6a5ea28a64fdcd7e99a770dfebb1968d +DIST prosite-20.72.tar.bz2 7521700 RMD160 5f48b403a05caeebf4136c2a626fa7a31e413b27 SHA1 164bc5ffc41aa2eb7e0a8588af577b84eca82040 SHA256 93b8664adecce63b14a96b6b9fbd970bcc2852a83413fd9b873df84dcfe07d12 diff --git a/sci-biology/prosite/metadata.xml b/sci-biology/prosite/metadata.xml new file mode 100644 index 000000000000..075d4b7bcf10 --- /dev/null +++ b/sci-biology/prosite/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + A protein families and domains database maintained at the Swiss + Institude for Bioinformatics. It consists of biologically significant + sites, patterns and profiles that help to reliably identify to which + known protein family (if any) a new sequence belongs. PROSITE currently + contains patterns and profiles specific for more than a thousand + protein families or domains. Each of these signatures comes with + documentation providing background information on the structure and + function of these proteins. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/prosite/prosite-19.36.ebuild b/sci-biology/prosite/prosite-19.36.ebuild new file mode 100644 index 000000000000..552c9193733f --- /dev/null +++ b/sci-biology/prosite/prosite-19.36.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A protein families and domains database" +LICENSE="swiss-prot" +HOMEPAGE="http://ca.expasy.org/prosite" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="amd64 ppc x86" + +DEPEND="emboss? ( sci-biology/emboss )" + +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir PROSITE + echo + einfo "Indexing PROSITE for usage with EMBOSS." + EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \ + "Indexing PROSITE failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins ${PN}.{doc,dat,lis} || die "Installing raw database failed." + fi + dodoc *.txt || die "Documentation installation failed." + dohtml *.htm || die "HTML documentation installation failed." + if use emboss; then + insinto /usr/share/EMBOSS/data/PROSITE + doins PROSITE/* || die "Installing EMBOSS data files failed." + fi +} diff --git a/sci-biology/prosite/prosite-20.36.ebuild b/sci-biology/prosite/prosite-20.36.ebuild new file mode 100644 index 000000000000..9bb65805bd27 --- /dev/null +++ b/sci-biology/prosite/prosite-20.36.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A protein families and domains database" +HOMEPAGE="http://ca.expasy.org/prosite" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="swiss-prot" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="amd64 ~ppc x86" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir PROSITE + echo + einfo "Indexing PROSITE for usage with EMBOSS." + EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \ + "Indexing PROSITE failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins *.{doc,dat} || die "Installing raw database failed." + fi + insinto /usr/share/doc/${PF} + doins *.pdf || die "PDF documentation installation failed." + if use emboss; then + insinto /usr/share/EMBOSS/data/PROSITE + doins PROSITE/* || die "Installing EMBOSS data files failed." + fi +} diff --git a/sci-biology/prosite/prosite-20.52.ebuild b/sci-biology/prosite/prosite-20.52.ebuild new file mode 100644 index 000000000000..69a997ed0987 --- /dev/null +++ b/sci-biology/prosite/prosite-20.52.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A protein families and domains database" +HOMEPAGE="http://ca.expasy.org/prosite" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="swiss-prot" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir PROSITE + echo + einfo "Indexing PROSITE for usage with EMBOSS." + EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \ + "Indexing PROSITE failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins *.{doc,dat} || die "Installing raw database failed." + fi + insinto /usr/share/doc/${PF} + doins *.pdf || die "PDF documentation installation failed." + if use emboss; then + insinto /usr/share/EMBOSS/data/PROSITE + doins PROSITE/* || die "Installing EMBOSS data files failed." + fi +} diff --git a/sci-biology/prosite/prosite-20.72.ebuild b/sci-biology/prosite/prosite-20.72.ebuild new file mode 100644 index 000000000000..799a5a432c14 --- /dev/null +++ b/sci-biology/prosite/prosite-20.72.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A protein families and domains database" +HOMEPAGE="http://ca.expasy.org/prosite" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="swiss-prot" +# Minimal build keeps only the indexed files (if applicable) and the +# documentation. The non-indexed database is not installed. +IUSE="emboss minimal" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" + +DEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${DEPEND}" + +src_compile() { + if use emboss; then + mkdir PROSITE + echo + einfo "Indexing PROSITE for usage with EMBOSS." + EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \ + "Indexing PROSITE failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins *.{doc,dat} || die "Installing raw database failed." + fi + insinto /usr/share/doc/${PF} + doins *.pdf || die "PDF documentation installation failed." + if use emboss; then + insinto /usr/share/EMBOSS/data/PROSITE + doins PROSITE/* || die "Installing EMBOSS data files failed." + fi +} diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest new file mode 100644 index 000000000000..1c17d7b94a74 --- /dev/null +++ b/sci-biology/psipred/Manifest @@ -0,0 +1,7 @@ +DIST psipred3.3.tar.gz 1239746 SHA256 133eef16ba4ac6ff5e10a757290ef794552833f42ed8251ff866ae56d9527c40 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e WHIRLPOOL d3883df88bde12a0f5ba6e195dc37b7104db36d16b5846b978fb045def6c4452edce4361dcced27ed36937bbd8d0e8dd4391b8592dca390941b3450e49cc5d34 +DIST psipred3.4.tar.gz 1102416 SHA256 c0eb8877313eb0564d34fc4d0e2d8d22e09d84d245e41008227560a10e64da9d SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919 WHIRLPOOL bdb47f296db1172df08f84b8cf18782e8585a8bc49f190b9783192db0e9d632bd6660437e8a35c24bb5970ca7a556b368c5a93373772f20d4be9a98ef963b902 +DIST psipred3.5.tar.gz 1101579 SHA256 107979a6bee968ba1df1ac1ee63bc1611105b83a7d519ab814f848ed955b76d8 SHA512 a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2 WHIRLPOOL fb07fdf550af6c9942e131a4856942c74adb3a7954c433ac7bc27680d9ab2b3db82a5178a15bcea224f7bb0da3cd84c94a4e9188be4fcbd49851037f631732e3 +DIST psipred31.tar.gz 746797 SHA256 2150696cae281bc942a18fc5f1e2057ed70cb6ee7b492c9594cbd99b8f6987dd SHA512 a04482fc5a08de03b2c1ac3eafbc289d476906811ef2557681f00e3ba865488c6061a194c5e12fe3ff38d31f42f13f4e783de1ca4a04508dd38a93c3ad848710 WHIRLPOOL 288d161698726a944b40acb3e2c355e61bad3644bf5edca40fd5e478f9d37e3acc9a91ee199fbadea680ab3a8c974eb8f80dd700dfe790e84d8a862148538dff +DIST psipred32.tar.gz 747120 SHA256 0775b0f07df87b2afd4989a378fc9b47f462507a264aaf2d56dd0243d9d00343 SHA512 49660d1c3cb9aa4c3ab13e721e23b83d70d0b6ecb772b08bd1058d3293dbcc9642d63092dd9746aa2a3a9085a13ba91e9849172d36954228a4f7a16e6e81050d WHIRLPOOL 24413200771fcee89c123fad25033b3230de3fdd82016ad7d084ddb096c081c46537f35c06578dad84a79a62c493e03b8f7b51be296b04d9568ea00b94293360 +DIST psipred321.tar.gz 747151 SHA256 5e88f2402e333be401b3022937b0167a33203f6289a84dd344941546f550f1f8 SHA512 b742f5fd3151bd624452bf37761fa66d364ea5b28d9d005ae6ce6f52fc6f2b17df31d6f1e600bd6c57776a1812f22b1eafbca781b430811a010d74f157a75cd1 WHIRLPOOL bb7111851ffe533b30fd6b77fb1ae396f0dd6506ce941944974c3b5c73c41d1a5b04c5af3d7e697aeb0640c03168b78d8832747940ed0de087df784d2d27e9f1 +DIST tdbdata.tar.gz 40241247 SHA256 87b7743538898f6cdf89cc5c18e1ecd040bc6223a01821d2bfc3109f4571851f SHA512 f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c WHIRLPOOL 37bc0912c6a71d1396489161465c690fb63d28167694d2e43553b6684c1f1f88866b2bf71f9531c7a7f41fc8ca81a6c93c2895ed498a07e3c4836f8c8bf4a34e diff --git a/sci-biology/psipred/files/2.6.1-Makefile.patch b/sci-biology/psipred/files/2.6.1-Makefile.patch new file mode 100644 index 000000000000..0a6df743ec83 --- /dev/null +++ b/sci-biology/psipred/files/2.6.1-Makefile.patch @@ -0,0 +1,42 @@ +--- src/Makefile 2008-03-09 22:59:51.000000000 +0100 ++++ src/Makefile.new 2009-04-09 12:31:38.669457918 +0200 +@@ -6,9 +6,7 @@ + #### CFLAGS Flags to pass to C compiler. + + INCDIR = . +-CC = cc + +-CFLAGS = -O + LIBS = -lm + + all: psipred psipass2 seq2mtx pfilt +@@ -20,13 +18,13 @@ + /bin/rm -f psipred psipass2 seq2mtx pfilt + + psipred: sspred_avpred.c ssdefs.h sspred_net.h +- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred ++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred + + psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h +- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 ++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 + + seq2mtx: seq2mtx.c +- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx ++ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx + + pfilt: pfilt.c +- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt ++ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt +--- src/Makefile 2009-04-09 12:34:41.636939862 +0200 ++++ src/Makefile.new 2009-04-09 12:36:03.796098341 +0200 +@@ -12,7 +12,8 @@ + all: psipred psipass2 seq2mtx pfilt + + install: +- /bin/cp psipred psipass2 seq2mtx pfilt ../bin ++ /bin/mkdir -p $(DESTDIR)/usr/bin ++ /bin/cp psipred psipass2 seq2mtx pfilt $(DESTDIR)/usr/bin + + clean: + /bin/rm -f psipred psipass2 seq2mtx pfilt diff --git a/sci-biology/psipred/files/2.6.1-path.patch b/sci-biology/psipred/files/2.6.1-path.patch new file mode 100644 index 000000000000..9b8d6b9fecfa --- /dev/null +++ b/sci-biology/psipred/files/2.6.1-path.patch @@ -0,0 +1,34 @@ +--- runpsipred 2008-04-05 00:14:36.000000000 +0200 ++++ runpsipred.new 2009-04-09 12:40:46.376203036 +0200 +@@ -14,13 +14,13 @@ + set dbname = nr + + # Where the NCBI programs have been installed +-set ncbidir = /usr/local/bin ++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V2 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V2 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t +--- runpsipred_single 2008-04-05 00:14:38.000000000 +0200 ++++ runpsipred_single.new 2009-04-09 12:41:10.086067082 +0200 +@@ -10,10 +10,10 @@ + # NOTE: Script modified to be more cluster friendly (DTJ April 2008) + + # Where the PSIPRED V2 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V2 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t diff --git a/sci-biology/psipred/files/3.0-path.patch b/sci-biology/psipred/files/3.0-path.patch new file mode 100644 index 000000000000..ebf9b2a61f4e --- /dev/null +++ b/sci-biology/psipred/files/3.0-path.patch @@ -0,0 +1,38 @@ +diff --git a/runpsipred b/runpsipred +index e133686..6ad57cc 100755 +--- a/runpsipred ++++ b/runpsipred +@@ -14,13 +14,13 @@ + set dbname = uniref90 + + # Where the NCBI programs have been installed +-set ncbidir = /usr/local/bin ++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V3 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V3 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t +diff --git a/runpsipred_single b/runpsipred_single +index 1f7680b..7bd5bc3 100755 +--- a/runpsipred_single ++++ b/runpsipred_single +@@ -10,10 +10,10 @@ + # NOTE: Script modified to be more cluster friendly (DTJ April 2008) + + # Where the PSIPRED V3 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V3 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t diff --git a/sci-biology/psipred/files/3.1-Makefile.patch b/sci-biology/psipred/files/3.1-Makefile.patch new file mode 100644 index 000000000000..0c70b6868565 --- /dev/null +++ b/sci-biology/psipred/files/3.1-Makefile.patch @@ -0,0 +1,38 @@ +diff --git a/src/Makefile b/src/Makefile +index abed8af..26061fa 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -6,9 +6,9 @@ + #### CFLAGS Flags to pass to C compiler. + + INCDIR = . +-CC = cc ++CC ?= gcc + +-CFLAGS = -O ++CFLAGS ?= -O2 + LIBS = -lm + + all: psipred psipass2 chkparse seq2mtx pfilt +@@ -20,16 +20,16 @@ clean: + /bin/rm -f psipred psipass2 chkparse seq2mtx pfilt + + psipred: sspred_avpred.c ssdefs.h sspred_net.h +- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred ++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred + + psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h +- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 ++ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2 + + chkparse: chkparse.c +- $(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse ++ $(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse + + seq2mtx: seq2mtx.c +- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx ++ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx + + pfilt: pfilt.c +- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt ++ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt diff --git a/sci-biology/psipred/files/3.1-fgets.patch b/sci-biology/psipred/files/3.1-fgets.patch new file mode 100644 index 000000000000..e58d677258e0 --- /dev/null +++ b/sci-biology/psipred/files/3.1-fgets.patch @@ -0,0 +1,13 @@ +diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c +index 4d8e5ff..0d82483 100644 +--- a/src/sspred_avpred.c ++++ b/src/sspred_avpred.c +@@ -213,7 +213,7 @@ predict(int argc, char **argv) + int getmtx(FILE *lfil) + { + int aa, i, j, naa; +- char buf[256], *p; ++ char buf[65536], *p; + + if (fscanf(lfil, "%d", &naa) != 1) + fail("Bad mtx file - no sequence length!"); diff --git a/sci-biology/psipred/files/3.1-path.patch b/sci-biology/psipred/files/3.1-path.patch new file mode 100644 index 000000000000..564e9c8a1ef9 --- /dev/null +++ b/sci-biology/psipred/files/3.1-path.patch @@ -0,0 +1,38 @@ +diff --git a/runpsipred b/runpsipred +index 4ccf44e..34dee99 100755 +--- a/runpsipred ++++ b/runpsipred +@@ -14,13 +14,13 @@ + set dbname = uniref90filt + + # Where the NCBI programs have been installed +-set ncbidir = /usr/local/bin ++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V2 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V2 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t +diff --git a/runpsipred_single b/runpsipred_single +index 1f7680b..7bd5bc3 100755 +--- a/runpsipred_single ++++ b/runpsipred_single +@@ -10,10 +10,10 @@ + # NOTE: Script modified to be more cluster friendly (DTJ April 2008) + + # Where the PSIPRED V3 programs have been installed +-set execdir = ./bin ++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin + + # Where the PSIPRED V3 data files have been installed +-set datadir = ./data ++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data + + set basename = $1:r + set rootname = $basename:t diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch new file mode 100644 index 000000000000..ec06d141ee34 --- /dev/null +++ b/sci-biology/psipred/files/3.2-fgets.patch @@ -0,0 +1,13 @@ +diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c +index 37b1332..4f04ab6 100644 +--- a/src/sspred_avpred.c ++++ b/src/sspred_avpred.c +@@ -223,7 +223,7 @@ predict(int argc, char **argv) + int getmtx(FILE *lfil) + { + int aa, i, j, naa; +- char buf[256], *p; ++ char buf[65536], *p; + + if (fscanf(lfil, "%d", &naa) != 1) + fail("Bad mtx file - no sequence length!"); diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml new file mode 100644 index 000000000000..655b161c218d --- /dev/null +++ b/sci-biology/psipred/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/psipred/psipred-3.1.ebuild b/sci-biology/psipred/psipred-3.1.ebuild new file mode 100644 index 000000000000..b81c4149b568 --- /dev/null +++ b/sci-biology/psipred/psipred-3.1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils prefix toolchain-funcs versionator + +MY_P="${PN}$(delete_all_version_separators)" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}" + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/${PV}-Makefile.patch \ + "${FILESDIR}"/${PV}-path.patch \ + "${FILESDIR}"/${PV}-fgets.patch + eprefixify runpsipred* +} + +src_compile() { + emake -C src CC=$(tc-getCC) || die "emake failed" +} + +src_install() { + emake -C src DESTDIR="${D}" install || die "installation failed" + dobin runpsipred* bin/* BLAST+/runpsipred* || die + insinto /usr/share/${PN} + doins -r data || die "failed to install data" + dodoc README || die "nothing to read" +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.2.1.ebuild b/sci-biology/psipred/psipred-3.2.1.ebuild new file mode 100644 index 000000000000..6b2158ef81e9 --- /dev/null +++ b/sci-biology/psipred/psipred-3.2.1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils prefix toolchain-funcs versionator + +MY_P="${PN}$(delete_all_version_separators)" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}" + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README + newdoc BLAST+/README README-blast +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.2.ebuild b/sci-biology/psipred/psipred-3.2.ebuild new file mode 100644 index 000000000000..418179c41278 --- /dev/null +++ b/sci-biology/psipred/psipred-3.2.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=3 + +inherit eutils prefix toolchain-funcs versionator + +MY_P="${PN}$(delete_all_version_separators)" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI="http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}" + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/${PV}-fgets.patch + eprefixify runpsipred* +} + +src_compile() { + emake -C src CC=$(tc-getCC) || die "emake failed" +} + +src_install() { + emake -C src DESTDIR="${D}" install || die "installation failed" + dobin runpsipred* bin/* BLAST+/runpsipred* || die + insinto /usr/share/${PN} + doins -r data || die "failed to install data" + dodoc README || die "nothing to read" +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.3.ebuild b/sci-biology/psipred/psipred-3.3.ebuild new file mode 100644 index 000000000000..3727fc29ad25 --- /dev/null +++ b/sci-biology/psipred/psipred-3.3.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils prefix toolchain-funcs versionator + +#MY_P="${PN}$(delete_all_version_separators)" +MY_P="${PN}${PV}" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI=" + http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz + test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* + emake -C src clean +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild new file mode 100644 index 000000000000..95d859b7898d --- /dev/null +++ b/sci-biology/psipred/psipred-3.4.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils prefix toolchain-funcs versionator + +#MY_P="${PN}$(delete_all_version_separators)" +MY_P="${PN}${PV}" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI=" + http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz + test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + app-shells/tcsh + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* + emake -C src clean +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild new file mode 100644 index 000000000000..95d859b7898d --- /dev/null +++ b/sci-biology/psipred/psipred-3.5.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils prefix toolchain-funcs versionator + +#MY_P="${PN}$(delete_all_version_separators)" +MY_P="${PN}${PV}" + +DESCRIPTION="Protein Secondary Structure Prediction" +HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/" +SRC_URI=" + http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz + test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )" + +LICENSE="psipred" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + app-shells/tcsh + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )" +DEPEND="" + +S="${WORKDIR}"/${PN} + +src_prepare() { + rm -f bin/* + epatch \ + "${FILESDIR}"/3.1-Makefile.patch \ + "${FILESDIR}"/3.1-path.patch \ + "${FILESDIR}"/3.2-fgets.patch + eprefixify runpsipred* + emake -C src clean +} + +src_compile() { + emake -C src CC=$(tc-getCC) +} + +src_install() { + emake -C src DESTDIR="${D}" install + dobin runpsipred* bin/* BLAST+/runpsipred* + insinto /usr/share/${PN} + doins -r data + dodoc README +} + +pkg_postinst() { + elog "Please use the update_blastdb.pl in order to" + elog "maintain your own local blastdb" +} diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest new file mode 100644 index 000000000000..4aea08f2d664 --- /dev/null +++ b/sci-biology/pysam/Manifest @@ -0,0 +1 @@ +DIST pysam-0.6.tar.gz 841790 SHA256 081c980481f31a81acb06f6fa5638b899321eddfd9eeb5075393e4dad84a1fc8 SHA512 b60df4551600f04e8ae67aec0f2745846d2411e2a1cc4c874ef296ee80ab075256190ebb0ec64eb78231d4d7b59670c5259818cd315f52c923774cc4c0b8b391 WHIRLPOOL eddeb19f3ebf0c6326f7c1b6b7224b2b8cb708e0bf7ceb66b1cac18909abafd1704b264452b70ee6721af4b3b360b51285dcffd7f137c6128920f91dc0dec7b2 diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml new file mode 100644 index 000000000000..49afc3c3d532 --- /dev/null +++ b/sci-biology/pysam/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="google-code">pysam</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/pysam/pysam-0.6-r1.ebuild b/sci-biology/pysam/pysam-0.6-r1.ebuild new file mode 100644 index 000000000000..3873100fa45f --- /dev/null +++ b/sci-biology/pysam/pysam-0.6-r1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="5" + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam" +SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" + +python_compile() { + python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" + distutils-r1_python_compile +} diff --git a/sci-biology/qrna/Manifest b/sci-biology/qrna/Manifest new file mode 100644 index 000000000000..b939f54fb27d --- /dev/null +++ b/sci-biology/qrna/Manifest @@ -0,0 +1 @@ +DIST qrna-2.0.3c.tar.bz2 6423705 SHA256 fc88b58dddab26f20477a50340453e9d360ea34956ba526f7db6959283399b1c SHA512 98710bcf8993e2c09ec1eb33632a18ac993ab817dc95a865200b0868f79b95ff61f5f7d3f0c1c33de6d26f674025ea11a8c7d8175b96071e4594daa252fa52b5 WHIRLPOOL f7c788629f6580e3f1c2ccaa5109ba13d8f103abfd3a88f3ef127577fc825fdc7deef102325ab2645a24ba1215d59b21e2c77448631c90d6eae47aa95a9463e5 diff --git a/sci-biology/qrna/files/26qrna b/sci-biology/qrna/files/26qrna new file mode 100644 index 000000000000..53a90b90ed78 --- /dev/null +++ b/sci-biology/qrna/files/26qrna @@ -0,0 +1 @@ +QRNADB="/usr/share/qrna/data" diff --git a/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch new file mode 100644 index 000000000000..dfa1b2a29e94 --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch @@ -0,0 +1,328 @@ +diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c +--- qrna-2.0.3c.orig/squid/sqio.c 2005-05-11 19:30:51.000000000 +0300 ++++ qrna-2.0.3c/squid/sqio.c 2009-08-05 22:27:20.000000000 +0300 +@@ -215,7 +215,7 @@ + } + + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + readline(V->f, V->sbuffer); + } +@@ -277,7 +277,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -305,7 +305,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -314,7 +314,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -323,7 +323,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -337,7 +337,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -355,7 +355,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -367,7 +367,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -389,7 +389,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -398,7 +398,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -416,7 +416,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -427,7 +427,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -460,11 +460,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -494,12 +494,12 @@ + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); + +- getline(V); /*skip title-junk line*/ ++ get_line(V); /*skip title-junk line*/ + + readLoop(0, endNBRF, V); + + while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>'))) +- getline(V); ++ get_line(V); + } + + +@@ -529,7 +529,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -549,7 +549,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -571,7 +571,7 @@ + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -598,7 +598,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -607,7 +607,7 @@ + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -631,7 +631,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -647,7 +647,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -658,7 +658,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -680,7 +680,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -692,7 +692,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -700,7 +700,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -732,14 +732,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -747,7 +747,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -786,7 +786,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -800,7 +800,7 @@ + SeqfilePosition(SQFILE *sqfp, long offset) + { + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -817,7 +817,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -912,7 +912,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -991,7 +991,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -1098,7 +1098,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + +@@ -1204,7 +1204,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch new file mode 100644 index 000000000000..d03f650dd39e --- /dev/null +++ b/sci-biology/qrna/files/qrna-2.0.3c-ldflags.patch @@ -0,0 +1,28 @@ +diff --git a/src/Makefile b/src/Makefile +index 1d1631b..4fa3af9 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -131,17 +131,17 @@ DEMOS = + all: $(PROGS) + + main: $(OBJ) main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(LIBS) + cfgbuild: $(OBJ) cfgbuild.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna: $(OBJ) eqrna.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + eqrna_sample: $(OBJ) eqrna_sample.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + shuffle: $(OBJ) shuffle.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR) $@.o $(OBJ) $(LIBS) + rnamat_main: $(OBJ2) rnamat_main.o +- $(CC) $(CFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ -L$(SQUIDDIR02) $@.o $(OBJ2) $(LIBS) + + main.o: ../src/main.c + $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $? diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml new file mode 100644 index 000000000000..d4648212cbad --- /dev/null +++ b/sci-biology/qrna/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/qrna/qrna-2.0.3c-r1.ebuild b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild new file mode 100644 index 000000000000..f8834630acee --- /dev/null +++ b/sci-biology/qrna/qrna-2.0.3c-r1.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Prototype ncRNA genefinder" +HOMEPAGE="http://selab.janelia.org/software.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~ppc x86" +IUSE="" + +RDEPEND=" + dev-lang/perl + sci-biology/hmmer" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-glibc-2.10.patch \ + "${FILESDIR}"/${P}-ldflags.patch + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "/^AR/s:ar:$(tc-getAR):g" \ + -e "/^RANLIB/s:ranlib:$(tc-getRANLIB):g" \ + -e "/CFLAGS/s:=.*$:= ${CFLAGS}:" \ + -i {src,squid,squid02}/Makefile || die + rm -v squid*/*.a +} + +src_compile() { + local dir + for dir in squid squid02 src; do + emake -C ${dir} + done +} + +src_install () { + dobin src/{cfgbuild,eqrna,eqrna_sample,rnamat_main} scripts/* + + newdoc 00README README + insinto /usr/share/doc/${PF} + doins documentation/* + + insinto /usr/share/${PN}/data + doins lib/* + insinto /usr/share/${PN}/demos + doins Demos/* + + # Sets the path to the QRNA data files. + doenvd "${FILESDIR}"/26qrna +} diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest new file mode 100644 index 000000000000..7e64fe420af6 --- /dev/null +++ b/sci-biology/raxml/Manifest @@ -0,0 +1 @@ +DIST RAxML-7.2.6.tar.bz2 202803 SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868 SHA512 b0027a7e583e6471a774d9e784a0be1ff63b3824a8cfbebca68bf9e414adab297206ea2d43c9b97456e6acc0a6a15f55ca33983381dd6150f9e7ea71ddecdcd3 WHIRLPOOL 7fe7ac66412c979d3ecca17e2c06a32566fefe7bdcf39664a0885fcdebc2b8187c222ca5e29cf2685085fba21a8aff0a2aefceec08823cab155a5f62f8b59490 diff --git a/sci-biology/raxml/files/raxml-7.2.5-makefile.patch b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch new file mode 100644 index 000000000000..8b381e50cb58 --- /dev/null +++ b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch @@ -0,0 +1,29 @@ + Makefile.gcc | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile.gcc b/Makefile.gcc +index 8d09549..59af556 100644 +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,10 +1,10 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> + +-CC = gcc ++CC ?= gcc + + +-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 ++CFLAGS += -D_GNU_SOURCE + #-Wall -std=c99 -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -pedantic-errors -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + + +@@ -19,7 +19,7 @@ all : raxmlHPC + GLOBAL_DEPS = axml.h globalVariables.h + + raxmlHPC : $(objs) +- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) ++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) + + classify.o : classify.c $(GLOBAL_DEPS) + evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch new file mode 100644 index 000000000000..ae83e2eef4e7 --- /dev/null +++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch @@ -0,0 +1,29 @@ + Makefile.gcc | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile.gcc b/Makefile.gcc +index 716b6c6..f0c1de2 100644 +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,10 +1,10 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> + +-CC = gcc ++CC ?= gcc + + +-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse ++CFLAGS += -D_GNU_SOURCE + + + +@@ -19,7 +19,7 @@ all : raxmlHPC + GLOBAL_DEPS = axml.h globalVariables.h + + raxmlHPC : $(objs) +- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) ++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) + + classify.o : classify.c $(GLOBAL_DEPS) + evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/raxml/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild new file mode 100644 index 000000000000..b9ace2a0ec0f --- /dev/null +++ b/sci-biology/raxml/raxml-7.2.6.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" +HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" +SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse3 +threads" + +REQUIRED_USE="cpu_flags_x86_sse3" + +# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS +DEPEND="" # mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/RAxML-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-makefile.patch + + use cpu_flags_x86_sse3 && append-cflags -D__SIM_SSE3 + use threads && \ + append-cflags -D_USE_PTHREADS && \ + append-ldflags -pthread + + tc-export CC +} + +src_compile() { + emake -f Makefile.gcc +} + +src_install() { + dobin raxmlHPC +} diff --git a/sci-biology/readseq/Manifest b/sci-biology/readseq/Manifest new file mode 100644 index 000000000000..bcd1dfa237bf --- /dev/null +++ b/sci-biology/readseq/Manifest @@ -0,0 +1,2 @@ +DIST readseq-20100513.zip 628406 SHA256 878b689828bdf59a73c377c314fe504b9f18569ed5cd512acdb264cf90e72601 SHA512 6e2a2207e3a1f14e5cc4f7ffd2c74563b6deb088dda02727611359a17e1b157d9c661715d1f896d1573786cb88f61d3b952ab7a53e6dc30f2dcbcead58604b32 WHIRLPOOL 6f5b7ff075a081f521971689d014ad3ea6ffdc50db1b24766712d21fb86f83d7767f9afa76473f0be6f36560c8572c7051337cde8020cb9562dfef96a2bfdc8a +DIST readseq-source-20080420.zip 627341 SHA256 d91ccadcbf5fde29525c639ece6ae132e0db863a7e63f96f69647e591617e8dd SHA512 cbc7afa46d2f0cfb30aa75ab88e4942a18ddf46a03a4cfb8d7e07bd23bce3fe015483899d371b947a0f1d6ec464b8c1238df7f7fc89753bb75dbb284f1e07b48 WHIRLPOOL fb180c53cb0555887d5278871498d66840d1d27da47ef6a947f0cd048bfb79762faf9493a645be6909bf41c5627131f3ced8d29b8241372d1e6034dc7524004d diff --git a/sci-biology/readseq/files/20080420-no-bundling.patch b/sci-biology/readseq/files/20080420-no-bundling.patch new file mode 100644 index 000000000000..f2e1708f8821 --- /dev/null +++ b/sci-biology/readseq/files/20080420-no-bundling.patch @@ -0,0 +1,14 @@ +diff --git a/build.xml b/build.xml +index e3d723c..4b44d6f 100644 +--- a/build.xml ++++ b/build.xml +@@ -229,9 +229,6 @@ + + <!-- for now, unjar xml classes into build/classes and rejar in readseq.jar --> + +- <unjar overwrite="false" src="${orgxml.jar}" dest="${build.home}/classes" /> +- <unjar overwrite="false" src="${xml.jar}" dest="${build.home}/classes" /> +- + <!-- <copy todir="${build.home}/classes""> --> + <!-- <src dir="${basedir}/META-INF"/> --> + <!-- </copy> --> diff --git a/sci-biology/readseq/metadata.xml b/sci-biology/readseq/metadata.xml new file mode 100644 index 000000000000..b198f044f3f5 --- /dev/null +++ b/sci-biology/readseq/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + Reads and writes nucleic/protein sequences in various formats. Data + files may have multiple sequences. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/readseq/readseq-20080420-r1.ebuild b/sci-biology/readseq/readseq-20080420-r1.ebuild new file mode 100644 index 000000000000..43c538beb596 --- /dev/null +++ b/sci-biology/readseq/readseq-20080420-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +MY_P="${PN}-source-${PV}" +DESCRIPTION="Reads and writes nucleic/protein sequences in various formats" +HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/" +# Originally unversioned at +# http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq-source.zip. +# Renamed to the date of the modification and mirrored +SRC_URI="http://dev.gentoo.org/~dberkholz/distfiles/${MY_P}.zip" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="!=sci-biology/meme-4.8.1 + >=virtual/jre-1.4" +DEPEND=">=virtual/jdk-1.4 + app-arch/unzip" + +S=${WORKDIR} + +java_prepare() { + rm "${S}"/lib/* || die + epatch "${FILESDIR}"/${PV}-* +} + +src_install() { + java-pkg_dojar build/readseq.jar + java-pkg_dolauncher +} + +pkg_postinst() { + elog "Documentation is available at" + elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html" +} diff --git a/sci-biology/readseq/readseq-20100513.ebuild b/sci-biology/readseq/readseq-20100513.ebuild new file mode 100644 index 000000000000..6539ebd427cc --- /dev/null +++ b/sci-biology/readseq/readseq-20100513.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Reads and writes nucleic/protein sequences in various formats" +HOMEPAGE="http://iubio.bio.indiana.edu/soft/molbio/readseq/" +SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.zip" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="!=sci-biology/meme-4.8.1 + >=virtual/jre-1.4" +DEPEND=">=virtual/jdk-1.4 + app-arch/unzip" + +S=${WORKDIR} + +java_prepare() { + rm "${S}"/lib/* || die + epatch "${FILESDIR}"/20080420-* +} + +src_install() { + java-pkg_dojar build/readseq.jar + java-pkg_dolauncher +} + +pkg_postinst() { + elog "Documentation is available at" + elog "http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html" +} diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest new file mode 100644 index 000000000000..632fbeb3bc72 --- /dev/null +++ b/sci-biology/rebase/Manifest @@ -0,0 +1,2 @@ +DIST rebase-1507.tar.xz 68538212 SHA256 87880a3f8cd49f537abf0a3d3fe00dca928ab5299cfd436351a279051f358efe SHA512 9fcb61d0f53f227485ecdaa86709b3fb7c20d8a430c456d2c24f68154691028709358d8dc25d4be2662d368e3cdd13d15eb316342dfb0f1aa8447b3742b80375 WHIRLPOOL f8cfc127890e17529d557f69c20be7ad90cd9e01ff9e112d41bb8c88359f7310744977253e8f82c71301ef1ea449f2e4cee9189e3b552edc242ab1033dca0b5e +DIST rebase-1508.tar.xz 69944352 SHA256 579ef686b0efea32d88633f85411da9c1396572eec0d20bd163ca7bf615c7b04 SHA512 d5dc9eb704ce28ab7951ab2a8781de76dcbd7a4b6d6c6634abcd36766c8dce77b6d8a712789fe6293a6ddc66cd9103e17121b0ff52f0d3fbabfc5bf47c2f2100 WHIRLPOOL f082a3096cef636a61a176d3d3fe5b993bc83e3b332d134ebc20201d21f2f66e3400ffc5d561018c63fb3201c5fc0862126a32c17c5c96f118859b62a618d341 diff --git a/sci-biology/rebase/metadata.xml b/sci-biology/rebase/metadata.xml new file mode 100644 index 000000000000..734fcff7e215 --- /dev/null +++ b/sci-biology/rebase/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + The Restriction Enzyme data BASE is a collection of information about + restriction enzymes and related proteins. It is maintained by New + England Biolabs. It contains published and unpublished references, + recognition and cleavage sites, isoschizomers, commercial availability, + methylation sensitivity, crystal and sequence data. DNA + methyltransferases, homing endonucleases, nicking enzymes, specificity + subunits and control proteins are also included. More recently, + putative DNA methyltransferases and restriction enzymes, as predicted + from analysis of genomic sequences, are also listed. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/rebase/rebase-1507.ebuild b/sci-biology/rebase/rebase-1507.ebuild new file mode 100644 index 000000000000..6b32ba231a2e --- /dev/null +++ b/sci-biology/rebase/rebase-1507.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PV=${PV#1} + +DESCRIPTION="A restriction enzyme database" +HOMEPAGE="http://rebase.neb.com" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" +IUSE="emboss minimal" + +RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" +DEPEND="${RDEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + echo; einfo "Indexing Rebase for usage with EMBOSS." + mkdir REBASE || die + EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ + -protofile proto.${MY_PV} -equivalences \ + || die "Indexing Rebase failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins withrefm.${MY_PV} proto.${MY_PV} + fi + newdoc REBASE.DOC README + if use emboss; then + insinto /usr/share/EMBOSS/data/REBASE + doins REBASE/embossre.{enz,ref,sup} + insinto /usr/share/EMBOSS/data + doins REBASE/embossre.equ + fi +} diff --git a/sci-biology/rebase/rebase-1508.ebuild b/sci-biology/rebase/rebase-1508.ebuild new file mode 100644 index 000000000000..f171a569ee83 --- /dev/null +++ b/sci-biology/rebase/rebase-1508.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PV=${PV#1} + +DESCRIPTION="A restriction enzyme database" +HOMEPAGE="http://rebase.neb.com" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" +IUSE="emboss minimal" + +RDEPEND="emboss? ( >=sci-biology/emboss-5.0.0 )" +DEPEND="${RDEPEND}" + +RESTRICT="binchecks strip" + +src_compile() { + if use emboss; then + echo; einfo "Indexing Rebase for usage with EMBOSS." + mkdir REBASE || die + EMBOSS_DATA="." rebaseextract -auto -infile withrefm.${MY_PV} \ + -protofile proto.${MY_PV} -equivalences \ + || die "Indexing Rebase failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN} + doins withrefm.${MY_PV} proto.${MY_PV} + fi + newdoc REBASE.DOC README + if use emboss; then + insinto /usr/share/EMBOSS/data/REBASE + doins REBASE/embossre.{enz,ref,sup} + insinto /usr/share/EMBOSS/data + doins REBASE/embossre.equ + fi +} diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest new file mode 100644 index 000000000000..d779bd4735c4 --- /dev/null +++ b/sci-biology/recon/Manifest @@ -0,0 +1 @@ +DIST RECON1.06.tar.gz 109484 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461 SHA512 0df3ecb4b569d087ffce6b4f326f6c8686e78b08864dff09b7441d4f4067e72baf80ecb211366c23f7b49ed123426f612347309ceb5ae052d9bb371070525d32 WHIRLPOOL d1f66533d16bc1b5cb4cc51b35278a25c5cd1b797a4178987a873757f9b8f591527f84d65a0dfd4f8b165c35bf336c94f8c465235a3ebc101992e5af970cccec diff --git a/sci-biology/recon/files/1.06-buffer-overflow.patch b/sci-biology/recon/files/1.06-buffer-overflow.patch new file mode 100644 index 000000000000..29d220c7310d --- /dev/null +++ b/sci-biology/recon/files/1.06-buffer-overflow.patch @@ -0,0 +1,13 @@ +diff --git a/src/eledef.c b/src/eledef.c +index 964890b..a001ec4 100644 +--- a/src/eledef.c ++++ b/src/eledef.c +@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp, + + void img_charge(IPROT_t **shadow, int ct, FILE *input) { + int i=0, pos=0; +- char line[100]; ++ char line[256]; + int scan_flag; + MSP_t msp; + diff --git a/sci-biology/recon/files/recon-1.06-respect.patch b/sci-biology/recon/files/recon-1.06-respect.patch new file mode 100644 index 000000000000..a02038d84784 --- /dev/null +++ b/sci-biology/recon/files/recon-1.06-respect.patch @@ -0,0 +1,24 @@ + src/Makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/Makefile b/src/Makefile +index 36ef59b..e45a0f2 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -13,14 +13,14 @@ MANDIR = $(HOME)/man + #SRCDIR = . + + ## your compiler +-CC = gcc ++CC ?= gcc + #CC = cc # for SGI Origin200 compiler# + + ## any special compiler flags you want + # -pedantic clashes with -DMEMDEBUG?? + # + #CFLAGS = -g -Wall -pedantic +-CFLAGS = -O ++CFLAGS ?= -O + #CFLAGS = -g + #CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler# + diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/recon/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/recon/recon-1.06-r1.ebuild b/sci-biology/recon/recon-1.06-r1.ebuild new file mode 100644 index 000000000000..86e820f49e9f --- /dev/null +++ b/sci-biology/recon/recon-1.06-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit eutils + +DESCRIPTION="Automated de novo identification of repeat families from genomic sequences" +HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html" +SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="examples" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/RECON${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-buffer-overflow.patch + sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die +} + +src_compile() { + emake -C src +} + +src_install() { + dobin scripts/* + exeinto /usr/libexec/${PN} + doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} + dodoc 00README + insinto /usr/share/${PN} + use examples && doins -r Demos +} diff --git a/sci-biology/recon/recon-1.06-r2.ebuild b/sci-biology/recon/recon-1.06-r2.ebuild new file mode 100644 index 000000000000..12a9207c9f42 --- /dev/null +++ b/sci-biology/recon/recon-1.06-r2.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit eutils toolchain-funcs + +DESCRIPTION="Automated de novo identification of repeat families from genomic sequences" +HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html" +SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="examples" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}/RECON${PV}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-buffer-overflow.patch \ + "${FILESDIR}"/${P}-respect.patch + sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die + tc-export CC +} + +src_compile() { + emake -C src +} + +src_install() { + dobin scripts/* + exeinto /usr/libexec/${PN} + doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} + dodoc 00README + insinto /usr/share/${PN} + use examples && doins -r Demos +} diff --git a/sci-biology/repeatmasker-libraries/Manifest b/sci-biology/repeatmasker-libraries/Manifest new file mode 100644 index 000000000000..599aa33f9dd1 --- /dev/null +++ b/sci-biology/repeatmasker-libraries/Manifest @@ -0,0 +1 @@ +DIST repeatmaskerlibraries-20120418.tar.gz 28059668 SHA256 7bd44a70ee33ef60ab829b4cb84a2a82a6fa923e2992071f374b7a473e4dac62 SHA512 254d47faeee72ee62e6854ebc389578691d66e99d9d5e2a0c2462bf752ac5b4d2171c9e6b45d4f87f548a96b62753bb9c37c2d2c00e06544e91dd09fe2bbfe32 WHIRLPOOL 1da932f84c591221c61177116d734d00c36c52d588bcdab73ed63e8128b9c90a63f855bf4e8e603167e059f98465460b5b2e7e00e4a724bec230d27b1b32a31a diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/repeatmasker-libraries/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild new file mode 100644 index 000000000000..4c6b6b6ba01e --- /dev/null +++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20120418.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="A special version of RepBase used by RepeatMasker" +HOMEPAGE="http://repeatmasker.org/" +SRC_URI="repeatmaskerlibraries-${PV}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/Libraries" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please register and download repeatmaskerlibraries-${PV}.tar.gz" + einfo 'at http://www.girinst.org/' + einfo '(select the "Repbase Update - RepeatMasker edition" link)' + einfo 'and place it in '${DISTDIR} +} + +src_install() { + insinto /usr/share/repeatmasker/Libraries + doins "${S}"/RepeatMaskerLib.embl + dodoc README + dohtml README.html +} diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest new file mode 100644 index 000000000000..5f4296e01d47 --- /dev/null +++ b/sci-biology/repeatmasker/Manifest @@ -0,0 +1 @@ +DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL f2d67ea6e97a0667ac9ce89f8ed8c590b911d9cd4fc4482bdc48c0ea7ca07161a8bec267ed3e2a950f6d8c501f992ceadc62e1211a80b6bc1c90d293cbf45e77 diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/repeatmasker/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild new file mode 100644 index 000000000000..acef7d5caf4b --- /dev/null +++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PV=${PV//\./-} + +DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA" +HOMEPAGE="http://repeatmasker.org/" +SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz" + +LICENSE="OSL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + sci-biology/rmblast + sci-biology/trf + sci-biology/repeatmasker-libraries" + +S="${WORKDIR}/RepeatMasker" + +src_configure() { + sed -i -e 's/system( "clear" );//' \ + -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die + echo " +env +/usr/share/${PN} +/usr/bin +2 +/opt/rmblast/bin +Y +5" | "${S}/configure" || die "configure failed" + sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \ + -e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \ + -e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \ + "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die +} + +src_install() { + exeinto /usr/share/${PN} + for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do + doexe $i || die + dosym /usr/share/${PN}/$i /usr/bin/$i || die + done + + dodir /usr/share/${PN}/lib + insinto /usr/share/${PN}/lib + doins "${S}"/*.pm || die + + insinto /usr/share/${PN} + doins -r util Matrices Libraries taxonomy.dat *.help || die + keepdir /usr/share/${PN}/Libraries + + dodoc README INSTALL *.help +} diff --git a/sci-biology/rmblast/Manifest b/sci-biology/rmblast/Manifest new file mode 100644 index 000000000000..00c455fce326 --- /dev/null +++ b/sci-biology/rmblast/Manifest @@ -0,0 +1 @@ +DIST rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz 10744076 SHA256 996be9886189364fff8ed39d4668122b2e5b8b010be47d929602416d95628eef SHA512 e7c2ebd114aee045ea3f3f462cf2658440e13a2d1eb777648386e1c5eeda9f8083af383c019f9b5802d935d6eb2367eef20822afc45233ddb44a426b4dd7ddb6 WHIRLPOOL aa3ada4297812a97614b0fe218de65d7474edfb5910e156eb09b625d45338a97b35f46876f5edf6105ead8b321a28f55ed7de2ad251bbc48ffd0cfa65ee2ac7a diff --git a/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch new file mode 100644 index 000000000000..70200d59ea4a --- /dev/null +++ b/sci-biology/rmblast/files/rmblast-1.2-gcc47.patch @@ -0,0 +1,865 @@ + c++/include/corelib/ncbiexpt.hpp | 4 +- + c++/include/corelib/ncbimisc.hpp | 2 + + c++/include/corelib/ncbiobj.hpp | 2 +- + c++/include/corelib/ncbistl.hpp | 6 +- + c++/include/corelib/ncbistr.hpp | 2 +- + c++/include/corelib/test_boost.hpp | 44 +++++- + c++/include/dbapi/driver/dbapi_object_convert.hpp | 8 +- + .../dbapi/driver/impl/dbapi_driver_utils.hpp | 2 +- + c++/include/serial/impl/stltypes.hpp | 16 ++- + c++/include/serial/iterator.hpp | 6 +- + c++/include/serial/serialbase.hpp | 8 +- + c++/include/util/bitset/bmfunc.h | 7 + + c++/include/util/linkedset.hpp | 16 +-- + c++/include/util/rangemap.hpp | 4 +- + c++/src/connect/ncbi_gnutls.c | 19 ++- + c++/src/corelib/ncbifile.cpp | 2 +- + c++/src/corelib/test_boost.cpp | 156 ++++++++++++++++++++- + c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp | 2 +- + c++/src/serial/stdtypes.cpp | 8 +- + 19 files changed, 269 insertions(+), 45 deletions(-) + +diff --git a/c++/include/corelib/ncbiexpt.hpp b/c++/include/corelib/ncbiexpt.hpp +index a9cf850..6d90e74 100644 +--- a/c++/include/corelib/ncbiexpt.hpp ++++ b/c++/include/corelib/ncbiexpt.hpp +@@ -831,7 +831,7 @@ const TTo* UppermostCast(const TFrom& from) + exception_class(const exception_class& other) \ + : base_class(other) \ + { \ +- x_Assign(other); \ ++ this->x_Assign(other); \ + } \ + public: \ + virtual ~exception_class(void) throw() {} \ +@@ -1154,7 +1154,7 @@ public: + : TBase( other) + { + m_Errno = other.m_Errno; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +diff --git a/c++/include/corelib/ncbimisc.hpp b/c++/include/corelib/ncbimisc.hpp +index f45d280..f0c030d 100644 +--- a/c++/include/corelib/ncbimisc.hpp ++++ b/c++/include/corelib/ncbimisc.hpp +@@ -57,6 +57,8 @@ + * @{ + */ + ++#include <stdlib.h> ++ + #ifndef NCBI_ESWITCH_DEFINED + #define NCBI_ESWITCH_DEFINED + +diff --git a/c++/include/corelib/ncbiobj.hpp b/c++/include/corelib/ncbiobj.hpp +index 4f83db4..815c188 100644 +--- a/c++/include/corelib/ncbiobj.hpp ++++ b/c++/include/corelib/ncbiobj.hpp +@@ -2128,7 +2128,7 @@ public: + CIRef<Interface, TThisType> ref( + dynamic_cast<Interface*>(proxy->GetLockedObject()), *this); + if (ref.NotNull()) { +- Unlock(ref.GetPointer()); ++ this->Unlock(ref.GetPointer()); + } + return ref; + } +diff --git a/c++/include/corelib/ncbistl.hpp b/c++/include/corelib/ncbistl.hpp +index 0bf465a..0618d9d 100644 +--- a/c++/include/corelib/ncbistl.hpp ++++ b/c++/include/corelib/ncbistl.hpp +@@ -37,7 +37,6 @@ + + #include <common/ncbi_export.h> + +- + // Get rid of some warnings in MSVC++ 6.00 + #if (_MSC_VER >= 1200) + // too long identificator name in the debug info; truncated +@@ -162,6 +161,9 @@ typedef int NCBI_NAME2(T_EAT_SEMICOLON_,UniqueName) + #endif + + #if defined(NCBI_COMPILER_GCC) || defined(NCBI_COMPILER_WORKSHOP) ++# if defined(NCBI_COMPILER_GCC) && NCBI_COMPILER_VERSION >= 400 ++# include <algorithm> ++# endif + // This template is used by some stl algorithms (sort, reverse...) + // We need to have our own implementation because some C++ Compiler vendors + // implemented it by using a temporary variable and an assignment operator +@@ -174,7 +176,7 @@ template<typename Iter> + inline + void iter_swap( Iter it1, Iter it2 ) + { +- swap( *it1, * it2 ); ++ swap( *it1, *it2 ); + } + + END_STD_SCOPE +diff --git a/c++/include/corelib/ncbistr.hpp b/c++/include/corelib/ncbistr.hpp +index db7054f..63e3299 100644 +--- a/c++/include/corelib/ncbistr.hpp ++++ b/c++/include/corelib/ncbistr.hpp +@@ -2583,7 +2583,7 @@ public: + : TBase(other) + { + m_Pos = other.m_Pos; +- x_Assign(other); ++ this->x_Assign(other); + } + + /// Destructor. +diff --git a/c++/include/corelib/test_boost.hpp b/c++/include/corelib/test_boost.hpp +index 69c41f3..4cd77d3 100644 +--- a/c++/include/corelib/test_boost.hpp ++++ b/c++/include/corelib/test_boost.hpp +@@ -56,10 +56,18 @@ + # undef BOOST_AUTO_TEST_MAIN + #endif + ++#ifdef NCBI_COMPILER_MSVC ++# pragma warning(push) ++// 'class' : class has virtual functions, but destructor is not virtual ++# pragma warning(disable: 4265) ++#endif ++ ++#include <boost/version.hpp> + #include <boost/test/auto_unit_test.hpp> + #include <boost/test/floating_point_comparison.hpp> + #include <boost/test/framework.hpp> + #include <boost/test/execution_monitor.hpp> ++#include <boost/test/parameterized_test.hpp> + + #include <boost/preprocessor/tuple/rem.hpp> + #include <boost/preprocessor/repeat.hpp> +@@ -72,6 +80,7 @@ + #undef BOOST_CHECK_THROW_IMPL + #undef BOOST_CHECK_NO_THROW_IMPL + #undef BOOST_FIXTURE_TEST_CASE ++#undef BOOST_PARAM_TEST_CASE + + #define BOOST_CHECK_THROW_IMPL( S, E, P, prefix, TL ) \ + try { \ +@@ -109,6 +118,12 @@ catch( ... ) { \ + } \ + /**/ + ++#if BOOST_VERSION >= 104200 ++# define NCBI_BOOST_LOCATION() , boost::execution_exception::location() ++#else ++# define NCBI_BOOST_LOCATION() ++#endif ++ + #define BOOST_FIXTURE_TEST_CASE( test_name, F ) \ + struct test_name : public F { void test_method(); }; \ + \ +@@ -124,7 +139,8 @@ static void BOOST_AUTO_TC_INVOKER( test_name )() \ + ::framework::current_test_case().p_name \ + << "\"" << ex); \ + throw boost::execution_exception( \ +- boost::execution_exception::cpp_exception_error, ""); \ ++ boost::execution_exception::cpp_exception_error, "" \ ++ NCBI_BOOST_LOCATION() ); \ + } \ + } \ + \ +@@ -142,6 +158,12 @@ BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) ( \ + void test_name::test_method() \ + /**/ + ++#define BOOST_PARAM_TEST_CASE( function, begin, end ) \ ++ ::NCBI_NS_NCBI::NcbiTestGenTestCases( function, \ ++ BOOST_TEST_STRINGIZE( function ), \ ++ (begin), (end) ) \ ++/**/ ++ + /// Set timeout value for the test case created using auto-registration + /// facility. + #define BOOST_AUTO_TEST_CASE_TIMEOUT(test_name, n) \ +@@ -158,6 +180,26 @@ static struct BOOST_JOIN( test_name, _timeout_spec ) \ + } BOOST_JOIN( test_name, _timeout_spec_inst ); \ + /**/ + ++/// Automatic registration of the set of test cases based on some function ++/// accepting one parameter. Set of parameters used to call that function is ++/// taken from iterator 'begin' which is incremented until it reaches 'end'. ++/// ++/// @sa BOOST_PARAM_TEST_CASE ++#define BOOST_AUTO_PARAM_TEST_CASE( function, begin, end ) \ ++ BOOST_AUTO_TU_REGISTRAR(function) ( \ ++ BOOST_PARAM_TEST_CASE(function, begin, end)) \ ++/**/ ++ ++#define BOOST_TIMEOUT(M) \ ++ do { \ ++ static string s(M); \ ++ throw boost::execution_exception( \ ++ boost::execution_exception::timeout_error, s \ ++ NCBI_BOOST_LOCATION()); \ ++ } while (0) \ ++/**/ ++ ++ + + #define NCBITEST_CHECK_IMPL(P, check_descr, TL, CT) \ + BOOST_CHECK_NO_THROW_IMPL(BOOST_CHECK_IMPL(P, check_descr, TL, CT), TL) +diff --git a/c++/include/dbapi/driver/dbapi_object_convert.hpp b/c++/include/dbapi/driver/dbapi_object_convert.hpp +index 6fcde61..eddde81 100644 +--- a/c++/include/dbapi/driver/dbapi_object_convert.hpp ++++ b/c++/include/dbapi/driver/dbapi_object_convert.hpp +@@ -67,7 +67,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +@@ -92,7 +92,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +@@ -133,7 +133,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +@@ -174,7 +174,7 @@ public: + operator const CTime&(void) const; + + private: +- mutable obj_type& m_Value; ++ obj_type& m_Value; + }; + + //////////////////////////////////////////////////////////////////////////////// +diff --git a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp +index 0792a6d..b6bd64b 100644 +--- a/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp ++++ b/c++/include/dbapi/driver/impl/dbapi_driver_utils.hpp +@@ -231,7 +231,7 @@ protected: + + private: + const string& m_SPName; +- mutable impl::CConnection& m_Conn; ++ impl::CConnection& m_Conn; + }; + + +diff --git a/c++/include/serial/impl/stltypes.hpp b/c++/include/serial/impl/stltypes.hpp +index d41ab94..7d9e3ce 100644 +--- a/c++/include/serial/impl/stltypes.hpp ++++ b/c++/include/serial/impl/stltypes.hpp +@@ -412,6 +412,7 @@ public: + typedef StlIterator TStlIterator; + typedef TypeInfoIterator TTypeInfoIterator; + typedef typename TTypeInfoIterator::TObjectPtr TObjectPtr; ++ typedef CStlClassInfoFunctions<Container> CParent; + + static TStlIterator& It(TTypeInfoIterator& iter) + { +@@ -437,7 +438,8 @@ public: + } + static bool InitIterator(TTypeInfoIterator& iter) + { +- TStlIterator stl_iter = Get(iter.GetContainerPtr()).begin(); ++ TStlIterator stl_iter ++ = CParent::Get(iter.GetContainerPtr()).begin(); + if ( sizeof(TStlIterator) <= sizeof(iter.m_IteratorData) ) { + void* data = &iter.m_IteratorData; + new (data) TStlIterator(stl_iter); +@@ -445,7 +447,7 @@ public: + else { + iter.m_IteratorData = new TStlIterator(stl_iter); + } +- return stl_iter != Get(iter.GetContainerPtr()).end(); ++ return stl_iter != CParent::Get(iter.GetContainerPtr()).end(); + } + static void ReleaseIterator(TTypeInfoIterator& iter) + { +@@ -466,7 +468,7 @@ public: + + static bool NextElement(TTypeInfoIterator& iter) + { +- return ++It(iter) != Get(iter.GetContainerPtr()).end(); ++ return ++It(iter) != CParent::Get(iter.GetContainerPtr()).end(); + } + static TObjectPtr GetElementPtr(const TTypeInfoIterator& iter) + { +@@ -503,7 +505,7 @@ public: + + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CParent::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + it = c->erase(it); + return it != c->end(); +@@ -511,7 +513,7 @@ public: + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CParent::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +@@ -542,7 +544,7 @@ public: + } + static bool EraseElement(TTypeInfoIterator& iter) + { +- TStlIterator& it = It(iter); ++ TStlIterator& it = CParent::It(iter); + Container* c = static_cast<Container*>(iter.GetContainerPtr()); + TStlIterator erase = it++; + c->erase(erase); +@@ -551,7 +553,7 @@ public: + static void EraseAllElements(TTypeInfoIterator& iter) + { + Container* c = static_cast<Container*>(iter.GetContainerPtr()); +- c->erase(It(iter), c->end()); ++ c->erase(CParent::It(iter), c->end()); + } + + static void SetIteratorFunctions(CStlOneArgTemplate* info) +diff --git a/c++/include/serial/iterator.hpp b/c++/include/serial/iterator.hpp +index 25e1193..cddb046 100644 +--- a/c++/include/serial/iterator.hpp ++++ b/c++/include/serial/iterator.hpp +@@ -491,13 +491,13 @@ protected: + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo) + : m_NeedType(needType) + { +- Init(beginInfo); ++ this->Init(beginInfo); + } + CTypeIteratorBase(TTypeInfo needType, const TBeginInfo& beginInfo, + const string& filter) + : m_NeedType(needType) + { +- Init(beginInfo, filter); ++ this->Init(beginInfo, filter); + } + + virtual bool CanSelect(const CConstObjectInfo& object) +@@ -599,7 +599,7 @@ public: + + CTypesIteratorBase<Parent>& operator=(const TBeginInfo& beginInfo) + { +- Init(beginInfo); ++ this->Init(beginInfo); + return *this; + } + +diff --git a/c++/include/serial/serialbase.hpp b/c++/include/serial/serialbase.hpp +index be6a4f9..d59fb25 100644 +--- a/c++/include/serial/serialbase.hpp ++++ b/c++/include/serial/serialbase.hpp +@@ -364,11 +364,15 @@ public: + // cast to object type + TObject& operator*(void) + { +- return *reinterpret_cast<TObject*>(m_Buffer); ++ TObject* ptr = static_cast<TObject*> ++ (static_cast<void*>(m_Buffer)); ++ return *ptr; + } + const TObject& operator*(void) const + { +- return *reinterpret_cast<const TObject*>(m_Buffer); ++ const TObject* ptr = static_cast<const TObject*> ++ (static_cast<const void*>(m_Buffer)); ++ return *ptr; + } + + // construct/destruct object +diff --git a/c++/include/util/bitset/bmfunc.h b/c++/include/util/bitset/bmfunc.h +index 5917ee5..a8c204b 100644 +--- a/c++/include/util/bitset/bmfunc.h ++++ b/c++/include/util/bitset/bmfunc.h +@@ -37,6 +37,13 @@ For more information please visit: http://bmagic.sourceforge.net + namespace bm + { + ++bm::id_t bit_block_any_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right); ++ ++bm::id_t bit_block_calc_count_range(const bm::word_t* block, ++ bm::word_t left, ++ bm::word_t right); + + /*! + @brief Structure with statistical information about bitset's memory +diff --git a/c++/include/util/linkedset.hpp b/c++/include/util/linkedset.hpp +index e8bbe6e..364164b 100644 +--- a/c++/include/util/linkedset.hpp ++++ b/c++/include/util/linkedset.hpp +@@ -268,10 +268,10 @@ public: + pair<iterator, bool> ins = m_Container.insert(value); + if ( ins.second ) { + if ( ins.first == begin() ) +- insertToStart(*ins.first); ++ this->insertToStart(*ins.first); + else { + iterator prev = ins.first; +- insertAfter(*--prev, *ins.first); ++ this->insertAfter(*--prev, *ins.first); + } + } + return ins; +@@ -280,10 +280,10 @@ public: + void erase(iterator iter) + { + if ( iter == begin() ) +- removeFromStart(*iter); ++ this->removeFromStart(*iter); + else { + iterator prev = iter; +- removeAfter(*--prev, *iter); ++ this->removeAfter(*--prev, *iter); + } + m_Container.erase(iter); + } +@@ -422,10 +422,10 @@ public: + { + iterator iter = m_Container.insert(value); + if ( iter == begin() ) +- insertToStart(get(iter)); ++ this->insertToStart(get(iter)); + else { + iterator prev = iter; +- insertAfter(get(--prev), get(iter)); ++ this->insertAfter(get(--prev), get(iter)); + } + return iter; + } +@@ -433,10 +433,10 @@ public: + void erase(iterator iter) + { + if ( iter == begin() ) +- removeFromStart(get(iter)); ++ this->removeFromStart(get(iter)); + else { + iterator prev = iter; +- removeAfter(get(--prev), get(iter)); ++ this->removeAfter(get(--prev), get(iter)); + } + m_Container.erase(iter); + } +diff --git a/c++/include/util/rangemap.hpp b/c++/include/util/rangemap.hpp +index c4f5f37..56e267d 100644 +--- a/c++/include/util/rangemap.hpp ++++ b/c++/include/util/rangemap.hpp +@@ -578,7 +578,7 @@ public: + // get level + + // insert element +- TSelectMapI selectIter = insertLevel(selectKey); ++ TSelectMapI selectIter = this->insertLevel(selectKey); + pair<TLevelMapI, bool> levelIns = selectIter->second.insert(value); + + pair<iterator, bool> ret; +@@ -640,7 +640,7 @@ public: + // insert element + iterator ret; + ret.m_Range = range_type::GetWhole(); +- ret.m_SelectIter = insertLevel(selectKey); ++ ret.m_SelectIter = this->insertLevel(selectKey); + ret.m_SelectIterEnd = this->m_SelectMap.end(); + ret.m_LevelIter = ret.m_SelectIter->second.insert(value); + return ret; +diff --git a/c++/src/connect/ncbi_gnutls.c b/c++/src/connect/ncbi_gnutls.c +index f0242b7..8b13713 100644 +--- a/c++/src/connect/ncbi_gnutls.c ++++ b/c++/src/connect/ncbi_gnutls.c +@@ -98,7 +98,6 @@ static const int kGnuTlsCertPrio[] = { + 0 + }; + static const int kGnuTlsCompPrio[] = { +- GNUTLS_COMP_LZO, + GNUTLS_COMP_ZLIB, + GNUTLS_COMP_NULL, + 0 +@@ -254,6 +253,24 @@ static EIO_Status s_GnuTlsOpen(void* session, int* error) + } + + ++/*ARGSUSED*/ ++static void x_set_errno(gnutls_session_t session, int error) ++{ ++# ifdef LIBGNUTLS_VERSION_NUMBER ++# if \ ++ LIBGNUTLS_VERSION_MAJOR > 1 || \ ++ LIBGNUTLS_VERSION_MINOR > 5 || \ ++ LIBGNUTLS_VERSION_PATCH > 3 ++ gnutls_transport_set_errno(session, error); ++ return; ++# endif /*LIBGNUTLS_VERSION >= 1.5.4*/ ++# endif /*LIBGNUTLS_VERSION_NUMBER*/ ++ /*NOTREACHED*/ ++ if (error) ++ errno = error; ++} ++ ++ + static ssize_t x_GnuTlsPull(gnutls_transport_ptr_t ptr, + void* buf, size_t size) + { +diff --git a/c++/src/corelib/ncbifile.cpp b/c++/src/corelib/ncbifile.cpp +index d751e62..fdc81c7 100644 +--- a/c++/src/corelib/ncbifile.cpp ++++ b/c++/src/corelib/ncbifile.cpp +@@ -51,8 +51,8 @@ + # include <dirent.h> + # include <pwd.h> + # include <fcntl.h> +-# include <sys/time.h> + # include <sys/mman.h> ++# include <sys/time.h> + # ifdef HAVE_SYS_STATVFS_H + # include <sys/statvfs.h> + # endif +diff --git a/c++/src/corelib/test_boost.cpp b/c++/src/corelib/test_boost.cpp +index dfd9cc8..f93d2ca 100644 +--- a/c++/src/corelib/test_boost.cpp ++++ b/c++/src/corelib/test_boost.cpp +@@ -41,6 +41,7 @@ + #ifndef BOOST_TEST_NO_LIB + # define BOOST_TEST_NO_LIB + #endif ++#define BOOST_TEST_NO_MAIN + #include <corelib/test_boost.hpp> + + #include <boost/preprocessor/cat.hpp> +@@ -95,6 +96,7 @@ const char* kTestResultTimeout = "timeout"; + const char* kTestResultAborted = "aborted"; + const char* kTestResultSkipped = "skipped"; + const char* kTestResultDisabled = "disabled"; ++const char* kTestResultToFix = "tofix"; + + + typedef but::results_reporter::format TBoostRepFormatter; +@@ -168,14 +170,24 @@ public: + unsigned long elapsed); + virtual + void test_unit_skipped(ostream& ostr, but::test_unit const& tu); ++#if BOOST_VERSION >= 104200 ++ virtual ++ void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd, ++ boost::execution_exception const& ex); ++ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up ++ using TBoostLogFormatter::log_exception; ++#else + virtual + void log_exception (ostream& ostr, but::log_checkpoint_data const& lcd, + but::const_string explanation); ++#endif + virtual + void log_entry_start (ostream& ostr, but::log_entry_data const& led, + log_entry_types let); + virtual + void log_entry_value (ostream& ostr, but::const_string value); ++ // Next line is necessary for compiling with ICC and Boost 1.41.0 and up ++ using TBoostLogFormatter::log_entry_value; + virtual + void log_entry_finish (ostream& ostr); + +@@ -402,10 +414,15 @@ public: + + /// Mark test case as failed due to hit of the timeout + void SetTestTimedOut(but::test_case* tc); ++ /// Register the fact of test failure ++ void SetTestErrored(but::test_case* tc); ++ /// Check if given test is marked as requiring fixing in the future ++ bool IsTestToFix(const but::test_unit* tu); + + /// Get number of actually executed tests + int GetRanTestsCount(void); +- ++ /// Get number of tests that were failed but are marked to be fixed ++ int GetToFixTestsCount(void); + /// Get string representation of result of test execution + string GetTestResultString(but::test_unit* tu); + +@@ -415,6 +432,11 @@ public: + /// Check if user initialization functions failed + bool IsInitFailed(void); + ++ /// Check if there were any test errors ++ bool HasTestErrors(void); ++ /// Check if there were any timeouted tests ++ bool HasTestTimeouts(void); ++ + private: + typedef list<TNcbiTestUserFunction> TUserFuncsList; + +@@ -493,6 +515,8 @@ private: + TUnitsSet m_DisabledTests; + /// List of all tests which result is a timeout + TUnitsSet m_TimedOutTests; ++ /// List of all tests marked as in need of fixing in the future ++ TUnitsSet m_ToFixTests; + /// List of all dependencies for each test having dependencies + TUnitToManyMap m_TestDeps; + /// Observer to make test dependencies and look for unit's timeouts +@@ -512,12 +536,18 @@ private: + /// String representation for whole test timeout (real value taken from + /// CHECK_TIMEOUT in Makefile). + string m_TimeoutStr; ++ /// Multiplicator for timeouts ++ double m_TimeMult; + /// Timer measuring elapsed time for the whole test + CStopWatch m_Timer; + /// Timeout that was set in currently executing unit before adjustment + /// + /// @sa AdjustTestTimeout() + unsigned int m_CurUnitTimeout; ++ /// Flag showing if there were some test errors ++ bool m_HasTestErrors; ++ /// Flag showing if there were some timeouted tests ++ bool m_HasTestTimeouts; + }; + + +@@ -794,7 +824,10 @@ CNcbiTestApplication::CNcbiTestApplication(void) + m_RunMode (0), + m_DummyTest(NULL), + m_Timeout (0), +- m_Timer (CStopWatch::eStart) ++ m_TimeMult (1), ++ m_Timer (CStopWatch::eStart), ++ m_HasTestErrors(false), ++ m_HasTestTimeouts(false) + { + m_Reporter = new CNcbiBoostReporter(); + m_Logger = new CNcbiBoostLogger(); +@@ -1244,6 +1277,24 @@ CNcbiTestApplication::GetRanTestsCount(void) + return result; + } + ++int ++CNcbiTestApplication::GetToFixTestsCount(void) ++{ ++ int result = 0; ++ ITERATE(TUnitsSet, it, m_ToFixTests) { ++ if (!but::results_collector.results((*it)->p_id).passed()) ++ ++result; ++ } ++ return result; ++} ++ ++inline bool ++CNcbiTestApplication::IsTestToFix(const but::test_unit* tu) ++{ ++ return m_ToFixTests.find(const_cast<but::test_unit*>(tu)) ++ != m_ToFixTests.end(); ++} ++ + inline void + CNcbiTestApplication::x_SetupBoostReporters(void) + { +@@ -1391,6 +1442,18 @@ CNcbiTestApplication::InitTestFramework(int argc, char* argv[]) + return NULL; + } + ++inline bool ++CNcbiTestApplication::HasTestErrors(void) ++{ ++ return m_HasTestErrors; ++} ++ ++inline bool ++CNcbiTestApplication::HasTestTimeouts(void) ++{ ++ return m_HasTestTimeouts; ++} ++ + void + CNcbiTestsCollector::visit(but::test_case const& test) + { +@@ -1431,9 +1494,20 @@ CNcbiTestsObserver::test_unit_finish(but::test_unit const& tu, + // elapsed comes in microseconds + if (timeout != 0 && timeout < elapsed / 1000000) { + boost::execution_exception ex( +- boost::execution_exception::timeout_error, "Timeout exceeded"); ++ boost::execution_exception::timeout_error, "Timeout exceeded" ++ NCBI_BOOST_LOCATION()); + but::framework::exception_caught(ex); + } ++ ++ but::test_results& tr = but::s_rc_impl().m_results_store[tu.p_id]; ++ if (!tr.passed() && s_GetTestApp().IsTestToFix(&tu)) { ++ static_cast<but::readwrite_property<bool>& >( ++ static_cast<but::class_property<bool>& >( ++ tr.p_skipped)).set(true); ++ static_cast<but::readwrite_property<but::counter_t>& >( ++ static_cast<but::class_property<but::counter_t>& >( ++ tr.p_assertions_failed)).set(0); ++ } + } + + void +@@ -1551,12 +1625,21 @@ CNcbiBoostLogger::test_unit_skipped(ostream& ostr, but::test_unit const& tu) + m_Upper->test_unit_skipped(ostr, tu); + } + ++#if BOOST_VERSION >= 104200 ++void ++CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd, ++ boost::execution_exception const& ex) ++{ ++ m_Upper->log_exception(ostr, lcd, ex); ++} ++#else + void + CNcbiBoostLogger::log_exception(ostream& ostr, but::log_checkpoint_data const& lcd, + but::const_string explanation) + { + m_Upper->log_exception(ostr, lcd, explanation); + } ++#endif + + void + CNcbiBoostLogger::log_entry_start(ostream& ostr, but::log_entry_data const& led, +@@ -1631,9 +1714,74 @@ NcbiTestGetUnit(CTempString test_name) + END_NCBI_SCOPE + + ++using namespace but; ++ + /// Global initialization function called from Boost framework +-but::test_suite* ++test_suite* + init_unit_test_suite(int argc, char* argv[]) + { + return NCBI_NS_NCBI::s_GetTestApp().InitTestFramework(argc, argv); + } ++ ++// This main() is mostly a copy from Boost's unit_test_main.ipp ++int ++main(int argc, char* argv[]) ++{ ++ int result = boost::exit_success; ++ ++ try { ++ framework::init( &init_unit_test_suite, argc, argv ); ++ ++ if( !runtime_config::test_to_run().is_empty() ) { ++ test_case_filter filter( runtime_config::test_to_run() ); ++ ++ traverse_test_tree( framework::master_test_suite().p_id, filter ); ++ } ++ ++ framework::run(); ++ ++ // Let's try to make report in case of any error after all catches. ++ //results_reporter::make_report(); ++ ++ if (!runtime_config::no_result_code()) { ++ result = results_collector.results( framework::master_test_suite().p_id ).result_code(); ++ if (!NCBI_NS_NCBI::s_GetTestApp().HasTestErrors() ++ && NCBI_NS_NCBI::s_GetTestApp().HasTestTimeouts()) ++ { ++ // This should certainly go to the output. So we can use only ++ // printf, nothing else. ++ printf("There were no test failures, only timeouts.\n" ++ " (for autobuild scripts: NCBI_UNITTEST_TIMEOUTS_BUT_NO_ERRORS)\n"); ++ } ++ } ++ } ++#if BOOST_VERSION >= 104200 ++ catch( framework::nothing_to_test const& ) { ++ result = boost::exit_success; ++ } ++#endif ++ catch( framework::internal_error const& ex ) { ++ results_reporter::get_stream() << "Boost.Test framework internal error: " << ex.what() << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ catch( framework::setup_error const& ex ) { ++ results_reporter::get_stream() << "Test setup error: " << ex.what() << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ catch( std::exception const& ex ) { ++ results_reporter::get_stream() << "Test framework error: " << ex.what() << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ catch( ... ) { ++ results_reporter::get_stream() << "Boost.Test framework internal error: unknown reason" << std::endl; ++ ++ result = boost::exit_exception_failure; ++ } ++ ++ results_reporter::make_report(); ++ ++ return result; ++} +diff --git a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp +index 92e817f..cfab8ab 100644 +--- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp ++++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp +@@ -1199,7 +1199,7 @@ private: + CSeqDBAtlasHolder m_AtlasHolder; + + /// Reference to memory management layer. +- mutable CSeqDBAtlas & m_Atlas; ++ CSeqDBAtlas & m_Atlas; + + /// The list of database names provided to the constructor. + string m_DBNames; +diff --git a/c++/src/serial/stdtypes.cpp b/c++/src/serial/stdtypes.cpp +index f6fa651..d6e8f80 100644 +--- a/c++/src/serial/stdtypes.cpp ++++ b/c++/src/serial/stdtypes.cpp +@@ -720,7 +720,7 @@ public: + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CParent::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -751,7 +751,7 @@ public: + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CParent::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } +@@ -786,7 +786,7 @@ public: + if ( IsSigned() ) { + // signed -> unsigned + // check for negative value +- if ( IsNegative(value) ) ++ if ( CParent::IsNegative(value) ) + ThrowIntegerOverflow(); + } + if ( sizeof(value) > sizeof(result) ) { +@@ -817,7 +817,7 @@ public: + // unsigned -> signed + if ( sizeof(value) == sizeof(result) ) { + // same size - check for sign change only +- if ( IsNegative(result) ) ++ if ( CParent::IsNegative(result) ) + ThrowIntegerOverflow(); + } + } diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/rmblast/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/rmblast/rmblast-1.2-r1.ebuild b/sci-biology/rmblast/rmblast-1.2-r1.ebuild new file mode 100644 index 000000000000..768b309813bc --- /dev/null +++ b/sci-biology/rmblast/rmblast-1.2-r1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +MY_NCBI_BLAST_V=2.2.23+ + +DESCRIPTION="RepeatMasker compatible version of NCBI BLAST+" +HOMEPAGE="http://www.repeatmasker.org/RMBlast.html" +SRC_URI="http://www.repeatmasker.org/rmblast-${PV}-ncbi-blast-${MY_NCBI_BLAST_V}-src.tar.gz" + +LICENSE="OSL-2.1" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-libs/boost" +DEPEND="${RDEPEND} + app-arch/cpio" + +S="${WORKDIR}/${P}-ncbi-blast-${MY_NCBI_BLAST_V}-src/c++" + +src_prepare() { + filter-ldflags -Wl,--as-needed + sed \ + -e 's/-print-file-name=libstdc++.a//' \ + -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ + -e "/DEF_FAST_FLAGS=/s:=\".*\":=\"${CFLAGS}\":g" \ + -i src/build-system/configure || die + epatch "${FILESDIR}"/${P}-gcc47.patch +} + +src_configure() { + tc-export CXX CC + + "${S}"/configure --without-debug \ + --with-mt \ + --without-static \ + --with-dll \ + --prefix="${ED}"/opt/${PN} \ + --with-boost="${EPREFIX}/usr/include/boost" \ + || die +} diff --git a/sci-biology/rnaview/Manifest b/sci-biology/rnaview/Manifest new file mode 100644 index 000000000000..f56b09e2659c --- /dev/null +++ b/sci-biology/rnaview/Manifest @@ -0,0 +1 @@ +DIST rnaview-20040713.tar.bz2 433916 SHA256 0961779c83e247a4b04c02d90d3850e8c4c889b630194ea1516cbeb6c6dbad17 SHA512 c63bb728bad0f358ab36f4ca18f4f9ef046811f21d3b8f3c6fdd3e6e6fcb367a9a52710476c5daea001f8f3262f72b64f0c0546f0c1423f463f2e0d288809e8e WHIRLPOOL 7ae8953a8028da0eb525a6b33964267b15721dbe148f5077cf2c7e47c7cc2e3a47616bcc944e7f8180c0696c27ac16c53bd3847d02db5a575df3cebba29dd169 diff --git a/sci-biology/rnaview/files/rnaview-20040713-implicit.patch b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch new file mode 100644 index 000000000000..009f6e79ae86 --- /dev/null +++ b/sci-biology/rnaview/files/rnaview-20040713-implicit.patch @@ -0,0 +1,13 @@ +Fix implicit function declaration + +--- src/xml2ps.c ++++ src/xml2ps.c +@@ -36,7 +36,7 @@ + void read_sugar_syn(char *inpfile, long **sugar_syn); + void get_sugar_syn(FILE *inp, char *value_ch); + void get_chain_broken(long nres, double **a, double **b, long *chain_broken); +- ++extern void get_BDIR(char *BDIR, char *filename); + + + FILE *psfile; diff --git a/sci-biology/rnaview/files/rnaview-20040713-makefile.patch b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch new file mode 100644 index 000000000000..1af72f581fbf --- /dev/null +++ b/sci-biology/rnaview/files/rnaview-20040713-makefile.patch @@ -0,0 +1,87 @@ + Makefile | 20 +++++++++++++++++--- + rnaml2ps/Makefile | 19 ++++++++++++------- + 2 files changed, 29 insertions(+), 10 deletions(-) + +diff --git a/Makefile b/Makefile +index 452e6c4..00d35f0 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,4 +1,4 @@ +-CC = cc ++CC ?= cc + + + +@@ -56,12 +56,17 @@ OBJ_FILE = $(OBJ)/rnaview.o \ + $(OBJ)/multiple.o \ + $(OBJ)/statistics.o + ++.PHONY: clean all install ++ ++SUBDIRS = rnaml2ps ++ + all: $(RNAVIEW) ++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} all ) ; done + +-CFLAGS = $(LINCLUDES) ++CFLAGS += $(LINCLUDES) + + $(RNAVIEW) : $(HFILES) $(OBJ_FILE) +- $(CC) $(CFLAGS) -o $@ $(OBJ_FILE) $(LDFLAGS) -lm $(MALLOCLIB) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJ_FILE) -lm $(MALLOCLIB) + + + +@@ -111,6 +116,15 @@ $(OBJ)/statistics.o : $(SRC)/statistics.c + clean: + @rm -f $(OBJ)/*.o + @rm -f $(ALLTARGETS) ++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} clean ) ; done ++ ++install: ++ install -D -m 0755 bin/rnaview $(DESTDIR)/usr/bin/rnaview ++ mkdir -p $(DESTDIR)/usr/share/rnaview/BASEPARS ++ install -m 0644 BASEPARS/* $(DESTDIR)/usr/share/rnaview/BASEPARS ++ mkdir -p $(DESTDIR)/usr/share/rnaview/test ++ install -m 0644 test/* $(DESTDIR)/usr/share/rnaview/test ++ for dir in ${SUBDIRS} ; do ( cd $$dir ; ${MAKE} install ) ; done + + export: + mkdir -p $(EXPORT_DIR) +diff --git a/rnaml2ps/Makefile b/rnaml2ps/Makefile +index d207655..2278ccc 100644 +--- a/rnaml2ps/Makefile ++++ b/rnaml2ps/Makefile +@@ -1,20 +1,25 @@ +-CFLAGS = -O +-CC = cc ++CFLAGS ?= -O ++CC ?= cc + + # ++++++++++++++++++++++++++++ Program RNADRAW + RNADRAW = rnaml2ps + OBJS_RNADRAW = rnaml2ps.o nrutil.o + ++all: $(RNADRAW) ++ + $(RNADRAW): $(OBJS_RNADRAW) +- $(CC) -o $(RNADRAW) $(OBJS_RNADRAW) -lm ++ $(CC) $(LDFLAGS) -o $(RNADRAW) $(OBJS_RNADRAW) -lm + + nrutil.o : nrutil.c +- cc -c nrutil.c ++ $(CC) $(CFLAGS) -c nrutil.c + + rnaml2ps.o : rnaml2ps.c +- cc -c rnaml2ps.c ++ $(CC) $(CFLAGS) -c rnaml2ps.c + + +-.PHONY : clean ++.PHONY : clean all install + clean: +- rm *.o ++ rm -f *.o ++ ++install: ++ install -D -m 0755 $(RNADRAW) $(DESTDIR)/usr/bin/$(RNADRAW) diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml new file mode 100644 index 000000000000..b243b0c8da63 --- /dev/null +++ b/sci-biology/rnaview/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + The RNAView program generates 2-dimensional displays of RNA/DNA + secondary structures with tertiary interactions. RNAView + automatically identifies and classifies the types of base pairs that + are formed in nucleic acid structures, fully implementing Leontis and + Westhof's (RNA (2001) 7, 499-512), convention for edge-to-edge + hydrogen bonding interactions. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/rnaview/rnaview-20040713-r2.ebuild b/sci-biology/rnaview/rnaview-20040713-r2.ebuild new file mode 100644 index 000000000000..ac9168c57512 --- /dev/null +++ b/sci-biology/rnaview/rnaview-20040713-r2.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 + +inherit eutils toolchain-funcs + +DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions" +HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" +LICENSE="public-domain" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +src_prepare() { + epatch "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-implicit.patch + cat <<- EOF > 22rnaview + RNAVIEW="/usr/share/${PN}" + EOF +} + +src_compile() { + emake CC="$(tc-getCC)" || die +} + +src_install() { + emake DESTDIR="${D}" install || die + dodoc README || die + doenvd 22rnaview || die +} diff --git a/sci-biology/rnaview/rnaview-20040713-r3.ebuild b/sci-biology/rnaview/rnaview-20040713-r3.ebuild new file mode 100644 index 000000000000..5f46e6bc586c --- /dev/null +++ b/sci-biology/rnaview/rnaview-20040713-r3.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions" +HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-implicit.patch + cat <<- EOF > 22rnaview + RNAVIEW="${EPREFIX}/usr/share/${PN}" + EOF + tc-export CC +} + +src_install() { + default + doenvd 22rnaview +} diff --git a/sci-biology/rnaview/rnaview-20040713.ebuild b/sci-biology/rnaview/rnaview-20040713.ebuild new file mode 100644 index 000000000000..9bbb7a81f3cf --- /dev/null +++ b/sci-biology/rnaview/rnaview-20040713.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2007 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs + +DESCRIPTION="Generates 2D displays of RNA/DNA secondary structures with tertiary interactions" +HOMEPAGE="http://ndbserver.rutgers.edu/services/download/index.html" +SRC_URI="mirror://gentoo/${P}.tar.bz2" +LICENSE="public-domain" + +SLOT="0" +KEYWORDS="~amd64 x86" +IUSE="" + +src_unpack() { + unpack ${A} + cd "${S}" + sed -e "s/CC = cc/CC = $(tc-getCC)/" \ + -e "s/CFLAGS =/CFLAGS = ${CFLAGS}/" \ + -i Makefile || die +} + +src_compile() { + make clean + make || die + cd "${S}"/rnaml2ps + make clean + make || die + cd "${S}"/test + rm '.#t' +} + +src_install() { + dobin bin/rnaview rnaml2ps/rnaml2ps || die + dodoc README || die + mkdir -p "${D}"/usr/share/${PN} + cp -r BASEPARS test "${D}"/usr/share/${PN} +} diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest new file mode 100644 index 000000000000..8178b5d5369f --- /dev/null +++ b/sci-biology/samtools/Manifest @@ -0,0 +1,5 @@ +DIST samtools-0.1.12a.tar.bz2 355633 SHA256 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac +DIST samtools-0.1.19.tar.bz2 514507 SHA256 d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 SHA512 d145f1d65eefefbdfb781945684b8b591419fb109ac7401a62cae65b9ca1e1271f001496e1038334ff9ab1c0e5bf9bcc059f70aaa273551193fbd68101fd188d WHIRLPOOL 7811388ae8b24c5d7a328d2da252b8d3afaefdab508bd97684d556d2d4ee60d9c8846ffa562beaa9d0c6a5e6bfac24fcd9d211dfee20383cf452609badc8ecd5 +DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 +DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 +DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 diff --git a/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch new file mode 100644 index 000000000000..d5ff3bd45da5 --- /dev/null +++ b/sci-biology/samtools/files/samtools-0.1.19-buildsystem.patch @@ -0,0 +1,183 @@ + Makefile | 22 +++++++++++----------- + bcftools/Makefile | 12 ++++++------ + misc/Makefile | 28 ++++++++++++++-------------- + 3 files changed, 31 insertions(+), 31 deletions(-) + +diff --git a/Makefile b/Makefile +index 2f51bfc..4dda5a4 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 +-#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 ++CC?= gcc ++CFLAGS?= -g -Wall -O2 ++#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ + bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ +@@ -21,14 +21,14 @@ LIBCURSES= -lcurses # -lXCurses + .PHONY: all lib + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all-recur lib-recur clean-recur cleanlocal-recur install-recur: + @target=`echo $@ | sed s/-recur//`; \ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -44,16 +44,16 @@ libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + + samtools:lib-recur $(AOBJS) +- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread + + bgzf.o:bgzf.c bgzf.h +- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -84,7 +84,7 @@ libbam.1.dylib-local:$(LOBJS) + libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -lm -lpthread + + dylib: + @$(MAKE) cleanlocal; \ +diff --git a/bcftools/Makefile b/bcftools/Makefile +index be831de..7ef796c 100644 +--- a/bcftools/Makefile ++++ b/bcftools/Makefile +@@ -1,6 +1,6 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE ++CC?= gcc ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o + OMISC= .. + AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o +@@ -11,14 +11,14 @@ SUBDIRS= . + .SUFFIXES:.c .o + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ + + all-recur lib-recur clean-recur cleanlocal-recur install-recur: + @target=`echo $@ | sed s/-recur//`; \ + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -31,7 +31,7 @@ libbcf.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + + bcftools:lib $(AOBJS) +- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread + + bcf.o:bcf.h + vcf.o:bcf.h +diff --git a/misc/Makefile b/misc/Makefile +index d36e7ac..7ae1dc3 100644 +--- a/misc/Makefile ++++ b/misc/Makefile +@@ -1,8 +1,8 @@ +-CC= gcc +-CXX= g++ +-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc +-CXXFLAGS= $(CFLAGS) +-DFLAGS= -D_FILE_OFFSET_BITS=64 ++CC?= gcc ++CXX?= g++ ++CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc ++CXXFLAGS?= $(CFLAGS) ++CPPFLAGS+= -D_FILE_OFFSET_BITS=64 + OBJS= + PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck + INCLUDES= -I.. +@@ -11,7 +11,7 @@ SUBDIRS= . + .SUFFIXES:.c .o + + .c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ + + all:$(PROG) + +@@ -20,7 +20,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: + wdir=`pwd`; \ + list='$(SUBDIRS)'; for subdir in $$list; do \ + cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ ++ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ + INCLUDES="$(INCLUDES)" $$target || exit 1; \ + cd $$wdir; \ + done; +@@ -28,31 +28,31 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur: + lib: + + bamcheck:bamcheck.o +- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz + + bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h + $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c + + ace2sam:ace2sam.o +- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz + + md5sum-lite:md5sum-lite.o +- $(CC) $(CFLAGS) -o $@ md5sum-lite.o ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o + + md5sum-lite.o:md5.c md5.h + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz + + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c diff --git a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch new file mode 100644 index 000000000000..53a8b66f918f --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch @@ -0,0 +1,59 @@ + Makefile | 26 ++++++++++++++++++-------- + 1 file changed, 18 insertions(+), 8 deletions(-) + +diff --git a/Makefile b/Makefile +index ae59abf..0d2788c 100644 +--- a/Makefile ++++ b/Makefile +@@ -21,11 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = $(DFLAGS) $(INCLUDES) +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LDLIBS = ++CC ?= gcc ++CPPFLAGS += $(DFLAGS) $(INCLUDES) ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LDLIBS += ++BAMLIB ?= libbam.a + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++bindir = $(exec_prefix)/lib + mandir = $(prefix)/share/man + man1dir = $(mandir)/man1 + +@@ -115,14 +117,22 @@ version.h: + .c.o: + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< + +-lib:libbam.a ++ ++lib:libbam.a libbam.so.1.0 + + libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +-samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.0 ++ ln -sf $@ libbam.so ++ ++samtools: $(AOBJS) $(HTSLIB) lib ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch new file mode 100644 index 000000000000..b9ae77de67d2 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch @@ -0,0 +1,153 @@ + Makefile | 76 ++++++++++++++++++++++++++++++++++++---------------------------- + 1 file changed, 43 insertions(+), 33 deletions(-) + +diff --git a/Makefile b/Makefile +index 43cefc3..743dd07 100644 +--- a/Makefile ++++ b/Makefile +@@ -21,11 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = $(DFLAGS) $(INCLUDES) +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LDLIBS = ++CC ?= gcc ++CPPFLAGS += $(DFLAGS) $(INCLUDES) ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LDLIBS += ++BAMLIB ?= libbam.a + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++libdir = $(exec_prefix)/lib + mandir = $(prefix)/share/man + man1dir = $(mandir)/man1 + +@@ -115,63 +117,71 @@ version.h: + .c.o: + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< + +-lib:libbam.a ++ ++lib:libbam.a libbam.so.1.0 + + libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +-samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.0 ++ ln -sf $@ libbam.so ++ ++samtools: $(AOBJS) lib ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h + bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) + bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) ++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) + sam_h = sam.h $(htslib_sam_h) $(bam_h) +-sample_h = sample.h $(HTSDIR)/htslib/kstring.h ++sample_h = sample.h + + bam.o: bam.c $(bam_h) sam_header.h +-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h ++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h + bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h + bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h + bam_aux.o: bam_aux.c + bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) + bam_color.o: bam_color.c $(bam_h) +-bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h +-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h +-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h ++bam_import.o: bam_import.c $(bam_h) ++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) ++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) + bam_mate.o: bam_mate.c $(bam_h) + bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h + bam_pileup.o: bam_pileup.c $(sam_h) + bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) ++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) + bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) +-bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h +-bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h +-bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) ++bam_rmdup.o: bam_rmdup.c $(sam_h) ++bam_rmdupse.o: bam_rmdupse.c $(sam_h) ++bam_sort.o: bam_sort.c $(htslib_sam_h) + bam_stat.o: bam_stat.c $(bam_h) samtools.h + bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) + bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c $(bam_tview_h) + bam_flags.o: bam_flags.c $(sam_h) +-bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h ++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h + bamtk.o: bamtk.c $(bam_h) version.h samtools.h +-bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h +-bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h ++bedcov.o: bedcov.c $(htslib_sam_h) ++bedidx.o: bedidx.c + cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) +-errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h ++errmod.o: errmod.c errmod.h + kaln.o: kaln.c kaln.h + kprobaln.o: kprobaln.c kprobaln.h + padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) +-phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h ++phase.o: phase.c $(htslib_sam_h) errmod.h + sam.o: sam.c $(htslib_faidx_h) $(sam_h) +-sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h +-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h +-sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h +-stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h +-stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) ++sam_header.o: sam_header.c sam_header.h ++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h ++sample.o: sample.c $(sample_h) ++stats_isize.o: stats_isize.c stats_isize.h ++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) + + + # test programs +@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib + # For tests that might use it, set $REF_PATH explicitly to use only reference + # areas within the test suite (or set it to ':' to use no reference areas). + # (regression.sh sets $REF_PATH to a subdirectory itself.) +-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) +- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) ++check test: samtools $(BUILT_TEST_PROGRAMS) ++ REF_PATH=: test/test.pl --exec bgzip=bgzip + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_pretty_header + test/merge/test_rtrans_build +@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o + misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz + +-misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h ++misc/ace2sam.o: misc/ace2sam.c + misc/md5.o: misc/md5.c misc/md5.h +-misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h +-misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h ++misc/md5fa.o: misc/md5fa.c misc/md5.h ++misc/wgsim.o: misc/wgsim.c + + misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch new file mode 100644 index 000000000000..2343b2245a29 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch @@ -0,0 +1,193 @@ + Makefile | 94 +++++++++++++++++++++++++++++++++++----------------------------- + 1 file changed, 52 insertions(+), 42 deletions(-) + +diff --git a/Makefile b/Makefile +index e368cee..9054526 100644 +--- a/Makefile ++++ b/Makefile +@@ -21,11 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = $(DFLAGS) $(INCLUDES) +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LDLIBS = ++CC ?= gcc ++CPPFLAGS += $(DFLAGS) $(INCLUDES) ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LDLIBS += ++BAMLIB ?= libbam.a + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++libdir = $(exec_prefix)/lib + mandir = $(prefix)/share/man + man1dir = $(mandir)/man1 + +@@ -115,62 +117,70 @@ version.h: + .c.o: + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< + +-lib:libbam.a ++ ++lib:libbam.a libbam.so.1.0 + + libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +-samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.0 ++ ln -sf $@ libbam.so ++ ++samtools: $(AOBJS) lib ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h + bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) + bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) ++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) + sam_h = sam.h $(htslib_sam_h) $(bam_h) +-sample_h = sample.h $(HTSDIR)/htslib/kstring.h ++sample_h = sample.h + + bam.o: bam.c $(bam_h) sam_header.h +-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h ++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h + bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h + bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h + bam_aux.o: bam_aux.c + bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) + bam_color.o: bam_color.c $(bam_h) +-bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h +-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h +-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h ++bam_import.o: bam_import.c $(bam_h) ++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) ++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) + bam_mate.o: bam_mate.c $(bam_h) + bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h + bam_pileup.o: bam_pileup.c $(sam_h) + bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) ++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) + bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) +-bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h +-bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h +-bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) ++bam_rmdup.o: bam_rmdup.c $(sam_h) ++bam_rmdupse.o: bam_rmdupse.c $(sam_h) ++bam_sort.o: bam_sort.c $(htslib_sam_h) + bam_stat.o: bam_stat.c $(bam_h) samtools.h + bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) + bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c $(bam_tview_h) + bam_flags.o: bam_flags.c $(sam_h) +-bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h ++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h + bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h +-bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h +-bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h ++bedcov.o: bedcov.c $(htslib_sam_h) ++bedidx.o: bedidx.c + cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) +-errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h ++errmod.o: errmod.c errmod.h + kprobaln.o: kprobaln.c kprobaln.h + padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) +-phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h ++phase.o: phase.c $(htslib_sam_h) errmod.h + sam.o: sam.c $(htslib_faidx_h) $(sam_h) +-sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h +-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h +-sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h +-stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h +-stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) ++sam_header.o: sam_header.c sam_header.h ++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h ++sample.o: sample.c $(sample_h) ++stats_isize.o: stats_isize.c stats_isize.h ++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) + + + # test programs +@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib + # For tests that might use it, set $REF_PATH explicitly to use only reference + # areas within the test suite (or set it to ':' to use no reference areas). + # (regression.sh sets $REF_PATH to a subdirectory itself.) +-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) +- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) ++check test: samtools $(BUILT_TEST_PROGRAMS) ++ REF_PATH=: test/test.pl --exec bgzip=bgzip + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_pretty_header + test/merge/test_rtrans_build +@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) + test/split/test_parse_args + + +-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) ++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) ++test/merge/test_pretty_header: test/merge/test_pretty_header.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) ++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) ++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) ++test/split/test_count_rg: test/split/test_count_rg.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) ++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) ++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) ++test/split/test_parse_args: test/split/test_parse_args.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) ++test/vcf-miniview: test/vcf-miniview.o + $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz + + test_test_h = test/test.h $(htslib_sam_h) +@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o + misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz + +-misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h ++misc/ace2sam.o: misc/ace2sam.c + misc/md5.o: misc/md5.c misc/md5.h +-misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h +-misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h ++misc/md5fa.o: misc/md5fa.c misc/md5.h ++misc/wgsim.o: misc/wgsim.c + + misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml new file mode 100644 index 000000000000..74dc02bc9826 --- /dev/null +++ b/sci-biology/samtools/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">samtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/samtools/samtools-0.1.12.ebuild b/sci-biology/samtools/samtools-0.1.12.ebuild new file mode 100644 index 000000000000..34720e4b9abb --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.12.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 + +MY_P="${P}a" + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://samtools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i 's/^CFLAGS=/CFLAGS+=/' "${S}"/{Makefile,misc/Makefile} +} + +src_install() { + dobin samtools || die + dobin $(find misc -type f -executable) || die + insinto /usr/share/${PN} + doins -r examples || die + doman ${PN}.1 || die + dodoc AUTHORS ChangeLog NEWS +} diff --git a/sci-biology/samtools/samtools-0.1.19-r2.ebuild b/sci-biology/samtools/samtools-0.1.19-r2.ebuild new file mode 100644 index 000000000000..133ababad9cc --- /dev/null +++ b/sci-biology/samtools/samtools-0.1.19-r2.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://samtools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND="sys-libs/ncurses" +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${P}-buildsystem.patch + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + tc-export CC AR +} + +src_compile() { + local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" + emake dylib LIBCURSES="${_ncurses}" + emake LIBCURSES="${_ncurses}" +} + +src_install() { + dobin samtools $(find bcftools misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + + dolib.so libbam$(get_libname 1) + dosym libbam$(get_libname 1) /usr/$(get_libdir)/libbam$(get_libname) + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild new file mode 100644 index 000000000000..802aefc91ada --- /dev/null +++ b/sci-biology/samtools/samtools-1.0-r1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses + sci-libs/htslib" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-1.0 -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + epatch "${FILESDIR}"/${P}-buildsystem.patch + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die + +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/samtools/samtools-1.0.ebuild b/sci-biology/samtools/samtools-1.0.ebuild new file mode 100644 index 000000000000..d1f1f507b45c --- /dev/null +++ b/sci-biology/samtools/samtools-1.0.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses + sci-libs/htslib" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-1.0 -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die + +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + CC="$(tc-getCC)" + LDFLAGS="${LDFLAGS}" + CFLAGS="${CFLAGS}" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + ) + emake "${mymakeargs[@]}" +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/samtools/samtools-1.1.ebuild b/sci-biology/samtools/samtools-1.1.ebuild new file mode 100644 index 000000000000..1f5b82ab4602 --- /dev/null +++ b/sci-biology/samtools/samtools-1.1.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses + ~sci-libs/htslib-${PV}" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-* -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + epatch "${FILESDIR}"/${P}-buildsystem.patch + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die + +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" +} + +src_test() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" test +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/samtools/samtools-1.2.ebuild b/sci-biology/samtools/samtools-1.2.ebuild new file mode 100644 index 000000000000..3a999e01e865 --- /dev/null +++ b/sci-biology/samtools/samtools-1.2.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses + >=sci-libs/htslib-${PV}" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-* -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + epatch "${FILESDIR}"/${P}-buildsystem.patch + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die + +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" +} + +src_test() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest new file mode 100644 index 000000000000..6bb12c484533 --- /dev/null +++ b/sci-biology/seaview/Manifest @@ -0,0 +1 @@ +DIST seaview_4.3.5.tar.gz 309530 SHA256 38050d6792eb799d61e5e849f76971a9c7d45f467e5c04fbc4363062d8e7100d SHA512 b20c018da9a29d79fe0393fed5d29117729492ea8f36e72d4aeb98044a3de4a13331bd29e76ca552a08f6da764e57e69f9fb0325fc031551514d7a54b56c849a WHIRLPOOL 82fc7324bf1d934d69712629808d6b4178a5f2cdcf25351fb2fe2784f9cea0c1ec0aaaba7a3a08c84795108eb049394ceaab052af8cc0efbb0975064fa4e80e0 diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml new file mode 100644 index 000000000000..33794f43ab01 --- /dev/null +++ b/sci-biology/seaview/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + SeaView is a graphical multiple sequence alignment editor developped by + Manolo Gouy. SeaView is able to read and write various alignment + formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to + manually edit the alignment, and also to run DOT-PLOT or CLUSTALW + programs to locally improve the alignment. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/seaview/seaview-4.3.5.ebuild b/sci-biology/seaview/seaview-4.3.5.ebuild new file mode 100644 index 000000000000..00abeb426064 --- /dev/null +++ b/sci-biology/seaview/seaview-4.3.5.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="A graphical multiple sequence alignment editor" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" +SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="+xft" + +CDEPEND=" + sys-libs/zlib + x11-libs/fltk:1 + x11-libs/libX11 + xft? ( + x11-libs/libXft + x11-libs/fltk:1[xft] )" +RDEPEND="${CDEPEND} + sci-biology/clustalw + || ( sci-libs/libmuscle sci-biology/muscle ) + sci-biology/phyml" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +src_prepare() { + # respect CXXFLAGS (package uses them as CFLAGS) + sed \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -e "s:^CXX.*:CXX = $(tc-getCXX):" \ + -e "s:\$(OPT):${CXXFLAGS}:" \ + -e "s:^OPT:#OPT:" \ + -e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \ + -e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \ + -e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \ + -e "s:^USE_XFT:#USE_XFT:" \ + -e "s:^#HELPFILE:HELPFILE:" \ + -e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \ + -e "s:^#PHYMLNAME:PHYMLNAME:" \ + -e 's:-lXinerama::g' \ + -e 's:-lpng::g' \ + -e 's:-ljpeg::g' \ + -e 's:-lfontconfig::g' \ + -i Makefile || die "sed failed while editing Makefile" + + if use xft; then + sed \ + -e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \ + -e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \ + -i Makefile || die "sed failed while editing Makefile to enable xft" + else + sed -i -e "s:-lXft::" Makefile || die + fi +} + +src_install() { + dobin seaview + + # /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile + insinto /usr/share/seaview + doins example.nxs seaview.html + + insinto /usr/share/seaview/images + doins seaview.xpm + + make_desktop_entry seaview Seaview + + doman seaview.1 +} diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest new file mode 100644 index 000000000000..134871573387 --- /dev/null +++ b/sci-biology/seqan/Manifest @@ -0,0 +1,3 @@ +DIST seqan-1.3.1.zip 8787521 SHA256 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512 dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4 WHIRLPOOL 5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b +DIST seqan-src-1.4.2.tar.gz 120601994 SHA256 2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a WHIRLPOOL 3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0 +DIST seqan-src-2.0.0.tar.gz 115731415 SHA256 69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28 SHA512 9823b109c27fa770b86a72530ebb4f6ca4541f8f6cf979724730cd8c59809192c14178c01a9ec13ef0277c997c4c37f00c80bba1fef5ef57c367ae8285b0215a WHIRLPOOL afa5dd41106390f63523990ce876ef74952ce7787a2772c2116bafd564d466e588809e4c5812b5aa1137408a0291de739b70a9a1e116d212967f68f5246217f4 diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch new file mode 100644 index 000000000000..5baee4d8ebc0 --- /dev/null +++ b/sci-biology/seqan/files/seqan-1.4.2-include.patch @@ -0,0 +1,16 @@ + core/include/seqan/index/index_qgram_openaddressing.h | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h +index 4a6c2e6..8cc9a42 100644 +--- a/core/include/seqan/index/index_qgram_openaddressing.h ++++ b/core/include/seqan/index/index_qgram_openaddressing.h +@@ -35,6 +35,8 @@ + #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H + #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H + ++#include <smmintrin.h> ++ + namespace SEQAN_NAMESPACE_MAIN + { + diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch new file mode 100644 index 000000000000..0f438ff07bce --- /dev/null +++ b/sci-biology/seqan/files/seqan-1.4.2-shared.patch @@ -0,0 +1,22 @@ + util/cmake/SeqAnBuildSystem.cmake | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake +index bcba2c0..d53cd01 100644 +--- a/util/cmake/SeqAnBuildSystem.cmake ++++ b/util/cmake/SeqAnBuildSystem.cmake +@@ -144,10 +144,10 @@ macro (seqan_register_apps) + set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1") + + # enable static linkage for seqan apps +- if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) +- set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") +- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") +- endif () ++# if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) ++# set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") ++# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") ++# endif () + + # Get all direct entries of the current source directory into ENTRIES. + file (GLOB ENTRIES diff --git a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch new file mode 100644 index 000000000000..de14e9d58b8e --- /dev/null +++ b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch @@ -0,0 +1,15 @@ + include/seqan/stream/zipstream/zutil.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/include/seqan/stream/zipstream/zutil.h b/include/seqan/stream/zipstream/zutil.h +index 2806344..f8b41e6 100644 +--- a/include/seqan/stream/zipstream/zutil.h ++++ b/include/seqan/stream/zipstream/zutil.h +@@ -152,6 +152,7 @@ extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */ + + /* functions */ + ++#define OF(x) x + #ifdef HAVE_STRERROR + extern char *strerror OF((int)); + # define zstrerror(errnum) strerror(errnum) diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/seqan/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/seqan/seqan-1.3.1-r1.ebuild b/sci-biology/seqan/seqan-1.3.1-r1.ebuild new file mode 100644 index 000000000000..a74eac3ccfce --- /dev/null +++ b/sci-biology/seqan/seqan-1.3.1-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic python-single-r1 + +DESCRIPTION="C++ Sequence Analysis Library" +HOMEPAGE="http://www.seqan.de/" +SRC_URI="http://ftp.seqan.de/releases/${P}.zip" + +SLOT="0" +LICENSE="BSD GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + sci-biology/samtools" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${P}/cmake + +src_prepare() { + append-cppflags -I"${EPREFIX}/usr/include/bam" + rm -rf "${S}"/../lib/samtools || die + + sed \ + -e "s:docs:docs/.:g" \ + -e "/DESTINATION/s:seqan:doc/${PF}/html:g" \ + -i CMakeLists.txt || die + + sed \ + -e "/DESTINATION/s:bin):share/${PN}):g" \ + -i apps/CMakeLists.txt || die + + cmake-utils_src_prepare +} diff --git a/sci-biology/seqan/seqan-1.4.2.ebuild b/sci-biology/seqan/seqan-1.4.2.ebuild new file mode 100644 index 000000000000..a7e436a2013b --- /dev/null +++ b/sci-biology/seqan/seqan-1.4.2.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic python-single-r1 + +DESCRIPTION="C++ Sequence Analysis Library" +HOMEPAGE="http://www.seqan.de/" +SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + sci-biology/samtools" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-shared.patch + "${FILESDIR}"/${P}-include.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} = "binary" ]] && return 0 + if use amd64; then + if ! echo "#include <smmintrin.h>" | gcc -E - 2>&1 > /dev/null; then + ewarn "Need at least SSE4.1 support" + die "Missing SSE4.1 support" + fi + fi +} + +src_prepare() { + rm -f \ + util/cmake/FindZLIB.cmake \ + || die + touch extras/apps/seqan_flexbar/README || die + sed \ + -e "s:share/doc:share/doc/${PF}:g" \ + -i docs/CMakeLists.txt util/cmake/SeqAnBuildSystem.cmake || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBoost_NO_BOOST_CMAKE=ON + ) + cmake-utils_src_configure +} + +src_install() { + mkdir -p "${BUILD_DIR}"/docs/html || die + cmake-utils_src_install + chmod 755 "${ED}"/usr/bin/*sh || die + + mv "${ED}"/usr/bin/{,seqan-}join || die +} + +pkg_postinst() { + elog "Due to filecollision the 'join' binary has been renamed to seqan-join" +} diff --git a/sci-biology/seqan/seqan-2.0.0.ebuild b/sci-biology/seqan/seqan-2.0.0.ebuild new file mode 100644 index 000000000000..5437e6df9f5b --- /dev/null +++ b/sci-biology/seqan/seqan-2.0.0.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic python-single-r1 + +DESCRIPTION="C++ Sequence Analysis Library" +HOMEPAGE="http://www.seqan.de/" +SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse4_1" + +REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1" + +RDEPEND="${PYTHON_DEPS} + dev-libs/boost:= + sci-biology/samtools" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${PN}-${PN}-v${PV} + +PATCHES=( + "${FILESDIR}"/${P}-zlib.patch +) + +src_prepare() { + rm -f \ + util/cmake/FindZLIB.cmake \ + || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBoost_NO_BOOST_CMAKE=ON + ) + cmake-utils_src_configure +} + +src_install() { + mkdir -p "${BUILD_DIR}"/docs/html || die + cmake-utils_src_install + chmod 755 "${ED}"/usr/bin/*sh || die +} diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest new file mode 100644 index 000000000000..ad017d9fc592 --- /dev/null +++ b/sci-biology/shrimp/Manifest @@ -0,0 +1,2 @@ +DIST SHRiMP_2_0_1.src.tar.gz 158535 SHA256 62557cf256421aea17a2b221ef485410be177cfc777a6bb8a3de89718d186f63 +DIST SHRiMP_2_2_3.src.tar.gz 4596867 SHA256 a8bed999baeda2ae17ae5c128b2161b20b896228d754e6e446439c1040d6dd8c SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 WHIRLPOOL 84325b9db3f2e10baa3db935d6e3e2ecae9fd0f47cf5666ea7493f7a975fcd31515f2c77dbe8fcf5cfa099ac2735973e791fa96f0fe8371c5279353bc3f9995a diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/shrimp/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild new file mode 100644 index 000000000000..771432f0bada --- /dev/null +++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit flag-o-matic toolchain-funcs + +MY_PV=${PV//./_} + +DESCRIPTION="SHort Read Mapping Package" +HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" +SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" + +LICENSE="shrimp" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="custom-cflags" + +# file collision on /usr/bin/utils #453044 +DEPEND=" + !sci-biology/emboss + !sci-mathematics/cado-nfs" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/SHRiMP_${MY_PV} + +pkg_setup() { + if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then + elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" + die "C compiler lacks OPENMP support" + fi +} + +src_prepare() { + sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die + # respect LDFLAGS wrt 331823 + sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \ + -e 's/-static//' Makefile || die +} + +src_compile() { + append-flags -fopenmp + use custom-cflags || append-flags -O3 # per instructions in BUILDING + tc-export CXX + emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm bin/README + dobin bin/* + insinto /usr/share/${PN} + doins -r utils + dodoc HISTORY README TODO SPLITTING_AND_MERGING +} diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild new file mode 100644 index 000000000000..7f2033d9054a --- /dev/null +++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit flag-o-matic python-single-r1 toolchain-funcs + +MY_PV=${PV//./_} + +DESCRIPTION="SHort Read Mapping Package" +HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" +SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" + +LICENSE="shrimp" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="custom-cflags +cpu_flags_x86_sse2" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +# file collision on /usr/bin/utils #453044 +DEPEND="!sci-mathematics/cado-nfs" +RDEPEND="${DEPEND} + ${PYTHON_DEPS}" + +S=${WORKDIR}/SHRiMP_${MY_PV} + +pkg_pretend() { + use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU" +} + +pkg_setup() { + if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then + elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" + die "C compiler lacks OPENMP support" + fi + python-single-r1_pkg_setup +} + +src_prepare() { + sed \ + -e '1 a #include <stdint.h>' \ + -i common/dag_glue.cpp || die + # respect LDFLAGS wrt 331823 + sed \ + -e "s/LDFLAGS/LIBS/" \ + -e "s/\$(LD)/& \$(LDFLAGS)/" \ + -e 's/-static//' \ + -i Makefile || die + + append-flags -fopenmp + if ! use custom-cflags; then + append-flags -O3 + replace-flags -O* -O3 + fi + tc-export CXX + + cd utils || die + sed -e '/^#!/d' -i *py || die + sed -e '1i#!/usr/bin/python' -i *py || die +} + +src_compile() { + emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + local i + newdoc bin/README README.bin && rm bin/README + dobin bin/* utils/split-contigs utils/temp-sink + dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES + + pushd utils > /dev/null + + python_doscript *py + + rm *.py *.o *.c split-contigs temp-sink || die + insinto /usr/share/${PN} + doins -r * +} diff --git a/sci-biology/sibsim4/Manifest b/sci-biology/sibsim4/Manifest new file mode 100644 index 000000000000..3a0be49f2116 --- /dev/null +++ b/sci-biology/sibsim4/Manifest @@ -0,0 +1 @@ +DIST SIBsim4-0.20.tar.gz 32118 SHA256 ee02ae5f678d6843cf3ba267140dfccf9648a60d1f01263ae70d405723a35463 SHA512 3802520095e83d3c691804b661696095a4198c4b2a16385c55ccdc8e4e836f82cc9c2251a5d37cb5918c2ee80aeb81737d751e6b065fbfe9c64f1aee3e0ea0c8 WHIRLPOOL b6117192170a7c8b6bcc441c8b31b392410116d25045203ce33e5274a0a65608de408626df5a29fddbbbe34973869b055603defd58d06cbc6240925556b63282 diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml new file mode 100644 index 000000000000..cfcd5be131d0 --- /dev/null +++ b/sci-biology/sibsim4/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">sibsim4</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild new file mode 100644 index 000000000000..ecef6870dea4 --- /dev/null +++ b/sci-biology/sibsim4/sibsim4-0.20.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="A rewrite and improvement upon sim4, a DNA-mRNA aligner" +HOMEPAGE="http://sibsim4.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/SIBsim4-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="" + +S="${WORKDIR}/SIBsim4-${PV}" + +src_prepare() { + sed \ + -e 's/CFLAGS = /CFLAGS +=/' \ + -e '/^CC/s:=:?=:' \ + -e '/^OPT/d' \ + -e "s:-o:${LDFLAGS} -o:g" \ + -i "${S}/Makefile" || die + tc-export CC +} + +src_install() { + dobin SIBsim4 + doman SIBsim4.1 +} diff --git a/sci-biology/sim4/Manifest b/sci-biology/sim4/Manifest new file mode 100644 index 000000000000..f2a25200b895 --- /dev/null +++ b/sci-biology/sim4/Manifest @@ -0,0 +1 @@ +DIST sim4.tar.gz 60814 RMD160 5acad71daa94893025a21b73b416dd3903078be5 SHA1 11a9170ea03990268d409056084415d725c6290b SHA256 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml new file mode 100644 index 000000000000..ea9731279003 --- /dev/null +++ b/sci-biology/sim4/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + sim4 is a similarity-based tool for aligning an expressed DNA sequence + (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects + end matches when the two input sequences overlap at one end (i.e., the + start of one sequence overlaps the end of the other).sim4 employs a + blast-based technique to first determine the basic matching blocks + representing the "exon cores". In this first stage, it detects all + possible exact matches of W-mers (i.e., DNA words of size W) between + the two sequences and extends them to maximal scoring gap-free + segments. In the second stage, the exon cores are extended into the + adjacent as-yet-unmatched fragments using greedy alignment algorithms, + and heuristics are used to favor configurations that conform to the + splice-site recognition signals (GT-AG, CT-AC). If necessary, the + process is repeated with less stringent parameters on the unmatched + fragments. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/sim4/sim4-20030921-r1.ebuild b/sci-biology/sim4/sim4-20030921-r1.ebuild new file mode 100644 index 000000000000..178bf92ab5da --- /dev/null +++ b/sci-biology/sim4/sim4-20030921-r1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs + +DESCRIPTION="A program to align cDNA and genomic DNA" +HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html" +SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz" +LICENSE="GPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +S=${WORKDIR}/${PN}.2003-09-21 + +src_compile() { + echo "$(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm" + $(tc-getCC) -o ${PN} ${LDFLAGS} -I. ${CFLAGS} *.c -lm || die +} + +src_install() { + dobin ${PN} || die + dodoc README.* VERSION || die +} diff --git a/sci-biology/sim4/sim4-20030921.ebuild b/sci-biology/sim4/sim4-20030921.ebuild new file mode 100644 index 000000000000..12d5231aa120 --- /dev/null +++ b/sci-biology/sim4/sim4-20030921.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2007 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A program to align cDNA and genomic DNA" +HOMEPAGE="http://globin.cse.psu.edu/html/docs/sim4.html" +SRC_URI="http://globin.cse.psu.edu/ftp/dist/sim4/sim4.tar.gz" +LICENSE="GPL-2" + +SLOT="0" +KEYWORDS="x86 ~ppc" +IUSE="" + +S="${WORKDIR}/${PN}.2003-09-21" + +src_install() { + dobin sim4 || die + dodoc README.psublast README.sim4 VERSION || die +} diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest new file mode 100644 index 000000000000..370468a92b39 --- /dev/null +++ b/sci-biology/snpfile/Manifest @@ -0,0 +1 @@ +DIST snpfile-2.0.1.tar.gz 171854 SHA256 71569e0dcd426447d1a5d215fb47615074a4c8d935cf70ef63c5f47a411b0b76 diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch new file mode 100644 index 000000000000..2b79c2492ede --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch @@ -0,0 +1,12 @@ +diff -ur snpfile-2.0.1.orig/input_archive.hh snpfile-2.0.1/input_archive.hh +--- snpfile-2.0.1.orig/input_archive.hh 2008-05-03 17:25:44.000000000 +0300 ++++ snpfile-2.0.1/input_archive.hh 2009-07-26 21:26:10.000000000 +0300 +@@ -26,6 +26,8 @@ + #ifndef INPUT_ARCHIVE_HH_INCLUDED + #define INPUT_ARCHIVE_HH_INCLUDED + ++#include <stdint.h> ++ + #include <string> + + #include "archive_common.hh" diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff new file mode 100644 index 000000000000..e6a8d60ec69c --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff @@ -0,0 +1,533 @@ +Fixing as-needed issues, provide shared libs + +https://bugs.gentoo.org/show_bug.cgi?id=294971 + +--- Makefile.am ++++ Makefile.am +@@ -1,440 +1,92 @@ + ACLOCAL_AMFLAGS = -I m4 + +-AM_CXXFLAGS = +-AM_CXXFLAGS += -Wall +-AM_CXXFLAGS += $(BOOST_CPPFLAGS) ++AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS) ++SUFFIXES = .cc + +- +-# for testing +-AM_CXXFLAGS += -g -O2 #-lefence +- +-# for profiling +-#CXXFLAGS += -O3 -g -pg +-#AM_CXXFLAGS += -O3 -g -pg +- +-# for production +-#CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG +-#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG +- +-# for coverage testing +-#CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations +-#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations +- +- +-lib_LIBRARIES = libsnpfile.a ++lib_LTLIBRARIES = libsnpfile.la + + noinst_PROGRAMS = +-TESTS = +-EXTRA_DIST = +-bin_PROGRAMS = + + # conversion tools +-bin_PROGRAMS += text2snpfile +-bin_PROGRAMS += snpfile2text +-bin_PROGRAMS += snpfile2fastPHASE +-bin_PROGRAMS += fastPHASE2snpfile +-bin_PROGRAMS += snpfile2haploview +-bin_PROGRAMS += beagle_phase_snpfile ++bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \ ++ snpfile2haploview beagle_phase_snpfile + + # data extraction tools +-bin_PROGRAMS += snpfile_genotype_count +-bin_PROGRAMS += snpfile_phenotypes +-bin_PROGRAMS += snpfile_markers +- +-bin_PROGRAMS += snpfile_metadata_info +-bin_PROGRAMS += snpfile_set_metadata +-bin_PROGRAMS += snpfile_get_metadata ++bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers ++ ++bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata + + # other tools + noinst_PROGRAMS += snpfile_split_on_column + + # tests +-noinst_PROGRAMS += matrix_test +-TESTS += matrix_test +-noinst_PROGRAMS += file_test +-TESTS += file_test +-noinst_PROGRAMS += file_matrix_test +-TESTS += file_matrix_test +-noinst_PROGRAMS += readonly_matrix_test +-TESTS += readonly_matrix_test +-noinst_PROGRAMS += archives_test +-TESTS += archives_test +-noinst_PROGRAMS += metadata_access_test +-TESTS += metadata_access_test +-noinst_PROGRAMS += metadata_types_test +-TESTS += metadata_types_test +-noinst_PROGRAMS += iterators_test +-TESTS += iterators_test +-noinst_PROGRAMS += tabulate_test +-TESTS += tabulate_test +-noinst_PROGRAMS += metadata_filtering_test +-TESTS += metadata_filtering_test ++TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \ ++ metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test ++ ++noinst_PROGRAMS += $(TESTS) + + #Utils for testing across different machines +-noinst_PROGRAMS += make_test_snpfile +-noinst_PROGRAMS += test_test_snpfile ++noinst_PROGRAMS += make_test_snpfile test_test_snpfile + + # other experiments... +-noinst_PROGRAMS += row_metadata_experiment +-noinst_PROGRAMS += metadata_cache_prototype +-noinst_PROGRAMS += matrix_benchmark +-noinst_PROGRAMS += matrix_benchmark_write +-noinst_PROGRAMS += matrix_benchmark_read +- +- +- +-matrix_test_LDADD = +-matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_test_SOURCES = +-matrix_test_SOURCES += test_util.hh test_util.cc +-matrix_test_SOURCES += matrix.hh matrix.cc +-matrix_test_SOURCES += array_matrix.hh array_matrix.cc +-matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-matrix_test_SOURCES += input_archive.hh +-matrix_test_SOURCES += output_archive.hh +-matrix_test_SOURCES += metadata.hh metadata.cc +-matrix_test_SOURCES += snpfile.hh snpfile.cc +-matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_test_SOURCES += matrix_test.cc +- +- +-file_test_LDADD = +-file_test_LDADD += $(BOOST_SIGNALS_LIB) +-file_test_SOURCES = +-file_test_SOURCES += test_util.hh test_util.cc +-file_test_SOURCES += metadata.hh metadata.cc +-file_test_SOURCES += snpfile.hh snpfile.cc +-file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-file_test_SOURCES += file_test.cc +-file_test_SOURCES += metadata_access.hh +-file_test_SOURCES += input_archive.hh +-file_test_SOURCES += output_archive.hh +- +-file_matrix_test_LDADD = +-file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-file_matrix_test_SOURCES = +-file_matrix_test_SOURCES += test_util.hh test_util.cc +-file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-file_matrix_test_SOURCES += matrix.hh matrix.cc +-file_matrix_test_SOURCES += input_archive.hh +-file_matrix_test_SOURCES += output_archive.hh +-file_matrix_test_SOURCES += metadata.hh metadata.cc +-file_matrix_test_SOURCES += snpfile.hh snpfile.cc +-file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-file_matrix_test_SOURCES += file_matrix_test.cc +- +- +-readonly_matrix_test_LDADD = +-readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-readonly_matrix_test_SOURCES = +-readonly_matrix_test_SOURCES += test_util.hh test_util.cc +-readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc +-readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-readonly_matrix_test_SOURCES += matrix.hh matrix.cc +-readonly_matrix_test_SOURCES += input_archive.hh +-readonly_matrix_test_SOURCES += output_archive.hh +-readonly_matrix_test_SOURCES += metadata.hh metadata.cc +-readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc +-readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-readonly_matrix_test_SOURCES += readonly_matrix_test.cc +- +- +-archives_test_SOURCES = +-archives_test_SOURCES += input_archive.hh +-archives_test_SOURCES += output_archive.hh +-archives_test_SOURCES += archives_test.cc +- +- +-metadata_access_test_LDADD = +-metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_access_test_SOURCES = +-metadata_access_test_SOURCES += test_util.hh test_util.cc +-metadata_access_test_SOURCES += metadata.hh metadata.cc +-metadata_access_test_SOURCES += snpfile.hh snpfile.cc +-metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-metadata_access_test_SOURCES += input_archive.hh +-metadata_access_test_SOURCES += output_archive.hh +-metadata_access_test_SOURCES += serialization_trait.hh +-metadata_access_test_SOURCES += metadata_access_test.cc +- +- +-metadata_types_test_LDADD = +-metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_types_test_SOURCES = +-metadata_types_test_SOURCES += test_util.hh test_util.cc +-metadata_types_test_SOURCES += metadata.hh metadata.cc +-metadata_types_test_SOURCES += snpfile.hh snpfile.cc +-metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-metadata_types_test_SOURCES += input_archive.hh +-metadata_types_test_SOURCES += output_archive.hh +-metadata_types_test_SOURCES += serialization_trait.hh +-metadata_types_test_SOURCES += metadata_types_test.cc +- +- +-iterators_test_SOURCES = +-iterators_test_SOURCES += iterators.hh +-iterators_test_SOURCES += array_matrix.hh array_matrix.cc +-iterators_test_SOURCES += matrix.hh matrix.cc +-iterators_test_SOURCES += iterators_test.cc +- +- +-tabulate_test_SOURCES = +-tabulate_test_SOURCES += tabulate.hh +-tabulate_test_SOURCES += array_matrix.hh array_matrix.cc +-tabulate_test_SOURCES += matrix.hh matrix.cc +-tabulate_test_SOURCES += tabulate_test.cc +- +- +-metadata_filtering_test_SOURCES = +-metadata_filtering_test_SOURCES += matrix.hh matrix.cc +-metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc +-metadata_filtering_test_SOURCES += metadata_filtering.hh +-metadata_filtering_test_SOURCES += metadata_filtering_test.cc +- +- +-make_test_snpfile_LDADD = +-make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-make_test_snpfile_SOURCES = +-make_test_snpfile_SOURCES += metadata.hh metadata.cc +-make_test_snpfile_SOURCES += snpfile.hh snpfile.cc +-make_test_snpfile_SOURCES += matrix.hh matrix.cc +-make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc +-make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc +-make_test_snpfile_SOURCES += input_archive.hh +-make_test_snpfile_SOURCES += output_archive.hh +-make_test_snpfile_SOURCES += make_test_snpfile.cc +- +- +-test_test_snpfile_LDADD = +-test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-test_test_snpfile_SOURCES = +-test_test_snpfile_SOURCES += metadata.hh metadata.cc +-test_test_snpfile_SOURCES += snpfile.hh snpfile.cc +-test_test_snpfile_SOURCES += matrix.hh matrix.cc +-test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc +-test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc +-test_test_snpfile_SOURCES += input_archive.hh +-test_test_snpfile_SOURCES += output_archive.hh +-test_test_snpfile_SOURCES += test_test_snpfile.cc +- +- +-row_metadata_experiment_LDADD = +-row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB) +-row_metadata_experiment_SOURCES = +-row_metadata_experiment_SOURCES += matrix.hh matrix.cc +-row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc +-row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc +-row_metadata_experiment_SOURCES += input_archive.hh +-row_metadata_experiment_SOURCES += output_archive.hh +-row_metadata_experiment_SOURCES += metadata.hh metadata.cc +-row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc +-row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc +-row_metadata_experiment_SOURCES += test_util.hh test_util.cc +-row_metadata_experiment_SOURCES += row_metadata_experiment.cc +- +- +-metadata_cache_prototype_SOURCES = +-metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc +-metadata_cache_prototype_LDFLAGS = +-metadata_cache_prototype_LDFLAGS += -L. +-metadata_cache_prototype_LDADD = +-metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_cache_prototype_LDADD += -lsnpfile +- +- +-matrix_benchmark_LDADD = +-matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_SOURCES = +-matrix_benchmark_SOURCES += test_util.hh test_util.cc +-matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc +-matrix_benchmark_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_SOURCES += input_archive.hh +-matrix_benchmark_SOURCES += output_archive.hh +-matrix_benchmark_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_SOURCES += timing.hh timing.cc +-matrix_benchmark_SOURCES += matrix_benchmark.cc +- +- +-matrix_benchmark_write_LDADD = +-matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_write_SOURCES = +-matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_write_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_write_SOURCES += input_archive.hh +-matrix_benchmark_write_SOURCES += output_archive.hh +-matrix_benchmark_write_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_write_SOURCES += timing.hh timing.cc +-matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc +- +- +-matrix_benchmark_read_LDADD = +-matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_read_SOURCES = +-matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_read_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_read_SOURCES += input_archive.hh +-matrix_benchmark_read_SOURCES += output_archive.hh +-matrix_benchmark_read_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_read_SOURCES += timing.hh timing.cc +-matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc ++noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ ++ matrix_benchmark_write matrix_benchmark_read ++ ++LDADD = $(top_builddir)/libsnpfile.la ++ ++matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc ++ ++file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \ ++ output_archive.hh ++ ++file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ file_matrix_test.cc ++ ++readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ readonly_matrix_test.cc + ++archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc ++ ++metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ serialization_trait.hh metadata_access_test.cc ++ ++metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ serialization_trait.hh metadata_types_test.cc ++ ++iterators_test_SOURCES = iterators.hh iterators_test.cc ++ ++tabulate_test_SOURCES = tabulate.hh tabulate_test.cc ++ ++metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc ++ ++make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc ++ ++test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc ++ ++row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \ ++ row_metadata_experiment.cc ++ ++matrix_benchmark_SOURCES = test_util.hh test_util.cc input_archive.hh \ ++ output_archive.hh timing.hh timing.cc matrix_benchmark.cc ++ ++matrix_benchmark_write_SOURCES = input_archive.hh output_archive.hh \ ++ timing.hh timing.cc matrix_benchmark_write.cc ++ ++matrix_benchmark_read_SOURCES = input_archive.hh output_archive.hh \ ++ timing.hh timing.cc matrix_benchmark_read.cc ++ ++snpfile_genotype_count_SOURCES = genotype_count.cc + + snpfileincludedir = $(includedir)/snpfile +-snpfileinclude_HEADERS = +-snpfileinclude_HEADERS += common.hh +-snpfileinclude_HEADERS += matrix.hh +-snpfileinclude_HEADERS += file_matrix.hh +-snpfileinclude_HEADERS += array_matrix.hh +-snpfileinclude_HEADERS += byte_order_handler.hh +-snpfileinclude_HEADERS += metadata.hh +-snpfileinclude_HEADERS += metadata_access.hh +-snpfileinclude_HEADERS += archive_common.hh +-snpfileinclude_HEADERS += archives.hh +-snpfileinclude_HEADERS += input_archive.hh +-snpfileinclude_HEADERS += output_archive.hh +-snpfileinclude_HEADERS += snpfile.hh +-snpfileinclude_HEADERS += serialization_trait.hh +-snpfileinclude_HEADERS += type_trait.hh +-snpfileinclude_HEADERS += iterators.hh +-snpfileinclude_HEADERS += tabulate.hh +- +-libsnpfile_a_SOURCES = +-libsnpfile_a_SOURCES += common.hh +-libsnpfile_a_SOURCES += matrix.hh matrix.cc +-libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc +-libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh +-libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh +-libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh +-libsnpfile_a_SOURCES += archive_common.hh +-libsnpfile_a_SOURCES += archives.hh +-libsnpfile_a_SOURCES += input_archive.hh +-libsnpfile_a_SOURCES += output_archive.hh +-libsnpfile_a_SOURCES += snpfile.hh snpfile.cc +-libsnpfile_a_SOURCES += serialization_trait.hh +-libsnpfile_a_SOURCES += type_trait.hh +- +-text2snpfile_SOURCES = +-text2snpfile_SOURCES += text2snpfile.cc +-text2snpfile_LDFLAGS = +-text2snpfile_LDFLAGS += -L. +-text2snpfile_LDADD = +-text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-text2snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-text2snpfile_LDADD += -lsnpfile +- +-snpfile2text_SOURCES = +-snpfile2text_SOURCES += snpfile2text.cc +-snpfile2text_LDFLAGS = +-snpfile2text_LDFLAGS += -L. +-snpfile2text_LDADD = +-snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2text_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2text_LDADD += -lsnpfile +- +- +-snpfile2fastPHASE_SOURCES = +-snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc +-snpfile2fastPHASE_LDFLAGS = +-snpfile2fastPHASE_LDFLAGS += -L. +-snpfile2fastPHASE_LDADD = +-snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2fastPHASE_LDADD += -lsnpfile +- +-fastPHASE2snpfile_SOURCES = +-fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc +-fastPHASE2snpfile_LDFLAGS = +-fastPHASE2snpfile_LDFLAGS += -L. +-fastPHASE2snpfile_LDADD = +-fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-fastPHASE2snpfile_LDADD += -lsnpfile +- +- +-snpfile2haploview_SOURCES = +-snpfile2haploview_SOURCES += snpfile2haploview.cc +-snpfile2haploview_LDFLAGS = +-snpfile2haploview_LDFLAGS += -L. +-snpfile2haploview_LDADD = +-snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2haploview_LDADD += -lsnpfile +- +- +-beagle_phase_snpfile_SOURCES = +-beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc +-beagle_phase_snpfile_LDFLAGS = +-beagle_phase_snpfile_LDFLAGS += -L. +-beagle_phase_snpfile_LDADD = +-beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-beagle_phase_snpfile_LDADD += -lsnpfile +- +-snpfile_genotype_count_SOURCES = +-snpfile_genotype_count_SOURCES += genotype_count.cc +-snpfile_genotype_count_LDFLAGS = +-snpfile_genotype_count_LDFLAGS += -L. +-snpfile_genotype_count_LDADD = +-snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_genotype_count_LDADD += -lsnpfile +- +-snpfile_phenotypes_SOURCES = +-snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc +-snpfile_phenotypes_LDFLAGS = +-snpfile_phenotypes_LDFLAGS += -L. +-snpfile_phenotypes_LDADD = +-snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_phenotypes_LDADD += -lsnpfile +- +-snpfile_markers_SOURCES = +-snpfile_markers_SOURCES += snpfile_markers.cc +-snpfile_markers_LDFLAGS = +-snpfile_markers_LDFLAGS += -L. +-snpfile_markers_LDADD = +-snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_markers_LDADD += -lsnpfile +- +-snpfile_metadata_info_SOURCES = +-snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc +-snpfile_metadata_info_LDFLAGS = +-snpfile_metadata_info_LDFLAGS += -L. +-snpfile_metadata_info_LDADD = +-snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_metadata_info_LDADD += -lsnpfile +- +-snpfile_set_metadata_SOURCES = +-snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc +-snpfile_set_metadata_LDFLAGS = +-snpfile_set_metadata_LDFLAGS += -L. +-snpfile_set_metadata_LDADD = +-snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_set_metadata_LDADD += -lsnpfile +- +-snpfile_get_metadata_SOURCES = +-snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc +-snpfile_get_metadata_LDFLAGS = +-snpfile_get_metadata_LDFLAGS += -L. +-snpfile_get_metadata_LDADD = +-snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_get_metadata_LDADD += -lsnpfile +- +-snpfile_split_on_column_SOURCES = +-snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc +-snpfile_split_on_column_LDFLAGS = +-snpfile_split_on_column_LDFLAGS += -L. +-snpfile_split_on_column_LDADD = +-snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_split_on_column_LDADD += -lsnpfile ++snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \ ++ byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \ ++ archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \ ++ type_trait.hh iterators.hh tabulate.hh ++ ++libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \ ++ array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \ ++ metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ ++ input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ ++ type_trait.hh ++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) ++ +--- configure.in ++++ configure.in +@@ -1,10 +1,11 @@ + AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) + AM_INIT_AUTOMAKE ++AC_CONFIG_MACRO_DIR([m4]) + AM_CONFIG_HEADER(config.hh) + ++LT_INIT + AC_PROG_CXX + AC_PROG_INSTALL +-AC_PROG_RANLIB + + if test "x$prefix" != xNONE; then + thePREFIX=$prefix diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch new file mode 100644 index 000000000000..2211aa36c0ca --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch @@ -0,0 +1,23 @@ + Makefile.am | 4 ++-- + 1 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 06fd733..5805c48 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -32,7 +32,7 @@ noinst_PROGRAMS += make_test_snpfile test_test_snpfile + noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ + matrix_benchmark_write matrix_benchmark_read + +-LDADD = $(top_builddir)/libsnpfile.la ++LDADD = $(top_builddir)/libsnpfile.la $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ + + matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc + +@@ -88,5 +88,5 @@ libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix + metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ + input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ + type_trait.hh +-libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) ++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ + diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/snpfile/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild new file mode 100644 index 000000000000..b06f628fa020 --- /dev/null +++ b/sci-biology/snpfile/snpfile-2.0.1-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools eutils multilib + +DESCRIPTION="A library and API for manipulating large SNP datasets" +HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/" +SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +KEYWORDS="amd64 x86" + +DEPEND="dev-libs/boost" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc44.patch \ + "${FILESDIR}"/${P}-gentoo.diff \ + "${FILESDIR}"/${P}-gold.patch + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + use static-libs || rm "${D}"/usr/$(get_libdir)/lib${PN}.la +} diff --git a/sci-biology/snpfile/snpfile-2.0.1.ebuild b/sci-biology/snpfile/snpfile-2.0.1.ebuild new file mode 100644 index 000000000000..6f57debb2930 --- /dev/null +++ b/sci-biology/snpfile/snpfile-2.0.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 +inherit eutils + +DESCRIPTION="A library and API for manipulating large SNP datasets" +HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/" +SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +RDEPEND="dev-libs/boost" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc44.patch +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" +} diff --git a/sci-biology/stride/Manifest b/sci-biology/stride/Manifest new file mode 100644 index 000000000000..cd6e1754804f --- /dev/null +++ b/sci-biology/stride/Manifest @@ -0,0 +1,2 @@ +DIST stride-20060723-update.patch.bz2 5621 SHA256 8d48627c294b4efba67acba10fba47b20c0a8d5f7e06c2775a2d7eaaa0aa7b81 SHA512 e06eb68b907615e12dc1a9981be157400e9ffed9391a906cb4eb3ef4067b7027c26cc600298053bfc5d2bbbebbbfefe0e6b18d0e4f6fef2172768e6f95498af1 WHIRLPOOL fbe19cd7da96a845a001f5fcfb6c0aed7b9c4c152b48ef9ab9df63b1d72c9a97e545c9a6e12c5c58823210dd48050392b0a9c0758c1d57c3677ac5092de863f9 +DIST stride.tar.gz 56441 SHA256 d272700bccd046199f6ea1faed31a2a2662a7d5f13b7663736a1818ac18c87b9 SHA512 cbd40fce4684728f363520540132fc1a0003126954a145d59aeff48adb20fdaa66520bd12b56ee5d2906e8ea97bf78a225204105b820f7f368aee5e790a6471b WHIRLPOOL 843c789eda18da69a670a134f8a19103381ac86d611a3e1f0b47e17c3d171a195b8064d131ec3f81a561a65d8536d5f8a8c3a490776646b50ecb6aee36c46536 diff --git a/sci-biology/stride/files/stride-LDFLAGS.patch b/sci-biology/stride/files/stride-LDFLAGS.patch new file mode 100644 index 000000000000..1761b12129bd --- /dev/null +++ b/sci-biology/stride/files/stride-LDFLAGS.patch @@ -0,0 +1,11 @@ +--- Makefile 2009-10-27 21:18:45.000000000 +0100 ++++ Makefile.new 2009-10-27 21:19:00.000000000 +0100 +@@ -12,7 +12,7 @@ + + + stride : $(OBJECT) +- $(CC) $(OBJECT) $(FLAGS) $(BINDIR)/stride ++ $(CC) $(LDFLAGS) $(OBJECT) $(FLAGS) $(BINDIR)/stride + + $(OBJECT) : stride.h protot.h + diff --git a/sci-biology/stride/metadata.xml b/sci-biology/stride/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/stride/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild new file mode 100644 index 000000000000..0848427631a0 --- /dev/null +++ b/sci-biology/stride/stride-20011129-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Protein secondary structure assignment from atomic coordinates" +HOMEPAGE="http://webclu.bio.wzw.tum.de/stride/" +SRC_URI=" + ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}/src/${PN}.tar.gz + http://dev.gentoo.org/~jlec/distfiles/${PN}-20060723-update.patch.bz2" + +SLOT="0" +LICENSE="STRIDE" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="" + +S="${WORKDIR}" + +RESTRICT="mirror bindist" + +src_prepare() { + # this patch updates the source to the most recent + # version which was kindly provided by the author + epatch \ + "${DISTDIR}/${PN}-20060723-update.patch.bz2" \ + "${FILESDIR}"/${PN}-LDFLAGS.patch + + # fix makefile + sed -e "/^CC/s|gcc -g|$(tc-getCC) ${CFLAGS}|" -i Makefile || \ + die "Failed to fix Makefile" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest new file mode 100644 index 000000000000..d7abf3e8ff7d --- /dev/null +++ b/sci-biology/t-coffee/Manifest @@ -0,0 +1,2 @@ +DIST T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz 3526354 SHA256 b8018433574ff7705c49cd974bebb06a48eb8bc5e38aaa9eb4f53f2e7778e72c SHA512 5c486411bae430cfca6f4623f4dff348e2d9ab7c2eb0edef8059c6cb9c01ee48347e06be0c5d19ee1ace4b9f597f19beee8da2d7eecba29c5a78c2aec800be92 WHIRLPOOL 205eb1b416b38c4d86722ec501d815cc3f9f974a79e07f6fff32855972a9d3a9849585ca345fa66bbcbe15dca8f16930e7bafe44ce5d39e23f9f73023da13b7c +DIST T-COFFEE_distribution_Version_9.03.r1318.tar.gz 3455629 SHA256 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c SHA512 40220c9fca5bee59b66757162ff2279c2ab221cca07532c64ed3606a95a787080cd4d6bf301ca6d20d8ba4f0c2166e5785fc0ad81ed6528eb527f24d59e79cc8 WHIRLPOOL a9d6b5abdf9851289d1de985fe0eda16f40d72ad23c74ee80ec7a365d9e6124ba12b4dc17894b98bd8d886f4dd0a25bce96cd4e2ec1bc7c2177d6ab8aa00bb65 diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch new file mode 100644 index 000000000000..5b15108b3bfa --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch @@ -0,0 +1,21 @@ + t_coffee_source/makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile +index 9e01ba0..026b714 100644 +--- a/t_coffee_source/makefile ++++ b/t_coffee_source/makefile +@@ -1,6 +1,6 @@ + + t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o +- $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm + + all: t_coffee TMalign + +@@ -8,4 +8,4 @@ clean: + rm *.o + + TMalign: +- $(FCC) TMalign.f -o TMalign ++ $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml new file mode 100644 index 000000000000..9a577185ee36 --- /dev/null +++ b/sci-biology/t-coffee/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + T-Coffee is a multiple sequence alignment package. Given a set of + sequences (Proteins or DNA), T-Coffee generates a multiple sequence + alignment. Version 2.00 and higher can mix sequences and structures. + T-Coffee allows the combination of a collection of multiple/pairwise, + global or local alignments into a single model. It also allows to + estimate the level of consistency of each position within the new + alignment with the rest of the alignments. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/t-coffee/t-coffee-11.00.ebuild b/sci-biology/t-coffee/t-coffee-11.00.ebuild new file mode 100644 index 000000000000..62e8b7033cbe --- /dev/null +++ b/sci-biology/t-coffee/t-coffee-11.00.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +MY_HASH="8cbe486" +MY_PV="${PV}.${MY_HASH}" +MY_P="T-COFFEE_distribution_Version_${MY_PV}" + +DESCRIPTION="A multiple sequence alignment package" +HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" +SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-biology/clustalw + sci-chemistry/tm-align" +DEPEND="" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed \ + -e '/@/s:.*;:\t:g' \ + -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ + -i t_coffee_source/makefile || die +} + +src_compile() { + [[ $(gcc-version) == "3.4" ]] || \ + [[ $(gcc-version) == "4.1" ]] && \ + append-flags -fno-unit-at-a-time + emake \ + V=1 \ + CC="$(tc-getCXX)" \ + CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \ + -C t_coffee_source t_coffee +} + +src_install() { + dobin t_coffee_source/t_coffee + + if use examples; then + insinto /usr/share/${PN} + doins -r example + fi +} diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild new file mode 100644 index 000000000000..4b56c05793b5 --- /dev/null +++ b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 toolchain-funcs versionator + +MY_PV="$(replace_version_separator 2 .r)" +MY_P="T-COFFEE_distribution_Version_${MY_PV}" + +DESCRIPTION="A multiple sequence alignment package" +HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" +SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc ~ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-biology/clustalw + sci-chemistry/tm-align" +DEPEND="" + +S="${WORKDIR}/${MY_P}" + +die_compile() { + echo + eerror "If you experience an internal compiler error (consult the above" + eerror "messages), try compiling t-coffee using very modest compiler flags." + eerror "See bug #114745 on the Gentoo Bugzilla for more details." + die "Compilation failed" +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-flags.patch +} + +src_compile() { + [[ $(gcc-version) == "3.4" ]] || \ + [[ $(gcc-version) == "4.1" ]] && \ + append-flags -fno-unit-at-a-time + emake \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + -C t_coffee_source t_coffee +} + +src_install() { + dobin t_coffee_source/t_coffee + + if use examples; then + insinto /usr/share/${PN} + doins -r example + fi +} diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest new file mode 100644 index 000000000000..2d7d1928582d --- /dev/null +++ b/sci-biology/tophat/Manifest @@ -0,0 +1,6 @@ +DIST tophat-1.0.12.tar.gz 468781 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2 +DIST tophat-1.4.1.tar.gz 1420422 SHA256 97fd6e09e3cafa90b969dac152585ce5bab4c86f32a980ce2c8ecaac846cd937 +DIST tophat-2.0.0.tar.gz 1750811 SHA256 1c45812225906fd014ed9671a3696727c6ed0cc5be8f330b3c5ec39a9234be97 SHA512 5bd1dcc79c301dc0b464dd95d6da2b2ed69c4e003bc1f9c5cb556a7974bcdb86cbe6f7d8912856691ca89e9a5a10cbe10fa7391c4bbdc163408e1e57afed7295 WHIRLPOOL ace795553630bcd1e9966cae2ed2c42195dea2f3845fe778d591ad0214afef28ca389f32f0bd53ad01d1e3a520be140e77305313992be16259c111a9aa5e8514 +DIST tophat-2.0.2.tar.gz 1759933 SHA256 f9e40ae123dab24d2f2d6896ebf191c8ae3c05c80da6d4d965defe7579d553e0 SHA512 8341d406bfc2b86323932a151ad60469c6d50031bace433c5e3b6678a92eaed3516744fb9077d0e8944018275642050e2e9aca0126b4dd69423754c3dc9ae83c WHIRLPOOL 45a52fc96b258f4ae0b5b7a4d1dc4c22885e0b9230891dde1db85671deeceb3213008de02878cc3b1f9dc6af68b40bc897f691a1835bd4abf29d1a2bde42e1c2 +DIST tophat-2.0.8.tar.gz 1757036 SHA256 07d323d295effc99d4e261439c5ba2e10d5530af078e5de97c1a7bf1cbdd0da1 SHA512 c69360cc2f558c37d14b6a0e006f2483771ce5cdb42dc8397dd15a944a61d762843158adbf7c2bc89c2d4db46d9a02633dbd2721bf3376ef5d3ae6fb153db100 WHIRLPOOL a97ad6d47be23089605578a6f8ff9434afcb27a9fa58118b5b923af1d79530614af9fcaf5ebda2043603bf2dd8b10c2b7636e7b14662b9ab4f6e2059da4cb2b2 +DIST tophat-2.0.9.tar.gz 1766681 SHA256 9b506bbfdbb14b296d804557a50f41cc167480dfeed66a31c33e2ffb580afd38 SHA512 a81b801ee6c1f643d1fa507c2372d43ccdf4922d3f7ab76a34442c96aee78a3afc4a47ba164d46c6b6b6451aeae78b711c44c118e584da742940f74af7bc9610 WHIRLPOOL a67392251e592df62deb3fe58dcc4eadd0d0b1fe0a09389e48f1f30a7c591343794d1e1b2a27467c0a0f5a0e84dd5a5fbdef538a5bcf1b80ba8972e6ec02fbcf diff --git a/sci-biology/tophat/files/tophat-2.0.2-flags.patch b/sci-biology/tophat/files/tophat-2.0.2-flags.patch new file mode 100644 index 000000000000..ac1ca62da254 --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.0.2-flags.patch @@ -0,0 +1,124 @@ + configure.ac | 6 +++--- + src/Makefile.am | 30 +++++++++++++++--------------- + 2 files changed, 18 insertions(+), 18 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 314a78e..f6933e6 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -68,7 +68,8 @@ AC_CANONICAL_HOST + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++#generic_CFLAGS="-Wall -Wno-strict-aliasing -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2], +@@ -84,7 +85,7 @@ AC_ARG_ENABLE([optim], + [if test "x$enable_optim" = xyes; then enable_optim=3; fi], + [enable_optim=3]) + +-AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) ++#AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"]) + AS_IF([test "x$enable_debug" = xyes], + [debug_CFLAGS="-DDEBUG"], + [debug_CFLAGS="-DNDEBUG"]) +@@ -92,7 +93,6 @@ AS_IF([test "x$enable_debug" = xyes], + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}" + CXXFLAGS="$CFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3" +-LDFLAGS="$ext_LDFLAGS" + + AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) + +diff --git a/src/Makefile.am b/src/Makefile.am +index aa17841..42f9c0c 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -2,7 +2,7 @@ + + #SUBDIRS = samtools + +-#AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3 ++AM_CXXFLAGS = -I$(top_srcdir)/src/SeqAn-1.3 + + # Generated with + # find SeqAn-1.3 -type f -print | grep -v ".svn" | sed 's/$/ \\/g' +@@ -550,7 +550,7 @@ CLEANFILES = \ + tophat2 + + tophat2: tophat2.in +- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2 ++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2 + + #SUFFIXES = .py + #.py: +@@ -621,53 +621,53 @@ libgc_a_SOURCES = \ + #-- program sources + + prep_reads_SOURCES = prep_reads.cpp +-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++prep_reads_LDADD = libtophat.a $(BAM_LIB) + prep_reads_LDFLAGS = $(BAM_LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB) ++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB) + segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB) ++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB) + long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) ++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB) + gtf_juncs_LDFLAGS = $(BAM_LDFLAGS) + + juncs_db_SOURCES = juncs_db.cpp +-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++juncs_db_LDADD = libtophat.a $(BAM_LIB) + juncs_db_LDFLAGS = $(BAM_LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB) ++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BAM_LIB) + tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp +-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB) + fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS) + + bam2fastx_SOURCES = bam2fastx.cpp +-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB) ++bam2fastx_LDADD = libgc.a $(BAM_LIB) + bam2fastx_LDFLAGS = $(BAM_LDFLAGS) + + bam_merge_SOURCES = bam_merge.cpp +-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB) ++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB) + bam_merge_LDFLAGS = $(BAM_LDFLAGS) + + closure_juncs_SOURCES = closures.cpp +-closure_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++closure_juncs_LDADD = libtophat.a $(BAM_LIB) + closure_juncs_LDFLAGS = $(BAM_LDFLAGS) + + sam_juncs_SOURCES = sam_juncs.cpp +-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) ++sam_juncs_LDADD = libtophat.a $(BAM_LIB) + sam_juncs_LDFLAGS = $(BAM_LDFLAGS) + + map2gtf_SOURCES = map2gtf.cpp +-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) ++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB) + map2gtf_LDFLAGS = $(BAM_LDFLAGS) + + gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp +-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) ++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB) + gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) diff --git a/sci-biology/tophat/files/tophat-2.0.8-flags.patch b/sci-biology/tophat/files/tophat-2.0.8-flags.patch new file mode 100644 index 000000000000..604f657d4c42 --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.0.8-flags.patch @@ -0,0 +1,105 @@ + configure.ac | 3 ++- + src/Makefile.am | 50 +++++++++++++++++++++++++------------------------- + 2 files changed, 27 insertions(+), 26 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 75e9218..98b05d2 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -68,7 +68,8 @@ AC_CANONICAL_HOST + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + user_LDFLAGS="$LDFLAGS" +diff --git a/src/Makefile.am b/src/Makefile.am +index dde692e..ebb9fcd 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -545,7 +545,7 @@ CLEANFILES = \ + tophat2 + + tophat2: tophat2.in +- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2 ++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2 + + #SUFFIXES = .py + #.py: +@@ -617,49 +617,49 @@ libgc_a_SOURCES = \ + #-- program sources + + prep_reads_SOURCES = prep_reads.cpp +-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++prep_reads_LDADD = libtophat.a $(BAM_LIB) ++prep_reads_LDFLAGS = $(BAM_LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_juncs_LDFLAGS = $(BAM_LDFLAGS) + + juncs_db_SOURCES = juncs_db.cpp +-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++juncs_db_LDADD = libtophat.a $(BAM_LIB) ++juncs_db_LDFLAGS = $(BAM_LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp +-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB) ++fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS) + + bam2fastx_SOURCES = bam2fastx.cpp +-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam2fastx_LDADD = libgc.a $(BAM_LIB) ++bam2fastx_LDFLAGS = $(BAM_LDFLAGS) + + bam_merge_SOURCES = bam_merge.cpp +-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB) ++bam_merge_LDFLAGS = $(BAM_LDFLAGS) + + sam_juncs_SOURCES = sam_juncs.cpp +-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++sam_juncs_LDADD = libtophat.a $(BAM_LIB) ++sam_juncs_LDFLAGS = $(BAM_LDFLAGS) + + map2gtf_SOURCES = map2gtf.cpp +-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB) ++map2gtf_LDFLAGS = $(BAM_LDFLAGS) + + gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp +-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch new file mode 100644 index 000000000000..af89e72084bf --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.0.9-flags.patch @@ -0,0 +1,109 @@ + configure.ac | 3 ++- + src/Makefile.am | 50 +++++++++++++++++++++++++------------------------- + 2 files changed, 27 insertions(+), 26 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 75e9218..98b05d2 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -68,7 +68,8 @@ AC_CANONICAL_HOST + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + user_LDFLAGS="$LDFLAGS" +diff --git a/src/Makefile.am b/src/Makefile.am +index dde692e..ebb9fcd 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -545,10 +545,10 @@ CLEANFILES = \ + tophat2 + + tophat2: tophat2.in +- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2 ++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2 + + tophat: tophat.py +- sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat ++ sed -e 's|__VERSION__|$(VERSION)|' $(top_srcdir)/src/tophat.py > tophat + + #SUFFIXES = .py + #.py: +@@ -617,49 +617,49 @@ libgc_a_SOURCES = \ + #-- program sources + + prep_reads_SOURCES = prep_reads.cpp +-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++prep_reads_LDADD = libtophat.a $(BAM_LIB) ++prep_reads_LDFLAGS = $(BAM_LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_juncs_LDFLAGS = $(BAM_LDFLAGS) + + juncs_db_SOURCES = juncs_db.cpp +-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++juncs_db_LDADD = libtophat.a $(BAM_LIB) ++juncs_db_LDFLAGS = $(BAM_LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp +-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB) ++fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS) + + bam2fastx_SOURCES = bam2fastx.cpp +-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam2fastx_LDADD = libgc.a $(BAM_LIB) ++bam2fastx_LDFLAGS = $(BAM_LDFLAGS) + + bam_merge_SOURCES = bam_merge.cpp +-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB) ++bam_merge_LDFLAGS = $(BAM_LDFLAGS) + + sam_juncs_SOURCES = sam_juncs.cpp +-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++sam_juncs_LDADD = libtophat.a $(BAM_LIB) ++sam_juncs_LDFLAGS = $(BAM_LDFLAGS) + + map2gtf_SOURCES = map2gtf.cpp +-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB) ++map2gtf_LDFLAGS = $(BAM_LDFLAGS) + + gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp +-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml new file mode 100644 index 000000000000..36cf4a138940 --- /dev/null +++ b/sci-biology/tophat/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="bam">Compile support for the BAM format</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/tophat/tophat-1.0.12.ebuild b/sci-biology/tophat/tophat-1.0.12.ebuild new file mode 100644 index 000000000000..88870c93982b --- /dev/null +++ b/sci-biology/tophat/tophat-1.0.12.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit autotools + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="" +RDEPEND="sci-biology/bowtie" + +src_prepare() { + # fix missing includes + sed -i '/#include <string>/ a #include <stdio.h>' "${S}/src/gff_juncs.cpp" || die + sed -i \ + -e '/#include <stdio.h>/ a #include <unistd.h>' \ + "${S}/src/prep_reads.cpp" \ + "${S}/src/extract_reads.cpp" || die + # fix parallel make race + sed -i -e 's/\$(top_builddir)\/src\///g' src/Makefile.am || die + # remove broken arch-dependent CFLAGS setting + perl -i -ne 'print unless /case "\${host_cpu}-\${host_os}" in/../^esac/' configure.ac || die + eautoreconf +} + +src_install() { + einstall || die + dodoc AUTHORS NEWS THANKS +} diff --git a/sci-biology/tophat/tophat-1.4.1.ebuild b/sci-biology/tophat/tophat-1.4.1.ebuild new file mode 100644 index 000000000000..3130c0d7c9c7 --- /dev/null +++ b/sci-biology/tophat/tophat-1.4.1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit flag-o-matic autotools + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="+bam" +KEYWORDS="~amd64 ~x86" + +DEPEND="bam? ( sci-biology/samtools )" +RDEPEND="${DEPEND} + sci-biology/bowtie" + +MAKEOPTS="${MAKEOPTS} -j1" + +src_prepare() { + filter-ldflags -Wl,--as-needed + eautoreconf +} + +src_configure() { + econf \ + $(use_with bam) +} diff --git a/sci-biology/tophat/tophat-2.0.0.ebuild b/sci-biology/tophat/tophat-2.0.0.ebuild new file mode 100644 index 000000000000..93159f65c773 --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+bam debug" + +DEPEND=" + dev-libs/boost + bam? ( sci-biology/samtools )" +RDEPEND="${DEPEND} + sci-biology/bowtie" + +PATCHES=( "${FILESDIR}"/${PN}-2.0.2-flags.patch ) + +src_configure() { + local myeconfargs=( $(use_enable debug) ) + autotools-utils_src_configure +} diff --git a/sci-biology/tophat/tophat-2.0.2.ebuild b/sci-biology/tophat/tophat-2.0.2.ebuild new file mode 100644 index 000000000000..7f68695af743 --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.2.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+bam debug" + +DEPEND=" + dev-libs/boost + bam? ( sci-biology/samtools )" +RDEPEND="${DEPEND} + sci-biology/bowtie" + +PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_configure() { + local myeconfargs=( $(use_enable debug) ) + autotools-utils_src_configure +} diff --git a/sci-biology/tophat/tophat-2.0.8.ebuild b/sci-biology/tophat/tophat-2.0.8.ebuild new file mode 100644 index 000000000000..c20007cd6160 --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.8.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" + +DEPEND=" + dev-libs/boost + sci-biology/samtools + sci-biology/seqan" +RDEPEND="${DEPEND} + sci-biology/bowtie" + +PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_prepare() { + rm -rf src/SeqAn* || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/tophat/tophat-2.0.9.ebuild b/sci-biology/tophat/tophat-2.0.9.ebuild new file mode 100644 index 000000000000..91cc2d463330 --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.9.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="A fast splice junction mapper for RNA-Seq reads" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug" + +DEPEND=" + dev-libs/boost + sci-biology/samtools + sci-biology/seqan" +RDEPEND="${DEPEND} + sci-biology/bowtie" + +PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_prepare() { + rm -rf src/SeqAn* || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + python_fix_shebang "${ED}"/usr/bin/tophat +} diff --git a/sci-biology/transfac/Manifest b/sci-biology/transfac/Manifest new file mode 100644 index 000000000000..d9522e5cccb5 --- /dev/null +++ b/sci-biology/transfac/Manifest @@ -0,0 +1 @@ +DIST transfac32.tar.Z 3346266 RMD160 892164634a80f388ba3c588823576ff0b5582338 SHA1 1f950c981364b03819463536c8d0195fe7351f02 SHA256 cf5c64e6f23037d73562d66f9dde56a767a8f31974a1c0906ec68edea3731a7f diff --git a/sci-biology/transfac/metadata.xml b/sci-biology/transfac/metadata.xml new file mode 100644 index 000000000000..d07df4fd4dbf --- /dev/null +++ b/sci-biology/transfac/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + TRANSFAC® is a database of eukaryotic transcription factors, of their + genomic binding sites and DNA-binding profiles. TRANSFAC 3.2 is an old + public version available at the European Bioinformatics Institute. + TRANSFAC® is currently maintained by the BIOBASE company. Altough they + offer public access to a more recent version of the database, they + offer no free downloadable version. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/transfac/transfac-3.2.ebuild b/sci-biology/transfac/transfac-3.2.ebuild new file mode 100644 index 000000000000..e2cdd68565f2 --- /dev/null +++ b/sci-biology/transfac/transfac-3.2.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +DESCRIPTION="A database of eucaryotic transcription factors" +HOMEPAGE="http://www.gene-regulation.com/pub/databases.html" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z" +LICENSE="public-domain" + +SLOT="3" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="emboss minimal" +# Minimal build keeps only the indexed files (if applicable) and the documentation. +# The non-indexed database is not installed. + +DEPEND="emboss? ( sci-biology/emboss )" + +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +src_compile() { + if use emboss; then + echo + einfo "Indexing TRANSFAC for usage with EMBOSS." + EMBOSS_DATA=. tfextract -auto -infile class.dat || die \ + "Indexing TRANSFAC failed." + echo + fi +} + +src_install() { + if ! use minimal; then + insinto /usr/share/${PN}-${SLOT} + doins *.dat || die + fi + if use emboss; then + insinto /usr/share/EMBOSS/data + doins tf* || die + fi +} diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest new file mode 100644 index 000000000000..4b855c8b51b8 --- /dev/null +++ b/sci-biology/tree-puzzle/Manifest @@ -0,0 +1 @@ +DIST tree-puzzle-5.2.tar.gz 875142 SHA256 3396d3b80b03b0600afb479dc33f0bd3e5631298337295a4fa454211ac44c3fb SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751 WHIRLPOOL 145afdfc266809638d7b049beb65cdfc8fb6c108ecba831ba36fae938d58edd141fdf1762d9ce86269f0098043e7314b0ddefaa5e7f9b11cc6fd56a480b54d61 diff --git a/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch new file mode 100644 index 000000000000..93b960f5c2b4 --- /dev/null +++ b/sci-biology/tree-puzzle/files/tree-puzzle-impl-dec.patch @@ -0,0 +1,14 @@ + src/sprng/primes-lcg64.c | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/sprng/primes-lcg64.c b/src/sprng/primes-lcg64.c +index 8e5a7c9..fb04373 100644 +--- a/src/sprng/primes-lcg64.c ++++ b/src/sprng/primes-lcg64.c +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <stdlib.h> ++#include <string.h> + #include "primes-lcg64.h" + #include "primelist-lcg64.h" + diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml new file mode 100644 index 000000000000..cbdeede346fa --- /dev/null +++ b/sci-biology/tree-puzzle/metadata.xml @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + TREE-PUZZLE is a computer program to reconstruct phylogenetic trees + from molecular sequence data by maximum likelihood. It implements a + fast tree search algorithm, quartet puzzling, that allows analysis of + large data sets and automatically assigns estimations of support to + each internal branch. TREE-PUZZLE also computes pairwise maximum + likelihood distances as well as branch lengths for user specified + trees. Branch lengths can be calculated under the clock-assumption. In + addition, TREE-PUZZLE offers a novel method, likelihood mapping, to + investigate the support of a hypothesized internal branch without + computing an overall tree and to visualize the phylogenetic content of + a sequence alignment. TREE-PUZZLE also conducts a number of statistical + tests on the data set (chi-square test for homogeneity of base + composition, likelihood ratio clock test, Kishino-Hasegawa test). The + models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for + nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, + and F81 for two-state data. Rate heterogeneity is modeled by a discrete + Gamma distribution and by allowing invariable sites. The corresponding + parameters can be inferred from the data set. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild new file mode 100644 index 000000000000..fd2b06f1d159 --- /dev/null +++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data" +HOMEPAGE="http://www.tree-puzzle.de" +SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="mpi" + +DEPEND="mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +RESTRICT="test" + +pkg_setup () { + use mpi && [ $(tc-getCC) = icc ] && die "The parallelized version of tree-puzzle cannot be compiled using icc. + Either disable the \"mpi\" USE flag to compile only the non-parallelized + version of the program, or use gcc as your compiler (CC=\"gcc\")." +} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-impl-dec.patch +} + +src_configure() { + default + + if ! use mpi; then + sed \ + -e 's:bin_PROGRAMS = puzzle$(EXEEXT) ppuzzle:bin_PROGRAMS = puzzle :' \ + -e 's:DIST_SOURCES = $(ppuzzle_SOURCES) $(puzzle_SOURCES):DIST_SOURCES = $(puzzle_SOURCES):' \ + -i "${S}"/src/Makefile || die + fi +} + +src_install() { + dobin src/puzzle + use mpi && dobin src/ppuzzle + dodoc AUTHORS ChangeLog README + + # User manual + insinto /usr/share/doc/${PF} + doins doc/tree-puzzle.pdf + + # Example data files + insinto /usr/share/${PN}/data + rm data/Makefile* + doins data/* +} diff --git a/sci-biology/treeviewx/Manifest b/sci-biology/treeviewx/Manifest new file mode 100644 index 000000000000..024410ff1615 --- /dev/null +++ b/sci-biology/treeviewx/Manifest @@ -0,0 +1 @@ +DIST tv-0.5.1.tar.gz 426745 RMD160 27c92a0f43c59c8988fe2d1410adb6de429e94c9 SHA1 0b0887477ca0d9ded6d0ee8bef014b6208e1fc14 SHA256 118bdbefb3f21636b1ba9da92e1b2029cb4d7d9944f4d02d2deace4ebb14c2d1 diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch new file mode 100644 index 000000000000..33bd3b1741f6 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-gcc4.3.patch @@ -0,0 +1,77 @@ +diff -Naur tv-0.5.1/TreeLib/Parse.cpp tv-0.5.1.new/TreeLib/Parse.cpp +--- tv-0.5.1/TreeLib/Parse.cpp 2002-02-23 07:22:32.000000000 -0500 ++++ tv-0.5.1.new/TreeLib/Parse.cpp 2008-06-17 06:08:24.000000000 -0400 +@@ -24,6 +24,11 @@ + #include <ctype.h> + #include "Parse.h" + ++ ++ ++ ++#include <cstring> ++ + // Return the next token in the string + tokentype Parser::NextToken () + { +diff -Naur tv-0.5.1/TreeLib/TreeLib.cpp tv-0.5.1.new/TreeLib/TreeLib.cpp +--- tv-0.5.1/TreeLib/TreeLib.cpp 2004-05-13 08:22:11.000000000 -0400 ++++ tv-0.5.1.new/TreeLib/TreeLib.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -24,6 +24,8 @@ + #include "TreeLib.h" + #include "Parse.h" + ++ ++#include <cstdlib> + #include <vector> + + +diff -Naur tv-0.5.1/TreeLib/treereader.cpp tv-0.5.1.new/TreeLib/treereader.cpp +--- tv-0.5.1/TreeLib/treereader.cpp 2003-09-10 08:58:16.000000000 -0400 ++++ tv-0.5.1.new/TreeLib/treereader.cpp 2008-06-17 06:07:15.000000000 -0400 +@@ -28,6 +28,9 @@ + #include <stdlib.h> + #endif + ++#include <cstring> ++#include <cstdlib> ++ + //------------------------------------------------------------------------------ + TreeReader::TreeReader (Tokeniser &p) : parser (p) + { +diff -Naur tv-0.5.1/ncl-2.0/src/charactersblock.cpp tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp +--- tv-0.5.1/ncl-2.0/src/charactersblock.cpp 2002-12-10 06:35:49.000000000 -0500 ++++ tv-0.5.1.new/ncl-2.0/src/charactersblock.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,5 @@ ++ ++#include <cstring> + #include "nexusdefs.h" + #include "xnexus.h" + #include "nexustoken.h" +diff -Naur tv-0.5.1/ncl-2.0/src/nexus.cpp tv-0.5.1.new/ncl-2.0/src/nexus.cpp +--- tv-0.5.1/ncl-2.0/src/nexus.cpp 2002-12-10 06:35:50.000000000 -0500 ++++ tv-0.5.1.new/ncl-2.0/src/nexus.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,5 @@ ++ ++#include <cstring> + #include "nexusdefs.h" + #include "xnexus.h" + #include "nexustoken.h" +diff -Naur tv-0.5.1/ncl-2.0/src/nexustoken.cpp tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp +--- tv-0.5.1/ncl-2.0/src/nexustoken.cpp 2005-04-29 10:28:17.000000000 -0400 ++++ tv-0.5.1.new/ncl-2.0/src/nexustoken.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,5 @@ ++ ++#include <cstring> + #include "nexusdefs.h" + #include "xnexus.h" + #include "nexustoken.h" +diff -Naur tv-0.5.1/ncl-2.0/src/nxsstring.cpp tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp +--- tv-0.5.1/ncl-2.0/src/nxsstring.cpp 2001-02-02 07:55:40.000000000 -0500 ++++ tv-0.5.1.new/ncl-2.0/src/nxsstring.cpp 2008-06-17 05:58:17.000000000 -0400 +@@ -1,3 +1,6 @@ ++ ++#include <cstring> ++ + #ifdef __BORLANDC__ + // Undefine __MINMAX_DEFINED so that min and max are correctly defined + #ifdef __MINMAX_DEFINED diff --git a/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch new file mode 100644 index 000000000000..e3ba6b2fff50 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-0.5.1-wx28.patch @@ -0,0 +1,14 @@ +Fix build w/ wxGTK-2.8 +http://bugs.debian.org/567238 + +--- a/tview.cpp ++++ b/tview.cpp +@@ -994,7 +994,7 @@ END_EVENT_TABLE() + MyCanvas::MyCanvas(wxView *v, wxMDIChildFrame *frame, const wxPoint& pos, const wxSize& size, long style): + wxScrolledWindow(frame, -1, pos, size, style) + { +- SetBackgroundColour(wxColour("WHITE")); ++ SetBackgroundColour(wxColour(wxT("WHITE"))); + view = v; + magnification = 1; + } diff --git a/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch b/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch new file mode 100644 index 000000000000..9d64fabb6a9b --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-gcc-3.4.patch @@ -0,0 +1,73 @@ +--- TreeLib/nodeiterator.h.old 2002-02-24 15:37:17.000000000 -0500 ++++ TreeLib/nodeiterator.h 2005-02-27 14:23:30.971981368 -0500 +@@ -128,34 +128,34 @@ + + template <class N> N *PreorderIterator<N>::begin () + { +- cur = root; +- return cur; ++ this->cur = this->root; ++ return this->cur; + } + + template <class N> N *PreorderIterator<N>::next () + { +- if (cur->GetChild()) ++ if (this->cur->GetChild()) + { +- stk.push (cur); +- N *p = (N *)(cur->GetChild()); +- cur = p; ++ this->stk.push (this->cur); ++ N *p = (N *)(this->cur->GetChild()); ++ this->cur = p; + } + else + { +- while (!stk.empty() && (cur->GetSibling() == NULL)) ++ while (!this->stk.empty() && (this->cur->GetSibling() == NULL)) + { +- cur = stk.top(); +- stk.pop(); ++ this->cur = this->stk.top(); ++ this->stk.pop(); + } +- if (stk.empty()) +- cur = NULL; ++ if (this->stk.empty()) ++ this->cur = NULL; + else + { +- N *p = (N *)(cur->GetSibling()); +- cur = p; ++ N *p = (N *)(this->cur->GetSibling()); ++ this->cur = p; + } + } +- return cur; ++ return this->cur; + } + + +--- TreeLib/profile.h.old 2002-12-10 06:37:57.000000000 -0500 ++++ TreeLib/profile.h 2005-02-27 14:27:51.205419872 -0500 +@@ -77,7 +77,7 @@ + #include <ctime> + #endif + +- ++using namespace std; + + /** + *@typedef std::map <std::string, int, std::less<std::string> > LabelMap; +--- TreeLib/treedrawer.cpp.old 2003-08-22 06:47:28.000000000 -0400 ++++ TreeLib/treedrawer.cpp 2005-02-27 14:26:19.279394752 -0500 +@@ -406,7 +406,7 @@ + if (q->IsLeaf()) + { + double d = q->GetPathLength() - mMaxPathLength; +- mUltrametric = (std::fabs(d) <= 0.0001); ++ mUltrametric = (fabs(d) <= 0.0001); + // cout << mMaxPathLength << ":" << q->GetPathLength() << " " << d << endl; + } + q = u.next(); diff --git a/sci-biology/treeviewx/files/treeviewx-wxt.patch b/sci-biology/treeviewx/files/treeviewx-wxt.patch new file mode 100644 index 000000000000..b1c03bbb39f9 --- /dev/null +++ b/sci-biology/treeviewx/files/treeviewx-wxt.patch @@ -0,0 +1,50 @@ +--- tv.cpp~ 2005-10-01 16:47:35.000000000 -0400 ++++ tv.cpp 2005-10-01 16:52:30.000000000 -0400 +@@ -312,11 +312,15 @@ + { + #ifdef __WXMSW__ + file_menu->AppendSeparator(); +- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to metafile"); ++ file_menu->Append(SAVEAS_PICTURE_CMD, ++ wxT("Save As Picture...")), ++ wxT("Save picture of tree to metafile"); + #else + #ifdef USE_SVG + file_menu->AppendSeparator(); +- file_menu->Append(SAVEAS_PICTURE_CMD, "Save As Picture..."), wxT("Save picture of tree to SVG file"); ++ file_menu->Append(SAVEAS_PICTURE_CMD, ++ wxT("Save As Picture...")), ++ wxT("Save picture of tree to SVG file"); + #endif + #endif + file_menu->AppendSeparator(); +--- tview.cpp~ 2005-10-01 16:47:45.000000000 -0400 ++++ tview.cpp 2005-10-01 16:50:42.000000000 -0400 +@@ -184,10 +184,10 @@ + wxString pictureFileName = GetFrame()->GetTitle(); + pictureFileName += wxT(".emf"); + wxFrame *f = GetMainFrame(); +- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, +- "Enhanced metafile (*.emf)|*.emf", +- wxSAVE|wxOVERWRITE_PROMPT); +- ++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), ++ pictureFileName, wxT("Enhanced metafile (*.emf)|*.emf"), ++ wxSAVE|wxOVERWRITE_PROMPT); ++ + if (dialog.ShowModal() == wxID_OK) + { + wxMetafileDC pictureDC (dialog.GetPath(), 600, 650) ; +@@ -204,9 +204,9 @@ + #else + wxFrame *f = GetMainFrame(); + #endif +- wxFileDialog dialog((wxWindow *)f, "Save Picture as", "", pictureFileName, +- "SVG vector picture files (*.svg)|*.svg", +- wxSAVE|wxOVERWRITE_PROMPT); ++ wxFileDialog dialog((wxWindow *)f, wxT("Save Picture as"), wxT(""), ++ pictureFileName, wxT("SVG vector picture files (*.svg)|*.svg"), ++ wxSAVE|wxOVERWRITE_PROMPT); + + if (dialog.ShowModal() == wxID_OK) + { diff --git a/sci-biology/treeviewx/metadata.xml b/sci-biology/treeviewx/metadata.xml new file mode 100644 index 000000000000..e351ff6c1fa9 --- /dev/null +++ b/sci-biology/treeviewx/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + TreeView X is a program for displaying phylogenetic trees on Linux and + UNIX platforms. It can read and display NEXUS and Newick format tree + files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other + programs). + </longdescription> +</pkgmetadata> diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild new file mode 100644 index 000000000000..4ff83ca1f34c --- /dev/null +++ b/sci-biology/treeviewx/treeviewx-0.5.1-r2.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=2 + +WX_GTK_VER="2.8" +inherit eutils wxwidgets + +DESCRIPTION="A phylogenetic tree viewer" +HOMEPAGE="http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/" +SRC_URI="http://darwin.zoology.gla.ac.uk/~rpage/${PN}/download/0.5/tv-${PV}.tar.gz" +LICENSE="GPL-2" + +KEYWORDS="amd64 x86" +SLOT="0" +IUSE="" + +DEPEND="x11-libs/wxGTK:2.8[X]" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/tv-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-wxt.patch + epatch "${FILESDIR}"/${P}-gcc4.3.patch + epatch "${FILESDIR}"/${P}-wx28.patch +} + +src_install() { + emake install DESTDIR="${D}" || die "make install failed" +} diff --git a/sci-biology/trf/Manifest b/sci-biology/trf/Manifest new file mode 100644 index 000000000000..621d293009ea --- /dev/null +++ b/sci-biology/trf/Manifest @@ -0,0 +1 @@ +DIST trf404.linux 89853 SHA256 1b9e3917088684afc2287a078810858f7a8e50d90e7bad2d814d40dc24188058 SHA512 c1aa05e394d47ea153df3082258f9a089aa59976963e9ac5d5816ef9dcd95c47e2e46861d1b2aae52b5ea9950a823a2449dd0d8426b04f2b738f5552c319393e WHIRLPOOL 7817c7eeb2c452ece7f71c2b7548fd9cda8c6796d5e77b2de46911f50bb271290b1a9601545efc50b94574c718e0e5e65d4a4e27f5cfd66c3590e9d5b7c5856c diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/trf/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/trf/trf-4.04.ebuild b/sci-biology/trf/trf-4.04.ebuild new file mode 100644 index 000000000000..81d540251f07 --- /dev/null +++ b/sci-biology/trf/trf-4.04.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils + +MY_P="${PN}404" + +DESCRIPTION="Tandem Repeats Finder" +HOMEPAGE="http://tandem.bu.edu/trf/trf.html" +SRC_URI="http://tandem.bu.edu/trf/downloads/${MY_P}.linux" + +LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html +SLOT="0" +KEYWORDS="amd64 x86" +RESTRICT="mirror bindist" + +S="${WORKDIR}" + +QA_PREBUILT="opt/${PN}/.*" + +src_unpack() { + cp "${DISTDIR}/${MY_P}.linux" "${S}/${MY_P}.linux.exe" || die +} + +src_install() { + exeinto /opt/${PN} + doexe trf404.linux.exe + dosym /opt/${PN}/${MY_P}.linux.exe /opt/bin/trf + # GTK version (http://tandem.bu.edu/trf/downloads/trf400.linuxgtk.exe) has broken linking + #if use gtk; then + # doexe trf400.linuxgtk.exe || die + # make_desktop_entry /opt/${PN}/trf400.linuxgtk.exe "Tandem Repeats Finder" || die + #fi +} diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest new file mode 100644 index 000000000000..b82cf548c773 --- /dev/null +++ b/sci-biology/trnascan-se/Manifest @@ -0,0 +1,2 @@ +DIST trnascan-se-1.23.tar.bz2 482202 SHA256 a1d18a0b9decf4a93fa6cf02fb5867367729449fc8e47e3749c91678fc1f344a SHA512 4977febcecf8344fb77aad2eeb278637aebdb1d995fd26823e459b3767d4f40b20f57d343092cc2cb8024b0ccc385879f4b6406c69022f848aa1df0acf1a68d8 WHIRLPOOL 978328857eaef5666fcf38c22afabfb796984b5fa52a02a7167b653164ba0bc32fcb52d35159eef83732046245c598426739cd4ed63bf259ea85130dda17dd70 +DIST trnascan-se-1.31.tar.gz 740960 SHA256 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d WHIRLPOOL aef8b9f8d44799bac134a36af45374cdaba4b30c041e71e3095252aa8272fe9bd0aa76091211ac270ad609f67f388d577a83ec2ed2433997963fd5708c5b6665 diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch new file mode 100644 index 000000000000..e21da6e58db0 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch @@ -0,0 +1,292 @@ +diff -ur trnascan-se-1.23.orig/sqio.c trnascan-se-1.23/sqio.c +--- trnascan-se-1.23.orig/sqio.c 2002-04-12 23:12:04.000000000 +0300 ++++ trnascan-se-1.23/sqio.c 2009-08-05 21:45:53.000000000 +0300 +@@ -235,7 +235,7 @@ + } + + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + readline(V->f, V->sbuffer); + } +@@ -306,7 +306,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + done = feof(V->f); + done |= (*endTest)(V->sbuffer, &addend); + if (addend || !done) +@@ -332,7 +332,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -341,7 +341,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -350,7 +350,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -364,7 +364,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -382,7 +382,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -394,7 +394,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -416,7 +416,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -425,7 +425,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -443,7 +443,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -454,7 +454,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -487,11 +487,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -521,12 +521,12 @@ + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); + +- getline(V); /*skip title-junk line*/ ++ get_line(V); /*skip title-junk line*/ + + readLoop(0, endNBRF, V); + + while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>'))) +- getline(V); ++ get_line(V); + } + + +@@ -559,7 +559,7 @@ + } else Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -579,7 +579,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -625,7 +625,7 @@ + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -652,7 +652,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -661,7 +661,7 @@ + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -685,7 +685,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -701,7 +701,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -712,7 +712,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -734,7 +734,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -746,7 +746,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -754,7 +754,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -786,14 +786,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -801,7 +801,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -848,7 +848,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -862,7 +862,7 @@ + SeqfilePosition(SQFILE *sqfp, long offset) + { + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -954,7 +954,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch new file mode 100644 index 000000000000..783e4340823d --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/Makefile b/Makefile +index 53e5c5b..a2d3feb 100644 +--- a/Makefile ++++ b/Makefile +@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o + all: $(PROGS) tRNAscanSE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + + trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c + + tRNAscanSE: + $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch new file mode 100644 index 000000000000..f28b1e8f6bb0 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/Makefile b/Makefile +index 53e5c5b..a2d3feb 100644 +--- a/Makefile ++++ b/Makefile +@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + + trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c + + tRNAscan-SE: + $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml new file mode 100644 index 000000000000..55de1683677f --- /dev/null +++ b/sci-biology/trnascan-se/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA + genes, with a false positive rate of less than one per 15 gigabases, + and with a search speed of about 30 kb/second. It was implemented for + large-scale human genome sequence analysis, but is applicable to + other DNAs as well. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild b/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild new file mode 100644 index 000000000000..aa8abf707262 --- /dev/null +++ b/sci-biology/trnascan-se/trnascan-se-1.23-r2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="tRNA detection in large-scale genome sequences" +HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +RDEPEND="dev-lang/perl" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-glibc-2.10.patch + epatch "${FILESDIR}"/${P}-ldflags.patch + sed -e "s%BINDIR = \$(HOME)/bin%BINDIR = ${EPREFIX}/usr/bin%" \ + -e "s%LIBDIR = \$(HOME)/lib/tRNAscan-SE%LIBDIR = ${EPRFIX}/usr/$(get_libdir)/${PN}%" \ + -e "s%MANDIR = \$(HOME)/man%MANDIR = ${EPREFIX}/usr/share/man%" \ + -e "s%CC = gcc%CC = $(tc-getCC)%" \ + -e "s%CFLAGS = -O%CFLAGS = ${CFLAGS}%" \ + -i Makefile || die +} + +src_install() { + mv tRNAscan-SE.man tRNAscan-SE.man.1 || die + dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 || die + doman tRNAscan-SE.man.1 || die + dodoc MANUAL README Release.history || die + insinto /usr/$(get_libdir)/${PN}/ + doins *.cm gcode.* Dsignal TPCsignal || die + insinto /usr/share/doc/${PF} + doins Manual.ps || die +} + +src_test() { + make PATH="${S}:${PATH}" testrun || die +} diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild new file mode 100644 index 000000000000..aa9b3a03fd8f --- /dev/null +++ b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no + +inherit eutils perl-module toolchain-funcs + +DESCRIPTION="tRNA detection in large-scale genome sequences" +HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" +SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S="${WORKDIR}"/tRNAscan-SE-1.3.1/ + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-ldflags.patch + sed \ + -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \ + -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \ + -e "s:MANDIR = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \ + -i Makefile || die + + perl_set_version +} + +src_test() { + emake PATH="${S}:${PATH}" testrun +} + +src_install() { + dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 + + newman tRNAscan-SE.man tRNAscan-SE.man.1 + + dodoc MANUAL README Release.history + + insinto /usr/share/${PN}/ + doins *.cm gcode.* Dsignal TPCsignal + + dodoc Manual.ps + + insinto ${VENDOR_LIB} + doins -r tRNAscanSE +} diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest new file mode 100644 index 000000000000..e17b1c93e220 --- /dev/null +++ b/sci-biology/uchime/Manifest @@ -0,0 +1 @@ +DIST uchime4.2.40_src.tar.gz 66772 SHA256 cb6a3aea4e8b4343a6e0ddde3b2755bbec53492bae5d6252ce8a7091061f353d SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b WHIRLPOOL 28ad19892ac8b4db03e93fd1fca39b05d6675c241a97f7a2ab241765589b34c56684ab4923eaf568a5f9b0e1583ce1460be7f0edf9d9201e5d3db3da0efb0ee6 diff --git a/sci-biology/uchime/files/CMakeLists.txt b/sci-biology/uchime/files/CMakeLists.txt new file mode 100644 index 000000000000..54b0a3ba0d30 --- /dev/null +++ b/sci-biology/uchime/files/CMakeLists.txt @@ -0,0 +1,11 @@ +cmake_minimum_required(VERSION 2.6) +project(UCHIME) + +set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FILE_OFFSET_BITS=64 -DUCHIMES=1") + +# Simply copy the source files from the mk script +add_executable(uchime + addtargets2.cpp alignchime.cpp alignchimel.cpp alnparams.cpp alpha.cpp alpha2.cpp fractid.cpp getparents.cpp globalalign2.cpp make3way.cpp mx.cpp myutils.cpp path.cpp searchchime.cpp seqdb.cpp setnucmx.cpp sfasta.cpp tracebackbit.cpp uchime_main.cpp usort.cpp viterbifast.cpp writechhit.cpp) + +INSTALL(TARGETS uchime + DESTINATION bin) diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml new file mode 100644 index 000000000000..a3c0f91c8a08 --- /dev/null +++ b/sci-biology/uchime/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> +UCHIME is a new algorithm for detecting chimeric sequences. It was developed in +collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob +Knight. Chimeras are commonly created during DNA sample amplification by +PCR, especially in community sequencing experiments using single regions +such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can +detect chimeras using a reference database or de novo using abundance +information on the assumption that chimeras are less abundant than their +parents because they must have undergone fewer rounds of amplification. +</longdescription> +</pkgmetadata> diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild new file mode 100644 index 000000000000..19b55f5039e4 --- /dev/null +++ b/sci-biology/uchime/uchime-4.2.40.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils + +MY_P="${PN}${PV}_src" + +DESCRIPTION="Fast, accurate chimera detection" +HOMEPAGE="http://www.drive5.com/uchime/" +SRC_URI="http://drive5.com/${PN}/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die +} diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest new file mode 100644 index 000000000000..3cf6c6051f97 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/Manifest @@ -0,0 +1 @@ +DIST jksrc.v260.zip 59090224 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 WHIRLPOOL 669b0f342a97f84164b32707a3b2bb51f64219168beceb8f9d46211749351b2c65b21ffe830f82620e7112a332e88ca271d4327739d8f93afbe14e399e45e248 diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml new file mode 100644 index 000000000000..f1f3ccfb77e0 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild new file mode 100644 index 000000000000..d897ce479df7 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit toolchain-funcs flag-o-matic webapp + +DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath" +HOMEPAGE="http://genome.ucsc.edu/" +SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip" + +LICENSE="blat" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+mysql +server static-libs" + +REQUIRED_USE="server? ( mysql )" + +WEBAPP_MANUAL_SLOT="yes" + +DEPEND=" + app-arch/unzip + !<sci-biology/ucsc-genome-browser-223 + mysql? ( virtual/mysql ) + server? ( virtual/httpd-cgi )" # TODO: test with other webservers +RDEPEND="${DEPEND}" + +S="${WORKDIR}/kent" + +src_prepare() { + use server && webapp_src_preinst + sed \ + -e 's/-Werror//' \ + -e "/COPT/s:=.*$:=${LDFLAGS}:g" \ + -e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \ + -e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \ + -i src/inc/common.mk src/hg/lib/makefile || die + find -name makefile -or -name cgi_build_rules.mk \ + | xargs sed -i \ + -e 's/-${USER}//g' \ + -e 's/-$(USER)//g' \ + -e 's:-O2::g' \ + -e 's:-ggdb::g' \ + -e 's:-pipe::g' || die + sed \ + -e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \ + -i src/hg/genePredToMafFrames/makefile || die +} + +src_compile() { + export MACHTYPE=${MACHTYPE/-*/} \ + BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \ + SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \ + ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \ + PATH="${BINDIR}:${PATH}" \ + STRIP="echo 'skipping strip' " + + export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none" + + use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ + MYSQLINC="${ROOT}usr/include/mysql" + + use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \ + CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin" + + mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die + use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT" + + emake -C src clean + emake -C src/lib + emake -C src/jkOwnLib + emake -C src/utils/stringify + emake -C src blatSuite + if use mysql; then + emake -j1 -C src/hg utils + emake -j1 -C src utils + emake -C src libs userApps + if use server; then + emake -j1 -C src/hg + emake -j1 -C src + fi + fi +} + +src_install() { + use server && webapp_src_preinst + cp -ad "${WORKDIR}"/destdir/* "${D}" || die + use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a + echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}" + doenvd "${S}/98${PN}" + + use server && webapp_postinst_txt en src/product/README.QuickStart + use server && webapp_src_install + + insinto "/usr/include/${PN}" + doins src/inc/*.h + insinto "/usr/share/${PN}" + doins -r src/product + keepdir "/usr/share/doc/${PF}" + find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die +} + +pkg_postinst() { + use server && webapp_pkg_postinst +} diff --git a/sci-biology/unafold/Manifest b/sci-biology/unafold/Manifest new file mode 100644 index 000000000000..c9d5717af552 --- /dev/null +++ b/sci-biology/unafold/Manifest @@ -0,0 +1 @@ +DIST unafold-3.8.tar.bz2 282418 SHA256 7552724ce82ad8618167ec0524d8c931ac4383314669322c8424cafc06c2bf38 SHA512 4c83cf0122e4d4ec2b713833adb11eb608b0f880f5b68114aefd8c7fa980c8d02f9a6cfc0c88cd640b4457e65954b05189118e8ac5ed207b2f9910738ca71a6c WHIRLPOOL 9fd5744e66d8669817433b5427fc671ac5185760ffaf0682a7938fc5542f24cbe7b08f7722c7135cd3197af2d748740e0ca35a70a5f6c40a4a5d5aaa806ed923 diff --git a/sci-biology/unafold/metadata.xml b/sci-biology/unafold/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/unafold/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild new file mode 100644 index 000000000000..f47f9d02ab36 --- /dev/null +++ b/sci-biology/unafold/unafold-3.8-r1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit flag-o-matic + +DESCRIPTION="Unified Nucleic Acid Folding and hybridization package" +HOMEPAGE="http://mfold.rna.albany.edu/" +SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2" + +LICENSE="unafold" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="custom-cflags" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare() { + # recommended in README + use custom-cflags || append-flags -O3 + + sed \ + -e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \ + -i tests/hybrid.tml || die +} diff --git a/sci-biology/unafold/unafold-3.8.ebuild b/sci-biology/unafold/unafold-3.8.ebuild new file mode 100644 index 000000000000..5d258f941645 --- /dev/null +++ b/sci-biology/unafold/unafold-3.8.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit flag-o-matic + +DESCRIPTION="Unified Nucleic Acid Folding and hybridization package" +HOMEPAGE="http://mfold.rna.albany.edu/" +SRC_URI="http://dinamelt.bioinfo.rpi.edu/download/${P}.tar.bz2" + +LICENSE="unafold" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare() { + # recommended in README + append-flags -O3 + + sed \ + -e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \ + -i tests/hybrid.tml || die +} + +src_install() { + einstall || die +} diff --git a/sci-biology/update-blastdb/Manifest b/sci-biology/update-blastdb/Manifest new file mode 100644 index 000000000000..5d5b09e31d1f --- /dev/null +++ b/sci-biology/update-blastdb/Manifest @@ -0,0 +1 @@ +DIST ncbi_cxx--12_0_0.tar.gz 37925914 SHA256 432d5c72cc02dad263f1b2f1ab875e04e60b1ded0c5537ed54e8095b50554d20 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed WHIRLPOOL 16f0b6de7e0d898bca7a2a46a64a4aa0795f99673d4715a21cca2dc5aa728143b56f02ad9c108543195a8f86f4267777d2be9428dcf52f5495083a63961ad867 diff --git a/sci-biology/update-blastdb/metadata.xml b/sci-biology/update-blastdb/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/update-blastdb/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild new file mode 100644 index 000000000000..8dbd69344fff --- /dev/null +++ b/sci-biology/update-blastdb/update-blastdb-12.0.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit versionator + +MY_PV="$(replace_all_version_separators _)" + +DESCRIPTION="update_blastdb.pl for local blast db maintainance" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" +SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-lang/perl + !sci-biology/ncbi-tools++" +DEPEND="" + +S="${WORKDIR}" + +src_install() { + dobin ncbi_cxx--${MY_PV}/src/app/blast/update_blastdb.pl +} diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest new file mode 100644 index 000000000000..8276750cfdc6 --- /dev/null +++ b/sci-biology/vaal/Manifest @@ -0,0 +1,2 @@ +DIST VAAL_manual.doc 48128 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 WHIRLPOOL 3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175 +DIST vaal-46233.tar.gz 1148052 SHA256 a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 WHIRLPOOL e848bcd6b2dd0c0c52142a3d55acef6a98b816e37355d22386bf3a2fac21e1318a821a394ebd5851cd530aa9afb0d178debc3f74638ee0d0820209a0f432f59f diff --git a/sci-biology/vaal/files/vaal-1.2-as-needed.patch b/sci-biology/vaal/files/vaal-1.2-as-needed.patch new file mode 100644 index 000000000000..31649010dbe3 --- /dev/null +++ b/sci-biology/vaal/files/vaal-1.2-as-needed.patch @@ -0,0 +1,22 @@ +--- VAAL.orig/MakeDepend.cc 2008-12-18 17:05:48.000000000 +0100 ++++ VAAL/MakeDepend.cc 2010-02-14 13:42:23.734370178 +0100 +@@ -1195,9 +1195,6 @@ + } + } + mf << " -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; +- for ( set<string>::iterator dep_iter = lib_deps.begin(); +- dep_iter != lib_deps.end(); ++dep_iter ) +- mf << " " << "$(" << *dep_iter << "_LFLAGS)"; + for ( set<string>::iterator dep_iter = sharedlib_deps.begin(); + dep_iter != sharedlib_deps.end(); ++dep_iter ) { + // Extract the symbolic name of this library from its filename. +@@ -1208,6 +1205,9 @@ + mf << " -l" << sharedlib_name; + } + mf << " -l" << libname; ++ for ( set<string>::iterator dep_iter = lib_deps.begin(); ++ dep_iter != lib_deps.end(); ++dep_iter ) ++ mf << " " << "$(" << *dep_iter << "_LFLAGS)"; + mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n"; + } + } diff --git a/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch new file mode 100644 index 000000000000..c021fadb44b1 --- /dev/null +++ b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch @@ -0,0 +1,39 @@ +diff -durr VAAL.orig/SortKmersImpl.h VAAL/SortKmersImpl.h +--- VAAL.orig/SortKmersImpl.h 2009-11-12 13:02:40.116993289 +0000 ++++ VAAL/SortKmersImpl.h 2009-11-12 13:04:59.416388534 +0000 +@@ -98,7 +98,7 @@ + { if ( reads[l].size( ) < KSPAN ) continue; + unsigned int N = reads[l].size( ) - KSPAN + 1; + if ( S + 2*N >= R.size( ) ) { +- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); ++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<1>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } +@@ -180,7 +180,7 @@ + } + if ( q == N ) break; + if ( S + 2*N >= R.size( ) ) { +- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); ++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } +@@ -207,7 +207,7 @@ + top += Min( N - top, (unsigned int) 10000 ); + + if ( S + 20000 >= R.size( ) || S + 2*N >= R.size( ) ) { +- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); ++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } +@@ -318,7 +318,7 @@ + + top += Min( N - top, 10000 ); + if ( S + 2*(top - q) >= R.size( ) ) { +- unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (S + 2*(top - q)) ); ++ unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (unsigned) (S + 2*(top - q)) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<100>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } diff --git a/sci-biology/vaal/files/vaal-1.2-respect-flags.patch b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch new file mode 100644 index 000000000000..d3420556b608 --- /dev/null +++ b/sci-biology/vaal/files/vaal-1.2-respect-flags.patch @@ -0,0 +1,60 @@ +--- VAAL.orig/Makefile.in 2009-04-02 21:43:42.000000000 +0200 ++++ VAAL/Makefile.in 2010-02-14 14:20:26.222370302 +0100 +@@ -161,12 +161,16 @@ + COMPILER = @CC@ + CPLUSPLUS = @CXX@ + ++CFLAGS = @CFLAGS@ ++CXXFLAGS = @CXXFLAGS@ ++LDFLAGS = @LDFLAGS@ ++ + # QUIET=yes causes the compiler to be less verbose about warnings. + QUIET = no + + # DEBUG=yes forces out-of-date executables to be built with symbolic + # debugging information. Any other value is ignored. +-DEBUG = yes ++DEBUG = no + + # OPTIM=<compiler optimization> forces user-defined optimizations to be used, + # rather than the compiler-specific default. +@@ -174,7 +178,7 @@ + # If OPTIM=none, then no optimization is used. + # If unset, defaults are used. + # -fno-exceptions +-OPTIM = ++OPTIM = none + + # PROFILE=yes builds sampled-profiling (i.e. gprof) executables. Any other + # value is ignored. +@@ -317,6 +321,7 @@ + # Setup final compilation options: + + CPP_OPTIONS = \ ++ $(CXXFLAGS) \ + $(SYS_WARN) \ + $(SYS_OPT) \ + $(SYS_DEBUG) \ +@@ -328,6 +333,7 @@ + @INCLUDES@ + + LINK_OPTIONS = \ ++ $(LDFLAGS) \ + $(SYS_DEBUG) \ + $(SYS_LINK) \ + $(OMP_LINK) \ +@@ -406,12 +406,12 @@ + $(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc + + checkLock: $(SRC)/util/checkLock.cc +- $(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock ++ $(CPLUSPLUS) $(CXXFLAGS) $(SRC)/util/checkLock.cc $(LDFLAGS) -o $(BIN)/checkLock + + random/Random.o: random/Random.cc + @ mkdir -p $(OBJ)/${@D} + cp $(SRC)/random/Random.cc $(SRC)/random/Random.c +- $(CC) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o ++ $(CC) $(CFLAGS) $(SYS_LANG) -c $(SRC)/random/Random.cc -w -Drandom=randomx -Dsrandom=srandomx -o $(OBJ)/random/Random.o + rm $(SRC)/random/Random.c + + MemTracker.o: MemTracker.cc diff --git a/sci-biology/vaal/files/vaal-1.6-gcc47.patch b/sci-biology/vaal/files/vaal-1.6-gcc47.patch new file mode 100644 index 000000000000..0d80f08d3c21 --- /dev/null +++ b/sci-biology/vaal/files/vaal-1.6-gcc47.patch @@ -0,0 +1,153 @@ +Fix building with gcc-4.7 + +https://bugs.gentoo.org/show_bug.cgi?id=423497 + +Patch written by Kacper Kowalik <xarthisius@gentoo.org> +--- a/src/feudal/MasterVec.h ++++ b/src/feudal/MasterVec.h +@@ -62,20 +62,20 @@ + /// This function is deprecated: Use reserve() instead. + /// The pool size argument is ignored, anyway. + MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity ) +- { reserve(capacity); return *this; } ++ { this->reserve(capacity); return *this; } + + /// This function is deprecated: Use clear().shrink_to_fit(). + MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; } + + /// This function is deprecated: Use push_back(). + MasterVec& push_back_external( T const& val ) +- { push_back(val); return *this; } ++ { this->push_back(val); return *this; } + + /// This function is deprecated: Use push_back(). + MasterVec& push_back_reserve( T const& val, + size_type growthIncr = 0, + float growthFact = 1.3f ) +- { push_back(val,growthFact,growthIncr); return *this; } ++ { this->push_back(val,growthFact,growthIncr); return *this; } + + /// This function is deprecated: Use append(). + MasterVec& Append( MasterVec const& that ) +@@ -83,7 +83,7 @@ + + /// This function is deprecated: Use append(). + MasterVec& Append( MasterVec const& that, size_type from, size_type to ) +- { append(that.begin(from),that.begin(to)); return *this; } ++ { this->append(that.begin(from),that.begin(to)); return *this; } + + MasterVec const& WriteAll( String const& fileName ) const + { return WriteRange(fileName,0UL,BaseT::size()); return *this; } +@@ -108,7 +108,7 @@ + { if ( !append ) BaseT::clear(); + FeudalFileReader rdr(fileName.c_str()); + size_type siz = rdr.getNElements(); +- reserve(BaseT::size()+siz); ++ this->reserve(BaseT::size()+siz); + preAlloc(rdr,0,siz); + for ( size_type iii = 0; iii < siz; ++iii ) + appendFromReader(rdr,iii); +--- a/src/feudal/FeudalControlBlock.cc ++++ b/src/feudal/FeudalControlBlock.cc +@@ -24,6 +24,7 @@ + #include <string.h> + #include <errno.h> + #include <iostream> ++#include <unistd.h> + + using std::cout; + using std::endl; +--- a/src/feudal/SerfVec.h ++++ b/src/feudal/SerfVec.h +@@ -83,9 +83,9 @@ + { AssertLe(pos,that.size()); + AssertLe(len,that.size()-pos); + if ( this != &that ) +- { assign(that.begin(pos),that.begin(pos+len)); } ++ { this->assign(that.begin(pos),that.begin(pos+len)); } + else +- { erase(BaseT::begin(),BaseT::begin(pos)); ++ { this->erase(BaseT::begin(),BaseT::begin(pos)); + BaseT::resize(len); } + return *this; } + +--- a/src/system/ProcBuf.cc ++++ b/src/system/ProcBuf.cc +@@ -195,12 +195,12 @@ + Assert(M_internal_put_buffer == NULL); + M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE]; + M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE; +- setp(M_internal_put_buffer, ++ this->setp(M_internal_put_buffer, + M_internal_put_buffer_end); + } else if (!flush()) + return traits_type::eof(); + if (!traits_type::eq_int_type(c, traits_type::eof())) +- return sputc(c); ++ return this->sputc(c); + else + return traits_type::not_eof(c); + } +@@ -240,7 +240,7 @@ + // (which is start of buffer) + std::copy_backward(this->eback(), this->egptr(), this->egptr()+1); + *(this->gptr()) = traits_type::to_char_type(c); +- setg(this->eback(), this->gptr(), this->egptr()+1); ++ this->setg(this->eback(), this->gptr(), this->egptr()+1); + return traits_type::not_eof(c); + } else + return traits_type::eof(); +@@ -269,7 +269,7 @@ + // doing wchars and we write an odd # of bytes? + return false; + } else { +- setp(this->pbase(), this->epptr()); ++ this->setp(this->pbase(), this->epptr()); + return true; + } + } +@@ -283,7 +283,7 @@ + Assert(M_internal_get_buffer == NULL); + M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE]; + M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE; +- setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end); ++ this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end); + } + // The "get" pointer should be at the end of the buffer - that's + // why we need to fill it. +@@ -318,7 +318,7 @@ + // + // reset the get pointers + // +- setg(M_internal_get_buffer, ++ this->setg(M_internal_get_buffer, + M_internal_get_buffer, + M_internal_get_buffer+numusable/sizeof(char_type)); + return true; +--- a/src/system/SysConf.cc ++++ b/src/system/SysConf.cc +@@ -19,6 +19,7 @@ + #include "system/SysConf.h" + #include "system/Exit.h" + #include <iostream> ++#include <unistd.h> + + namespace + { +--- a/src/Vec.h ++++ b/src/Vec.h +@@ -261,11 +261,11 @@ + + template <class U> + void append( const vec<U>& y ) +- { insert( this->end( ), y.begin( ), y.end( ) ); } ++ { this->insert( this->end( ), y.begin( ), y.end( ) ); } + + void append( const vec<T>& y, size_type i, size_type j ) { +- if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) ); +- else insert( this->end( ), y.begin( ) + i, y.begin( ) + j ); ++ if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) ); ++ else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j ); + } + + // appends values in y, but only those whose indices are in entries diff --git a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch new file mode 100644 index 000000000000..152fb423e924 --- /dev/null +++ b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch @@ -0,0 +1,12 @@ +diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac +--- vaal-33805.orig/configure.ac 2010-09-20 04:37:49.858059826 +0000 ++++ vaal-33805/configure.ac 2010-09-20 04:39:41.178059477 +0000 +@@ -14,7 +14,7 @@ + AC_OPENMP + AC_OPENMP_CEHCK + +-CXXFLAGS=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3 -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ." ++CXXFLAGS+=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ." + + OS_RELEASE="`uname -r`" + AC_SUBST(CXXFLAGS) diff --git a/sci-biology/vaal/metadata.xml b/sci-biology/vaal/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/vaal/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/vaal/vaal-46233.ebuild b/sci-biology/vaal/vaal-46233.ebuild new file mode 100644 index 000000000000..6aee878ad2d1 --- /dev/null +++ b/sci-biology/vaal/vaal-46233.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/" +SRC_URI=" + ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz + ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc" + +LICENSE="Whitehead-MIT" +SLOT="0" +KEYWORDS="amd64" +IUSE="openmp" + +DEPEND=">=dev-libs/boost-1.41.0-r3" +RDEPEND="${DEPEND}" + +DOCS=( "${DISTDIR}/VAAL_manual.doc" ) + +src_prepare() { + sed \ + -e '/COPYING/d' \ + -i src/Makefile.am || die + + sed \ + -e 's:-ggdb::g' \ + -e '/AC_OPENMP_CEHCK/d' \ + -i configure.ac || die + autotools-utils_src_prepare +} + +src_configure(){ + local myeconfargs=( $(use_enable openmp) ) + autotools-utils_src_configure +} diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest new file mode 100644 index 000000000000..acbb2140b6da --- /dev/null +++ b/sci-biology/vcftools/Manifest @@ -0,0 +1 @@ +DIST vcftools_0.1.12b.tar.gz 631374 SHA256 9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512 803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd WHIRLPOOL 3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863 diff --git a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch new file mode 100644 index 000000000000..85197664a0d1 --- /dev/null +++ b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch @@ -0,0 +1,53 @@ +diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile +--- vcftools_0.1.12b.orig/cpp/Makefile 2014-08-01 21:11:22.000000000 +0200 ++++ vcftools_0.1.12b/cpp/Makefile 2015-04-03 17:24:38.830781049 +0200 +@@ -3,8 +3,8 @@ + # ($Revision: 1.1 $) + + # Compiler +-CC = gcc +-CPP = g++ ++CC ?= gcc ++CPP ?= g++ + # Output executable + EXECUTABLE = vcftools + # Flag used to turn on compilation of PCA routines +@@ -12,9 +12,9 @@ + VCFTOOLS_PCA = 0 + endif + # Compiler flags +-CFLAGS = -O2 -m64 ++CFLAGS ?= -O2 -m64 + #CFLAGS = -Wall -O2 -pg -m64 +-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 ++CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64 + #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64 + # Included libraries (zlib) + LIB = -lz +@@ -29,13 +29,13 @@ + # Define flag for PCA routine compilation + CPPFLAGS += -DVCFTOOLS_PCA + # Add LAPACK library +- LIB += -llapack ++ LIB += `$(PKG_CONFIG) --libs lapack` + # Add PCA source code + OBJS+= dgeev.o + endif + + vcftools: $(OBJS) +- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB) ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB) + ifdef BINDIR + cp $(CURDIR)/$@ $(BINDIR)/$@ + endif +@@ -47,8 +47,8 @@ + -include $(OBJS:.o=.d) + + %.o: %.cpp +- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o +- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d ++ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o ++ $(CXX) -MM $(CXXFLAGS) $(CPPFLAGS) $*.cpp > $*.d + + # remove compilation products + clean: diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml new file mode 100644 index 000000000000..c45e9f4dea06 --- /dev/null +++ b/sci-biology/vcftools/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">vcftools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild new file mode 100644 index 000000000000..ddc214c430c0 --- /dev/null +++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +MY_P="${PN}_${PV}" + +DESCRIPTION="Tools for working with VCF (Variant Call Format) files" +HOMEPAGE="http://vcftools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="lapack" + +RDEPEND="lapack? ( virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-buildsystem.patch + tc-export CXX PKG_CONFIG +} + +src_compile() { + local myconf + use lapack && myconf="VCFTOOLS_PCA=1" + emake -C cpp ${myconf} +} + +src_install(){ + perl_set_version + dobin cpp/${PN} + insinto ${VENDOR_LIB} + doins perl/*.pm + dobin perl/{fill,vcf}-* + dodoc README.txt +} diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest new file mode 100644 index 000000000000..08824f51b1cc --- /dev/null +++ b/sci-biology/velvet/Manifest @@ -0,0 +1,2 @@ +DIST velvet_1.0.18.tgz 7598196 SHA256 e6e108ef16f6c5974617b195ce79c7d2860d335a5122418a883217b8cc48473e SHA512 6823265bae085df85513f29e0ac5f17951de4d39aa62bce205f1b1579e274c08047360f25f1936c89361281f66b8a4b755f611890a6a98c02751c74e69ae03ad WHIRLPOOL 69dcb5a6760b66eba65d054562e873d2c000dc57b487cdcf2c977bc1c0106bf027a79ff3b7e81da8a0f82b00635b755c26135b34de51cae34f4d276f15c2be74 +DIST velvet_1.2.10.tgz 18818559 SHA256 884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874 WHIRLPOOL 595e40c92ab5724b3e9a5af11f023307da7c66628b0c96d2ac2c89617e2aaa8a84279252c397f52d4603119d6fcb4995d2bf6e38f7de8c7c9616bde3aefdcd64 diff --git a/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff new file mode 100644 index 000000000000..883211a557d6 --- /dev/null +++ b/sci-biology/velvet/files/velvet-0.7.62-gentoo.diff @@ -0,0 +1,126 @@ +Debundle zlib, fixes parallel build, respect user FLAGS + +--- src/readSet.c ++++ src/readSet.c +@@ -23,18 +23,13 @@ + #include <string.h> + #include <math.h> + #include <time.h> ++#include <zlib.h> + + #include "globals.h" + #include "tightString.h" + #include "readSet.h" + #include "utility.h" + +-#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32) +-#include "../third-party/zlib-1.2.3/Win32/include/zlib.h" +-#else +-#include "../third-party/zlib-1.2.3/zlib.h" +-#endif +- + #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) + # include <fcntl.h> + # include <io.h> + +--- Makefile ++++ Makefile +@@ -1,77 +1,62 @@ +-CC = gcc +-CFLAGS = -Wall +-DEBUG = -g +-LDFLAGS = -lm +-OPT = -O3 ++LIBS = -lm -lz + MAXKMERLENGTH=31 + CATEGORIES=2 + DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) + +-Z_LIB_DIR=third-party/zlib-1.2.3 +-Z_LIB_FILES=$(Z_LIB_DIR)/*.o +- +-# Mac OS users: uncomment the following lines +-# Z_LIB_FILES= +-# LDFLAGS = -lm -lz +-# CFLAGS = -Wall -m64 +- +-# Sparc/Solaris users: uncomment the following line +-# CFLAGS = -Wall -m64 +- + OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o + OBJDBG = $(subst obj,obj/dbg,$(OBJ)) ++OBJDE = $(subst obj,objde,$(OBJ)) + +-default : cleanobj zlib obj velveth velvetg doc ++default : cleanobj obj velveth velvetg + + clean : +- -rm obj/*.o obj/dbg/*.o ./velvet* +- cd $(Z_LIB_DIR) && make clean ++ -rm -f obj/*.o obj/dbg/*.o ./velvet* objde/*.o + -rm -f doc/manual_src/Manual.toc doc/manual_src/Manual.aux doc/manual_src/Manual.out doc/manual_src/Manual.log + + cleanobj: +- -rm obj/*.o obj/dbg/*.o +- +-zlib : +- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o ++ -rm -f obj/*.o obj/dbg/*.o objde/*.o + + velveth : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(LIBS) + + + velvetg : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(LIBS) + + debug : cleanobj obj/dbg +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(LIBS) + + color : cleanobj obj_de +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de objde/tightString.o objde/run.o objde/recycleBin.o objde/splay.o objde/splayTable.o objde/readSet.o objde/crc.o objde/utility.o objde/kmer.o $(LIBS) ++ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de objde/tightString.o objde/graph.o objde/run2.o objde/fibHeap.o objde/fib.o objde/concatenatedGraph.o objde/passageMarker.o objde/graphStats.o objde/correctedGraph.o objde/dfib.o objde/dfibHeap.o objde/recycleBin.o objde/readSet.o objde/shortReadPairs.o objde/scaffold.o objde/locallyCorrectedGraph.o objde/graphReConstruction.o objde/roadMap.o objde/preGraph.o objde/preGraphConstruction.o objde/concatenatedPreGraph.o objde/readCoherentGraph.o objde/utility.o objde/kmer.o $(LIBS) + + colordebug : cleanobj obj/dbg_de +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de objde/dbg/tightString.o objde/dbg/run.o objde/dbg/recycleBin.o objde/dbg/splay.o objde/dbg/splayTable.o objde/dbg/readSet.o objde/dbg/crc.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de objde/dbg/tightString.o objde/dbg/graph.o objde/dbg/run2.o objde/dbg/fibHeap.o objde/dbg/fib.o objde/dbg/concatenatedGraph.o objde/dbg/passageMarker.o objde/dbg/graphStats.o objde/dbg/correctedGraph.o objde/dbg/dfib.o objde/dbg/dfibHeap.o objde/dbg/recycleBin.o objde/dbg/readSet.o objde/dbg/shortReadPairs.o objde/dbg/scaffold.o objde/dbg/locallyCorrectedGraph.o objde/dbg/graphReConstruction.o objde/dbg/roadMap.o objde/dbg/preGraph.o objde/dbg/preGraphConstruction.o objde/dbg/concatenatedPreGraph.o objde/dbg/readCoherentGraph.o objde/dbg/utility.o objde/dbg/kmer.o $(LIBS) + + objdir: + mkdir -p obj ++ mkdir -p objde + +-obj: zlib objdir $(OBJ) ++obj: objdir $(OBJ) + +-obj_de: override DEF := $(DEF) -D COLOR +-obj_de: zlib cleanobj objdir $(OBJ) ++obj_de: cleanobj objdir $(OBJDE) + + obj/dbgdir: + mkdir -p obj/dbg + +-obj/dbg: zlib obj/dbgdir $(OBJDBG) ++obj/dbg: obj/dbgdir $(OBJDBG) + + obj/dbg_de: override DEF := $(DEF) -D COLOR +-obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG) ++obj/dbg_de: cleanobj obj/dbgdir $(OBJDBG) + + obj/%.o: src/%.c + $(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ + ++objde/%.o: src/%.c ++ $(CC) $(CFLAGS) $(OPT) $(DEF) -D COLOR -c $? -o $@ ++ + obj/dbg/%.o: src/%.c + $(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ + diff --git a/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff new file mode 100644 index 000000000000..ed53a1229b5b --- /dev/null +++ b/sci-biology/velvet/files/velvet-1.0.18-gentoo-r1.diff @@ -0,0 +1,72 @@ +diff -durr Makefile Makefile +--- Makefile 2011-01-27 16:52:58.853408562 +0000 ++++ Makefile 2011-01-27 17:01:45.088065521 +0000 +@@ -1,8 +1,4 @@ +-CC = gcc +-CFLAGS = -Wall +-DEBUG = -g +-LDFLAGS = -lm +-OPT = -O3 ++LIBS = -lm -lz + MAXKMERLENGTH=31 + CATEGORIES=2 + DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) +@@ -41,29 +37,29 @@ + -rm obj/*.o obj/dbg/*.o + + zlib : +- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o ++ echo "unbundled zlib" + + velveth : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(LIBS) + + + velvetg : obj +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) + + debug : override DEF := $(DEF) -D DEBUG + debug : cleanobj obj/dbg +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) + + color : override DEF := $(DEF) -D COLOR + color : cleanobj obj_de +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(LIBS) + + colordebug : override DEF := $(DEF) -D COLOR -D DEBUG + colordebug : cleanobj obj/dbg_de +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) +- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(LIBS) + + objdir: + mkdir -p obj +@@ -83,7 +79,7 @@ + obj/dbg_de: zlib cleanobj obj/dbgdir $(OBJDBG) + + obj/%.o: src/%.c +- $(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ ++ $(CC) $(CFLAGS) $(DEF) -c $? -o $@ + + obj/dbg/%.o: src/%.c + $(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ +diff -durr src/readSet.c src/readSet.c +--- src/readSet.c 2011-01-27 16:52:58.804084948 +0000 ++++ src/readSet.c 2011-01-27 17:02:55.380324786 +0000 +@@ -24,6 +24,7 @@ + #include <math.h> + #include <time.h> + #include <limits.h> ++#include <zlib.h> + + #include "globals.h" + #include "tightString.h" diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/velvet/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/velvet/velvet-1.0.18-r1.ebuild b/sci-biology/velvet/velvet-1.0.18-r1.ebuild new file mode 100644 index 000000000000..c0bfb929033e --- /dev/null +++ b/sci-biology/velvet/velvet-1.0.18-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils toolchain-funcs flag-o-matic + +MY_P=${PN}_${PV} + +DESCRIPTION="A sequence assembler for very short reads" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/" +SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="-doc" +KEYWORDS="amd64 x86" + +RDEPEND="sys-libs/zlib" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + # necessary? + # append-flags -O3 # as recommended by upstream + epatch "${FILESDIR}"/${P}-gentoo-r1.diff + use doc || sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die +} + +src_compile() { + tc-export CC + MAKE_XOPTS="" + if [[ $VELVET_MAXKMERLENGTH != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS MAXKMERLENGTH=$VELVET_MAXKMERLENGTH"; fi + if [[ $VELVET_CATEGORIES != "" ]]; then MAKE_XOPTS="$MAKE_XOPTS CATEGORIES=$VELVET_CATEGORIES"; fi + emake -j1 $MAKE_XOPTS || die + emake -j1 $MAKE_XOPTS color || die +} + +src_install() { + dobin velvet{g,h,g_de,h_de} || die + insinto /usr/share/${PN} + doins -r contrib || die + dodoc Manual.pdf CREDITS.txt ChangeLog || die +} + +pkg_postinst() { + elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual," + elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your" + elog "environment or /etc/make.conf, then re-emerge the package. For example:" + elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet" +} diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild new file mode 100644 index 000000000000..86b06ffcd125 --- /dev/null +++ b/sci-biology/velvet/velvet-1.2.10.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +MY_P=${PN}_${PV} + +DESCRIPTION="A sequence assembler for very short reads" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/" +SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc openmp" + +RDEPEND="" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + if ! use doc; then + sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die + fi + elog "Upstream recommendes using -O3 in CFLAGS" + echo + elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual," + elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your" + elog "environment or /etc/make.conf, then re-emerge the package. For example:" + elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet" + MAKEOPTS+=" -j1" + + if [[ $(tc-getCC) =~ gcc ]]; then + local eopenmp=-fopenmp + elif [[ $(tc-getCC) =~ icc ]]; then + local eopenmp=-openmp + else + elog "Cannot detect compiler type so not setting openmp support" + fi + append-flags -fPIC ${eopenmp} + append-ldflags ${eopenmp} + + tc-export CC + + MAKE_XOPTS=( + CC=$(tc-getCC) + CFLAGS="${CFLAGS}" + OPT="${CFLAGS}" + ) + if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi + if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi +} + +src_compile() { + emake "${MAKE_XOPTS[@]}" + emake "${MAKE_XOPTS[@]}" color +} + +src_test() { + emake "${MAKE_XOPTS[@]}" test +} + +src_install() { + dobin velvet{g,h,g_de,h_de} + insinto /usr/share/${PN} + doins -r contrib + dodoc Manual.pdf CREDITS.txt ChangeLog +} diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest new file mode 100644 index 000000000000..d53e2f5d3ab7 --- /dev/null +++ b/sci-biology/vienna-rna/Manifest @@ -0,0 +1,2 @@ +DIST ViennaRNA-2.1.1.tar.gz 5327215 SHA256 bfea440dface4562d5dfb0a1c83bf226c0697bb18aacae0dc84c555282cedebe SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5 WHIRLPOOL 48b6bcd96b2ff2523ba00335cac7fe141b6ed7f037a3192e6c174297266d0f967492a67afaaa6c05f8b28fdc0eb7c9b72d0d9daba286b5dd3dca4456cc058b1f +DIST ViennaRNA-2.1.8.tar.gz 5464683 SHA256 37a0a0b7c8a167bcdab1a85d88bcb1025ad8e00a4b00a147bf36d45dc8ca7560 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e WHIRLPOOL a79f30d49c9bbe047d9fe83054dc08e94535f17417ef1f412bbcdd374d1988a8f2faf679e154c1ed1d1a75799e6cc0232d30b3adf65b3fa19978322f67ace57e diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch new file mode 100644 index 000000000000..0a781667c70b --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch @@ -0,0 +1,22 @@ +diff -Naur ViennaRNA-1.6.5/Cluster/statgeom.c ViennaRNA-1.6.5.new/Cluster/statgeom.c +--- ViennaRNA-1.6.5/Cluster/statgeom.c 2001-04-05 04:36:41.000000000 -0400 ++++ ViennaRNA-1.6.5.new/Cluster/statgeom.c 2007-11-24 08:55:17.000000000 -0500 +@@ -5,6 +5,7 @@ + */ + + #include <stdio.h> ++#include <string.h> + #include <strings.h> + #include <ctype.h> + #include "utils.h" +diff -Naur ViennaRNA-1.6.5/Readseq/readseq.c ViennaRNA-1.6.5.new/Readseq/readseq.c +--- ViennaRNA-1.6.5/Readseq/readseq.c 1995-07-12 13:05:58.000000000 -0400 ++++ ViennaRNA-1.6.5.new/Readseq/readseq.c 2007-11-24 08:56:16.000000000 -0500 +@@ -173,6 +173,7 @@ + #include <stdio.h> + #include <string.h> + #include <ctype.h> ++#include <stdlib.h> + + #include "ureadseq.h" + diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch new file mode 100644 index 000000000000..37e2f8c6a880 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-LDFLAGS.patch @@ -0,0 +1,24 @@ +diff -Naur ViennaRNA-1.7.2/Perl/Makefile.am ViennaRNA-1.7.2.new/Perl/Makefile.am +--- ViennaRNA-1.7.2/Perl/Makefile.am 2007-12-19 05:33:14.000000000 -0500 ++++ ViennaRNA-1.7.2.new/Perl/Makefile.am 2008-10-06 14:20:54.000000000 -0400 +@@ -4,7 +4,7 @@ + RNA.i tmaps.i + + Makefile.perl: Makefile.PL Makefile +- @PerlCmd@ Makefile.PL ++ @PerlCmd@ Makefile.PL LDDLFLAGS="${LDFLAGS} -shared" + + # the perl command repairs some errors in the SWIG CVS version + RNA_wrap.c: RNA.i tmaps.i +diff -Naur ViennaRNA-1.7.2/Readseq/Makefile ViennaRNA-1.7.2.new/Readseq/Makefile +--- ViennaRNA-1.7.2/Readseq/Makefile 2008-01-23 05:32:00.000000000 -0500 ++++ ViennaRNA-1.7.2.new/Readseq/Makefile 2008-10-06 14:21:13.000000000 -0400 +@@ -40,7 +40,7 @@ + + build: $(SOURCES) + @echo "Compiling readseq..." +- $(CC) $(CFLAGS) -o readseq readseq.c ureadseq.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c + + # if using NCBI, uncomment these lines in place of build: above + #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch new file mode 100644 index 000000000000..2c5ac3041297 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch @@ -0,0 +1,16 @@ +# unfortunately, vienna-rna's build system is a little broken and sometimes detects +# gd in RNAforested but then realizes in g2 that it can't actually build it +# resulting in unresolved symbols. + +diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in +--- ViennaRNA-1.8.3.orig/RNAforester/configure.in 2009-09-10 13:05:40.507932827 +0000 ++++ ViennaRNA-1.8.3/RNAforester/configure.in 2009-09-10 13:06:15.171952984 +0000 +@@ -47,7 +47,7 @@ + save_CPPFLAGS=$CPPFLAGS + CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"] + +-AC_CHECK_LIB(gd,main,,) ++dnl AC_CHECK_LIB(gd,main,,) + + dnl Checks for header files. + AC_HEADER_STDC diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch new file mode 100644 index 000000000000..025822f45c91 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch @@ -0,0 +1,76 @@ +diff -durr ViennaRNA-1.8.3.orig/Cluster/AS_main.c ViennaRNA-1.8.3/Cluster/AS_main.c +--- ViennaRNA-1.8.3.orig/Cluster/AS_main.c 2009-09-10 11:56:01.636674988 +0000 ++++ ViennaRNA-1.8.3/Cluster/AS_main.c 2009-09-10 11:58:32.915952366 +0000 +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <string.h> ++#include <stdlib.h> + #include "distance_matrix.h" + #include "statgeom.h" + #include "split.h" +diff -durr ViennaRNA-1.8.3.orig/Cluster/statgeom.c ViennaRNA-1.8.3/Cluster/statgeom.c +--- ViennaRNA-1.8.3.orig/Cluster/statgeom.c 2009-09-10 11:56:01.636674988 +0000 ++++ ViennaRNA-1.8.3/Cluster/statgeom.c 2009-09-10 11:58:53.192452141 +0000 +@@ -7,6 +7,7 @@ + #include <stdio.h> + #include <string.h> + #include <strings.h> ++#include <stdlib.h> + #include <ctype.h> + #include "utils.h" + #include "PS3D.h" +diff -durr ViennaRNA-1.8.3.orig/Cluster/treeplot.c ViennaRNA-1.8.3/Cluster/treeplot.c +--- ViennaRNA-1.8.3.orig/Cluster/treeplot.c 2009-09-10 11:56:01.636674988 +0000 ++++ ViennaRNA-1.8.3/Cluster/treeplot.c 2009-09-10 11:59:22.457509165 +0000 +@@ -1,5 +1,6 @@ + #include <stdio.h> + #include <string.h> ++#include <stdlib.h> + #include <math.h> + #include "distance_matrix.h" + #include "utils.h" +diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp ViennaRNA-1.8.3/RNAforester/src/main.cpp +--- ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp 2009-09-10 11:56:01.624743558 +0000 ++++ ViennaRNA-1.8.3/RNAforester/src/main.cpp 2009-09-10 12:00:37.693252890 +0000 +@@ -19,6 +19,8 @@ + #include <list> + #include <sstream> + #include <string> ++#include <cstring> ++#include <climits> + #include <map> + + //#include <sys/timeb.h> +diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h +--- ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h 2009-09-10 11:56:01.624743558 +0000 ++++ ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h 2009-09-10 12:01:41.631932654 +0000 +@@ -16,6 +16,7 @@ + + #include <algorithm> + #include <cassert> ++#include <cstring> + + #include "misc.h" + #include "types.h" +diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h +--- ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h 2009-09-10 11:56:01.620703294 +0000 ++++ ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h 2009-09-10 12:02:29.687952726 +0000 +@@ -4,6 +4,7 @@ + #include <assert.h> + #include <algorithm> + #include <climits> ++#include <cstring> + + #include "algebra.h" + #include "debug.h" +diff -durr ViennaRNA-1.8.3.orig/Readseq/ureadseq.c ViennaRNA-1.8.3/Readseq/ureadseq.c +--- ViennaRNA-1.8.3.orig/Readseq/ureadseq.c 2009-09-10 11:56:01.632743452 +0000 ++++ ViennaRNA-1.8.3/Readseq/ureadseq.c 2009-09-10 12:03:15.343952776 +0000 +@@ -20,6 +20,7 @@ + #include <stdio.h> + #include <ctype.h> + #include <string.h> ++#include <stdlib.h> + + #define UREADSEQ_G + #include "ureadseq.h" diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch new file mode 100644 index 000000000000..76a5a259a862 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch new file mode 100644 index 000000000000..c3f5b52141e8 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch @@ -0,0 +1,47 @@ +Fix implicit function declarations and attempt to free non-heap obj + +--- lib/subopt.c ++++ lib/subopt.c +@@ -80,12 +80,12 @@ + #include <string.h> + #include <math.h> + #include "fold.h" ++#include "cofold.h" + #include "utils.h" + #include "energy_par.h" + #include "fold_vars.h" + #include "pair_mat.h" + #include "list.h" +-#include "subopt.h" + #include "params.h" + + #define true 1 +--- Progs/RNAfold.c ++++ Progs/RNAfold.c +@@ -20,6 +20,7 @@ + #include "MEA.h" + extern void read_parameter_file(const char fname[]); + extern plist * stackProb(double cutoff); ++extern void init_pf_circ_fold(int length); + + /*@unused@*/ + static char UNUSED rcsid[] = "$Id$"; +--- Cluster/AS_main.c ++++ Cluster/AS_main.c +@@ -1,6 +1,7 @@ + #include <stdio.h> + #include <string.h> + #include <stdlib.h> ++#include <unistd.h> + #include "distance_matrix.h" + #include "statgeom.h" + #include "split.h" +@@ -226,7 +227,7 @@ + for(j=0;j<nn[i];j++) free(ss[i][j]); + free(ss[i]); + } +- free(ss); ++ // free(ss); // attempt to free a non-heap object ‘ss’ + } + else { + printf_taxa_list(); diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch new file mode 100644 index 000000000000..cfadc70bc6f6 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-jobserver-fix.patch @@ -0,0 +1,18 @@ +diff -ur ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in +--- ViennaRNA-1.8.4-orig/RNAforester/g2-0.70/Makefile.in 2009-10-13 13:44:40.000000000 +0200 ++++ ViennaRNA-1.8.4/RNAforester/g2-0.70/Makefile.in 2010-03-27 21:39:21.000000000 +0100 +@@ -116,12 +116,12 @@ + + + clean: +- -(cd ./demo ; make clean) ++ -(cd ./demo ; $(MAKE) clean) + -rm -f $(OBJ) + -rm -f libg2.a config.cache config.log Makefile.bak config.status + -rm -f ./include/*.h + -$(FIND) . -name "*~" -exec rm -f {} \; +- -(cd ./g2_perl ; make clean) ++ -(cd ./g2_perl ; $(MAKE) clean) + -rm -f ./g2_perl/test.ps + -rm -f ./g2_perl/test.png + -rm -f ./g2_perl/test.jpg diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch new file mode 100644 index 000000000000..fcaa5f9a53b6 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch @@ -0,0 +1,26 @@ +Fix buffer overflows + +http://bugs.gentoo.org/show_bug.cgi?id=341089 + +--- Readseq/ureadseq.c ++++ Readseq/ureadseq.c +@@ -1579,7 +1579,7 @@ + + short linesout = 0, seqtype = kNucleic; + long i, j, l, l1, ibase; +- char idword[31], endstr[10]; ++ char idword[31], endstr[15]; + char seqnamestore[128], *seqname = seqnamestore; + char s[kMaxseqwidth], *cp; + char nameform[10], numform[10], nocountsymbols[10]; +--- lib/part_func_up.c ++++ lib/part_func_up.c +@@ -1438,7 +1438,7 @@ + PUBLIC int plot_free_pu_out(pu_out* res, interact *pint, char *ofile, char *head) { + int size,s,i,len; + double dG_u; +- char nan[4], *time, startl[2], dg[10];; ++ char nan[4], *time, startl[3], dg[10];; + FILE *wastl; + + wastl = fopen(ofile,"a"); diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py new file mode 100644 index 000000000000..0aeaf2a116d3 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.5-setup.py @@ -0,0 +1,27 @@ +from distutils.core import setup, Extension +import os +import sys + +old_filename = os.path.join("Perl", "RNA.py") +new_filename = os.path.join("Perl", "__init__.py") +if os.path.exists(old_filename): + os.rename(old_filename, new_filename) + +extra_link_args = [] + +extension = Extension("_RNA", + ["Perl/RNA_wrap.c"], + libraries=['RNA'], + library_dirs=['lib'], + extra_link_args=extra_link_args + ) + +setup(name="RNA", + version="1.8.5", + description="Vienna RNA", + author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", + url="http://www.tbi.univie.ac.at/RNA/", + package_dir = {'RNA':'Perl'}, + packages = ['RNA'], + ext_modules=[extension], + ) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch new file mode 100644 index 000000000000..6d35ecea9b0f --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch new file mode 100644 index 000000000000..de457f318e8e --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch @@ -0,0 +1,15 @@ + Readseq/readseq.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/Readseq/readseq.c b/Readseq/readseq.c +index 8af7b39..56a25ae 100644 +--- a/Readseq/readseq.c ++++ b/Readseq/readseq.c +@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' + #include <stdio.h> + #include <string.h> + #include <ctype.h> ++#include <stdlib.h> + + #include "ureadseq.h" + diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch new file mode 100644 index 000000000000..ee4aef5c3308 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch @@ -0,0 +1,30 @@ + Readseq/Makefile | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Readseq/Makefile b/Readseq/Makefile +index f073aaa..05f2edd 100644 +--- a/Readseq/Makefile ++++ b/Readseq/Makefile +@@ -6,11 +6,11 @@ + # + + # pick an ANSI C compiler (the default Sun CC is not ANSI) +-CC=gcc # Gnu C Compiler ++CC?=gcc # Gnu C Compiler + #CC=cc # SGI Irix + #CC=vcc # some DEC Ultrix + +-CFLAGS= ++CFLAGS?= + #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum + # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software + +@@ -40,7 +40,7 @@ all: build test + + build: $(SOURCES) + @echo "Compiling readseq..." +- $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c + + # if using NCBI, uncomment these lines in place of build: above + #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py new file mode 100644 index 000000000000..57f6b712ba3d --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py @@ -0,0 +1,27 @@ +from distutils.core import setup, Extension +import os +import sys + +old_filename = os.path.join("Perl", "RNA.py") +new_filename = os.path.join("Perl", "__init__.py") +if os.path.exists(old_filename): + os.rename(old_filename, new_filename) + +extra_link_args = [] + +extension = Extension("_RNA", + ["Perl/RNA_wrap.c"], + libraries=['RNA'], + library_dirs=['lib'], + extra_link_args=extra_link_args + ) + +setup(name="RNA", + version="2.1.1", + description="Vienna RNA", + author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna", + url="http://www.tbi.univie.ac.at/RNA/", + package_dir = {'RNA':'Perl'}, + packages = ['RNA'], + ext_modules=[extension], + ) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch new file mode 100644 index 000000000000..e54dff95b485 --- /dev/null +++ b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch @@ -0,0 +1,10 @@ +diff --git a/Utils/Makefile.am b/Utils/Makefile.am +index f42ebf4..d84a0f1 100644 +--- a/Utils/Makefile.am ++++ b/Utils/Makefile.am +@@ -1,4 +1,4 @@ +-pkgbindir = $(pkgdatadir)/bin ++pkgbindir = $(prefix)/bin + pkgbin_PROGRAMS = b2ct popt ct2db + + pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml new file mode 100644 index 000000000000..50f4e02d4a18 --- /dev/null +++ b/sci-biology/vienna-rna/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <longdescription> + The Vienna RNA Package consists of a C code library and several + stand-alone programs for the prediction and comparison of RNA secondary + structures. RNA secondary structure prediction through energy + minimization is the most used function in the package. We provide three + kinds of dynamic programming algorithms for structure prediction: the + minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a + single optimal structure, the partition function algorithm of + (McCaskill 1990) which calculates base pair probabilities in the + thermodynamic ensemble, and the suboptimal folding algorithm of + (Wuchty et.al 1999) which generates all suboptimal structures within a + given energy range of the optimal energy. For secondary structure + comparison, the package contains several measures of distance + (dissimilarities) using either string alignment or tree-editing + (Shapiro and Zhang 1990). Finally, we provide an algorithm to design + sequences with a predefined structure (inverse folding). +</longdescription> +</pkgmetadata> diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild new file mode 100644 index 000000000000..df5c8eb50f90 --- /dev/null +++ b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild @@ -0,0 +1,113 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_OPTIONAL=true +AUTOTOOLS_AUTORECONF=true +AUTOTOOLS_IN_SOURCE_BUILD=1 + +inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs + +DESCRIPTION="RNA secondary structure prediction and comparison" +HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" +SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${PV}.tar.gz" + +SLOT="0" +LICENSE="vienna-rna" +KEYWORDS="amd64 ppc x86" +IUSE="doc openmp python static-libs" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +DEPEND=" + dev-lang/perl + media-libs/gd + doc? ( dev-texlive/texlive-latex ) + python? ( + ${PYTHON_DEPS} + dev-lang/swig )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/ViennaRNA-${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-bindir.patch + "${FILESDIR}"/${P}-prll.patch + "${FILESDIR}"/${P}-impl-decl.patch +) + +src_prepare() { + sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die + sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die + + autotools-utils_src_prepare + + if use python; then + cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die + PATCHES=() + distutils-r1_src_prepare + fi +} + +src_configure() { + local myeconfargs=( + --with-cluster + $(use_enable openmp) ) + + use doc || \ + myeconfargs+=( + --without-doc-pdf + --without-doc-html + --without-doc + ) + autotools-utils_src_configure + sed \ + -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \ + -e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \ + -i RNAforester/g2-0.70/Makefile || die + sed \ + -e "s:CC=gcc:CC=$(tc-getCC):" \ + -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ + -i Readseq/Makefile || die + use python && distutils-r1_src_configure +} + +src_compile() { + autotools-utils_src_compile + autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) + + # TODO: Add (optional?) support for the NCBI toolkit. + if use python; then + pushd Perl > /dev/null + mv RNA_wrap.c{,-perl} || die + swig -python RNA.i || die + popd > /dev/null + distutils-r1_src_compile + mv Perl/RNA_wrap.c{-perl,} || die + fi +} + +src_test() { + autotools-utils_src_compile -C Perl check + autotools-utils_src_compile -C Readseq test +} + +src_install() { + autotools-utils_src_install + + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + fi + + newbin Readseq/readseq readseq-vienna + dodoc Readseq/Readseq.help + newdoc Readseq/Readme README.readseq + newdoc Readseq/Formats Formats.readseq + + # remove perlocal.pod to avoid file collisions (see #240358) + perl_delete_localpod || die "Failed to remove perlocal.pod" + use python && distutils-r1_src_install +} diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild new file mode 100644 index 000000000000..8b862403e25f --- /dev/null +++ b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild @@ -0,0 +1,114 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_OPTIONAL=true +AUTOTOOLS_AUTORECONF=true +AUTOTOOLS_IN_SOURCE_BUILD=1 + +inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs + +DESCRIPTION="RNA secondary structure prediction and comparison" +HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/" +SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz" + +SLOT="0" +LICENSE="vienna-rna" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="doc openmp python static-libs" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +DEPEND=" + dev-lang/perl + media-libs/gd + doc? ( dev-texlive/texlive-latex ) + python? ( + ${PYTHON_DEPS} + dev-lang/swig )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/ViennaRNA-${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-bindir.patch + "${FILESDIR}"/${PN}-2.1.1-prll.patch + "${FILESDIR}"/${PN}-2.1.1-impl-decl.patch +) + +src_prepare() { + sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die + sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die + + autotools-utils_src_prepare + + if use python; then + cd interfaces/Python || die + local PATCHES=() + distutils-r1_src_prepare + fi +} + +src_configure() { + local myeconfargs=( + --with-cluster + $(use_enable openmp) + ) + + use doc || \ + myeconfargs+=( + --without-doc-pdf + --without-doc-html + --without-doc + ) + autotools-utils_src_configure + sed \ + -e "s:CC=gcc:CC=$(tc-getCC):" \ + -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ + -i Readseq/Makefile || die + if use python; then + cd interfaces/Python || die + distutils-r1_src_configure + fi +} + +src_compile() { + autotools-utils_src_compile + autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) + + # TODO: Add (optional?) support for the NCBI toolkit. + if use python; then + cd interfaces/Python || die + emake RNA_wrap.c + distutils-r1_src_compile + fi +} + +src_test() { + autotools-utils_src_compile -C interfaces/Perl check + use python && autotools-utils_src_compile -C interfaces/Python check + autotools-utils_src_compile -C Readseq test +} + +src_install() { + autotools-utils_src_install + + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + fi + + newbin Readseq/readseq readseq-vienna + dodoc Readseq/Readseq.help + newdoc Readseq/Readme README.readseq + newdoc Readseq/Formats Formats.readseq + + # remove perlocal.pod to avoid file collisions (see #240358) + perl_delete_localpod || die "Failed to remove perlocal.pod" + if use python; then + cd interfaces/Python || die + distutils-r1_src_install + fi +} diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest new file mode 100644 index 000000000000..8a178bca08c9 --- /dev/null +++ b/sci-biology/wgs-assembler/Manifest @@ -0,0 +1,3 @@ +DIST wgs-5.4.tar.bz2 1876180 SHA256 698b22bd63fa2bb4fe7f164a92c92f82474bc8fc64c37704258ebb3bdc86d7bf +DIST wgs-6.1.tar.bz2 1900084 SHA256 e00c1b64e857ea01f7e9a9f115dd91e290a380ccda217dd6a386f57754a3cff8 SHA512 3a9cfff43967bf28f557c71b387b3ca8fd56dcdaf15fa0cd1d4b845b7b4d006e8f2692b2097d281925d59bbc41eaac1c789b6993877cffd0e233a5a9050af83c WHIRLPOOL 88e9a3f85ddee01a8a17e989248857bb6483fbde59ce211986f64d8729e82174b6fc04b2f771eb1fc131706a6adb9710c75fb90be3923db8bce6387764e3fa03 +DIST wgs-7.0.tar.bz2 1952253 SHA256 fee425cf2ec6aec6e98d580cc7e43b53eb37abd7ca14e3edc1f953d2c09b3a6c SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba WHIRLPOOL a158b882e51e8ff80fa4e6bcbe4322125fce65fc64900407882a728de9465b778f59cc6d543142ca65a255295e66e89e5303774eeef7a66362c5f492ae99a92b diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch new file mode 100644 index 000000000000..f7fb44743968 --- /dev/null +++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-build.patch @@ -0,0 +1,229 @@ + kmer/Make.rules | 4 ++-- + kmer/configure.sh | 20 +++++++++---------- + src/c_make.as | 58 +++++++++++++++++++++++++++---------------------------- + src/c_make.gen | 4 ++-- + 4 files changed, 43 insertions(+), 43 deletions(-) + +diff --git a/kmer/Make.rules b/kmer/Make.rules +index f904b13..5c2d477 100644 +--- a/kmer/Make.rules ++++ b/kmer/Make.rules +@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:% + ## EXE targets + ALL_C_EXES :=$(strip $(foreach x,${//},${${x:.=.C_EXES}})) + ${ALL_C_EXES}: +- ${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS} ++ ${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS} + __SUBGOALS__+=$${${1:.=.C_EXES}} + + ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}})) + ${ALL_CXX_EXES}: +- ${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS} ++ ${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS} + __SUBGOALS__+=$${${1:.=.CXX_EXES}} + + define .RULE-install-copy-C-CXX-EXES +diff --git a/kmer/configure.sh b/kmer/configure.sh +index 2f0d5ea..9daf89f 100755 +--- a/kmer/configure.sh ++++ b/kmer/configure.sh +@@ -254,13 +254,13 @@ EOF + # -*- makefile -*- + # Linux, optimized + CC := $CC +-SHLIB_FLAGS := -shared +-CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CLDFLAGS := -L/usr/local/lib ++SHLIB_FLAGS := -shared ${LDFLAGS} ++CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CLDFLAGS := + CLIBS := -pthread -ldl + CXX := $CXX +-CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CXXLDFLAGS := -L/usr/local/lib ++CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CXXLDFLAGS := + CXXLIBS := -pthread -ldl + ARFLAGS := ruvs + INSTALL/ := $target/ +@@ -272,13 +272,13 @@ EOF + # -*- makefile -*- + # Linux64, optimized + CC := $CC +-SHLIB_FLAGS := -shared +-CFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CLDFLAGS := -L/usr/local/lib ++SHLIB_FLAGS := -shared ${LDFLAGS} ++CFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CLDFLAGS := + CLIBS := -pthread -ldl + CXX := $CXX +-CXXFLAGS_COMPILE := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer +-CXXLDFLAGS := -L/usr/local/lib ++CXXFLAGS_COMPILE := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts ++CXXLDFLAGS := + CXXLIBS := -pthread -ldl + ARFLAGS := ruvs + INSTALL/ := $target/ +diff --git a/src/c_make.as b/src/c_make.as +index 0172807..4304589 100644 +--- a/src/c_make.as ++++ b/src/c_make.as +@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen + + ifeq ($(OSTYPE), Linux) + ifeq ($(MACHINETYPE), i686) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX + ARCH_LIB = /usr/X11R6/lib + endif + ifeq ($(MACHINETYPE), amd64) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX + ARCH_LIB = /usr/lib64 /usr/X11R6/lib64 + endif + ifeq ($(MACHINETYPE), ia64) +- ARCH_LDFLAGS += -pthread -lm +- ARCH_CFLAGS += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 ++ LINK_LIBS += -pthread -lm ++ ARCH_CFLAGS += -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 + ARCH_LIB = /usr/X11R6/lib + endif + + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -g +- ARCH_LDFLAGS += ++ ARCH_CFLAGS += ++ LINK_LIBS += + else +- ARCH_CFLAGS += -O2 +- ARCH_LDFLAGS += -Wl,-O1 ++ ARCH_CFLAGS += ++ LINK_LIBS += + endif + endif + +@@ -94,19 +94,19 @@ endif + + ifeq ($(OSTYPE), FreeBSD) + ifeq ($(MACHINETYPE), i386) +- ARCH_LDFLAGS += -pthread -lthr -lm +- ARCH_CFLAGS = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare +- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare ++ LINK_LIBS += -pthread -lthr -lm ++ ARCH_CFLAGS = -pthread -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare ++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare + endif + ifeq ($(MACHINETYPE), amd64) +- ARCH_LDFLAGS += -pthread -lthr -lm +- ARCH_CFLAGS = -pthread -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat +- ARCH_CFLAGS = -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat ++ LINK_LIBS += -pthread -lthr -lm ++ ARCH_CFLAGS = -pthread -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat ++ ARCH_CFLAGS = -pthread -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat + endif + + ifeq ($(BUILDCOVERAGE), 1) + ARCH_CFLAGS += -g -fprofile-arcs -ftest-coverage +- ARCH_LDFLAGS += -lgcov ++ LINK_LIBS += -lgcov + else + ifeq ($(BUILDDEBUG), 1) + ARCH_CFLAGS += -g +@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin) + + ifeq ($(MACHINETYPE), i386) + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g +- ARCH_LDFLAGS += -m64 -lm ++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g ++ LINK_LIBS += -m64 -lm + else + # Wow, -Wshorten-64-to-32 is tough +- ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast ++ ARCH_CFLAGS += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast + # ARCH_CFLAGS += -Wextra + # ARCH_CFLAGS += -pedantic (see above about pedantic) +- ARCH_LDFLAGS += -m64 -lm ++ LINK_LIBS += -m64 -lm + endif + endif + +@@ -161,23 +161,23 @@ endif + ifeq ($(OSTYPE), SunOS) + ifeq ($(MACHINETYPE), i86pc) + ARCH_CFLAGS = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -lm ++ LINK_LIBS += -lm + endif + + ifeq ($(MACHINETYPE), sparc32) + ARCH_CFLAGS = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -lm -lnsl -lsocket ++ LINK_LIBS += -lm -lnsl -lsocket + endif + + ifeq ($(MACHINETYPE), sparc64) + ARCH_CFLAGS = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads +- ARCH_LDFLAGS += -m64 -lm -lnsl -lsocket ++ LINK_LIBS += -lm -lnsl -lsocket + endif + + ifeq ($(BUILDDEBUG), 1) +- ARCH_CFLAGS += -g ++ ARCH_CFLAGS += + else +- ARCH_CFLAGS += -O ++ ARCH_CFLAGS += + endif + endif + +@@ -186,14 +186,14 @@ endif + + ifeq ($(BUILDPROFILE), 1) + ARCH_CFLAGS += -pg +- ARCH_LDFLAGS += -pg ++ LINK_LIBS += -pg + endif + + # One can argue that CXXFLAGS should be separate. For now, we only + # add to the flags. + + CFLAGS += $(ARCH_CFLAGS) +-CXXFLAGS += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS) ++CXXFLAGS += $(ARCH_CXXFLAGS) + LDFLAGS += $(ARCH_LDFLAGS) + + INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) +@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB) + OBJ_SEARCH_PATH = $(LOCAL_OBJ) + + ifeq ($(SITE_NAME), JCVI) +- LDFLAGS += -lcurl ++ LINK_LIBS += -lcurl + endif + + # The order of compilation here is very carefully chosen to be the +diff --git a/src/c_make.gen b/src/c_make.gen +index 7b5227c..c27b777 100644 +--- a/src/c_make.gen ++++ b/src/c_make.gen +@@ -396,12 +396,12 @@ $(LIBRARIES): + $(C_PROGS): + @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; + cd $(LOCAL_OBJ); \ +- $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) + + $(CXX_PROGS): + @ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; + cd $(LOCAL_OBJ); \ +- $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS) + + $(SCRIPT_PROGS): %.sh: + @echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++"; diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml new file mode 100644 index 000000000000..8e4a74368071 --- /dev/null +++ b/sci-biology/wgs-assembler/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">wgs-assembler</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild new file mode 100644 index 000000000000..1ad4d9cf9540 --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-5.4.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG" +HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" +SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +DEPEND="x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${PV}" + +src_configure() { + sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \ + -e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \ + "${S}"/src/c_make.as || die + sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \ + -e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \ + "${S}"/kmer/configure.sh || die + cd "${S}/kmer" + ./configure.sh || die +} + +src_compile() { + # not really an install target + emake -C kmer -j1 install || die + emake -C src -j1 SITE_NAME=LOCAL || die +} + +src_install() { + OSTYPE=$(uname) + MACHTYPE=$(uname -m) + MACHTYPE=${MACHTYPE/x86_64/amd64} + MY_S="${OSTYPE}-${MACHTYPE}" + sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die + + sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die + sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die + sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die + + dobin kmer/${MY_S}/bin/* || die + insinto /usr/$(get_libdir)/${PN} + doins kmer/${MY_S}/lib/* || die + # Collisions + # dolib.a kmer/${MY_S}/lib/* || die + insinto /usr/include/${PN} + doins kmer/${MY_S}/include/* + + insinto /usr/share/${PN} + doins -r ${MY_S}/bin/spec + insinto /usr/share/${PN}/lib + doins -r ${MY_S}/bin/TIGR || die + rm -rf ${MY_S}/bin/{TIGR,spec} + dobin ${MY_S}/bin/* || die + dolib.a ${MY_S}/lib/* || die + dodoc README +} diff --git a/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild new file mode 100644 index 000000000000..8a9114d9ecd5 --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG" +HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" +SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 x86" + +DEPEND="x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${PV}" + +src_configure() { + sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \ + -e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \ + "${S}"/src/c_make.as || die + sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \ + -e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \ + "${S}"/kmer/configure.sh || die + cd "${S}/kmer" + ./configure.sh || die +} + +src_compile() { + # not really an install target + emake -C kmer -j1 install || die + emake -C src -j1 SITE_NAME=LOCAL || die +} + +src_install() { + OSTYPE=$(uname) + MACHTYPE=$(uname -m) + MACHTYPE=${MACHTYPE/x86_64/amd64} + MY_S="${OSTYPE}-${MACHTYPE}" + sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die + + sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die + sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die + sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die + + dobin kmer/${MY_S}/bin/* || die + insinto /usr/$(get_libdir)/${PN} + doins kmer/${MY_S}/lib/* || die + # Collisions + # dolib.a kmer/${MY_S}/lib/* || die + insinto /usr/include/${PN} + doins kmer/${MY_S}/include/* + + insinto /usr/share/${PN} + doins -r ${MY_S}/bin/spec + insinto /usr/share/${PN}/lib + doins -r ${MY_S}/bin/TIGR || die + rm -rf ${MY_S}/bin/{TIGR,spec} + dobin ${MY_S}/bin/* || die + dolib.a ${MY_S}/lib/* || die + dodoc README +} diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild new file mode 100644 index 000000000000..b3ac7c30813b --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild @@ -0,0 +1,75 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +PYTHON_DEPEND=2 + +inherit eutils python toolchain-funcs + +DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG" +HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" +SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="static-libs" + +DEPEND=" + x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${PV}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_configure() { + cd "${S}/kmer" + ./configure.sh || die +} + +src_compile() { + # not really an install target + emake -C kmer -j1 install + emake -C src -j1 SITE_NAME=LOCAL +} + +src_install() { + OSTYPE=$(uname) + MACHTYPE=$(uname -m) + MACHTYPE=${MACHTYPE/x86_64/amd64} + MY_S="${OSTYPE}-${MACHTYPE}" + sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die + + sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die + sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die + sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die + + dobin kmer/${MY_S}/bin/* + insinto /usr/$(get_libdir)/${PN} + use static-libs && doins kmer/${MY_S}/lib/* + + insinto /usr/include/${PN} + doins kmer/${MY_S}/include/* + + insinto /usr/share/${PN}/lib + doins -r ${MY_S}/bin/TIGR + rm -rf ${MY_S}/bin/TIGR || die + dobin ${MY_S}/bin/* + use static-libs && dolib.a ${MY_S}/lib/* + dodoc README +} diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild new file mode 100644 index 000000000000..e25a27c40026 --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG" +HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" +SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${PV}" + +src_configure() { + sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \ + -e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \ + "${S}"/src/c_make.as || die + sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \ + -e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \ + "${S}"/kmer/configure.sh || die + cd "${S}/kmer" + ./configure.sh || die +} + +src_compile() { + # not really an install target + emake -C kmer -j1 install || die + emake -C src -j1 SITE_NAME=LOCAL || die +} + +src_install() { + OSTYPE=$(uname) + MACHTYPE=$(uname -m) + MACHTYPE=${MACHTYPE/x86_64/amd64} + MY_S="${OSTYPE}-${MACHTYPE}" + sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die + + sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die + sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die + sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die + + dobin kmer/${MY_S}/bin/* || die + insinto /usr/$(get_libdir)/${PN} + doins kmer/${MY_S}/lib/* || die + # Collisions + # dolib.a kmer/${MY_S}/lib/* || die + insinto /usr/include/${PN} + doins kmer/${MY_S}/include/* + + insinto /usr/share/${PN} + doins -r ${MY_S}/bin/spec + insinto /usr/share/${PN}/lib + doins -r ${MY_S}/bin/TIGR || die + rm -rf ${MY_S}/bin/{TIGR,spec} + dobin ${MY_S}/bin/* || die + dolib.a ${MY_S}/lib/* || die + dodoc README +} diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest new file mode 100644 index 000000000000..fc9cf9f0083c --- /dev/null +++ b/sci-biology/wise/Manifest @@ -0,0 +1 @@ +DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch new file mode 100644 index 000000000000..1ec433f19227 --- /dev/null +++ b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch @@ -0,0 +1,301 @@ +diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c +--- wise2.2.0.orig/src/HMMer2/sqio.c 2001-06-18 16:59:51.000000000 +0300 ++++ wise2.2.0/src/HMMer2/sqio.c 2009-08-05 22:39:04.000000000 +0300 +@@ -213,7 +213,7 @@ + } + } + +-/* Function: getline() ++/* Function: get_line() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -377,7 +377,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -411,7 +411,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -438,7 +438,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -515,7 +515,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -555,12 +555,12 @@ + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) get_line(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -587,7 +587,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -636,7 +636,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -669,7 +669,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -816,7 +816,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -853,7 +853,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -949,7 +949,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch new file mode 100644 index 000000000000..d3c17098105e --- /dev/null +++ b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch @@ -0,0 +1,407 @@ +diff --git a/src/base/makefile b/src/base/makefile +index 4620f19..a84e2c7 100644 +--- a/src/base/makefile ++++ b/src/base/makefile +@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \ + + + #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH +-CFLAGS = -c -O2 -DUNIX -pthread +-LFLAGS = -g -lm ++CFLAGS += -c -DUNIX -pthread ++LFLAGS = -lm + DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D + AR_OPTIONS = ru + +diff --git a/src/corba/makefile b/src/corba/makefile +index df3dd78..237a1ba 100644 +--- a/src/corba/makefile ++++ b/src/corba/makefile +@@ -1,10 +1,10 @@ + + +-CC = cc ++CC += gcc + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/ ++CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags` + LFLAGS = -L../base/ -lm -lpthread + AR_OPTIONS = ru + +@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile +index ef3334a..3a0bc2a 100644 +--- a/src/dnaindex/assembly/makefile ++++ b/src/dnaindex/assembly/makefile +@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o + + + CC = cc +-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` ++CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags` + + +-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm + + + .c.o : +diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile +index 285e6a0..8c6a0dc 100644 +--- a/src/dnaindex/makefile ++++ b/src/dnaindex/makefile +@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs` + + make_shotgun : make_shotgun.o shotgun.o + $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) +@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o + $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) + + CC = cc +-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` + + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm + + + .c.o : +diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile +index d1d77af..cad8900 100644 +--- a/src/dynlibsrc/makefile ++++ b/src/dynlibsrc/makefile +@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \ + + + +-CC = cc ++CC ?= gcc + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` ++CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` ++#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ + LFLAGS = -g -L../base/ -lm + AR_OPTIONS = ru +@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a + $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) -g -o test_seqhash `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +diff --git a/src/external/mott/makefile b/src/external/mott/makefile +index 8d7c1d4..940c438 100644 +--- a/src/external/mott/makefile ++++ b/src/external/mott/makefile +@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o + wise2_mott_bridge.o : wise2_mott_bridge.c + $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c + +-CC = cc ++CC ?= gcc + +-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c +-LFLAGS = -g -L../base/ -lm ++CFLAGS += -DPTHREAD -c ++LFLAGS = -L../base/ -lm + AR_OPTIONS = ru + + +diff --git a/src/makefile b/src/makefile +index bdff4ff..0d7c871 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -26,12 +26,12 @@ + + # Change the cc line to gcc if you get compiler errors + # Most likely you have a non ANSI C compiler +-CC ?= cc ++CC ?= gcc + + # These are the CFLAGS to use. These days Wise2 is inherently + # pthreaded, and everything is compiled with threads. More + # info on running threads can be found in the documentation +-CFLAGS = -c -pthread -O2 `glib-config --cflags` ++CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags` + + + +diff --git a/src/models/makefile b/src/models/makefile +index f518d0c..a297eff 100644 +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -50,6 +50,8 @@ NEWG = geneparser21.o \ + proteinsw.o \ + estquick3.o + ++EXTRALIBS += `pkg-config glib-2.0 --libs` ++ + all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a + + libmodel.a : $(NEWG) +@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c + $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. + + oldpostwise : oldpostwise.o $(NEWG) +- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm ++ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm + + testdna : testdna.o dnaalign.o seqaligndisplay.o + $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) +@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o + $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c +@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc. + + + scanwisep_wiseserver.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs` + + scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread ++ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs` + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c +@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap. + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) $(LDFLAGS) -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o + $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread +@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o + $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o +- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o +- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm ++ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm + + + efgw : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence ++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + edb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence ++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o +- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o +- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o +- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o +- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) ++ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) + + + HMMER_LIBS = ../HMMer2/ +@@ -345,11 +347,11 @@ HMMER_DEFINE = + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` ++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags` + #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` ++LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +diff --git a/src/network/makefile b/src/network/makefile +index 303c2da..e607310 100644 +--- a/src/network/makefile ++++ b/src/network/makefile +@@ -3,8 +3,8 @@ + + CC = cc + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` ++CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags` ++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +diff --git a/src/snp/makefile b/src/snp/makefile +index ccf750a..2b83c43 100644 +--- a/src/snp/makefile ++++ b/src/snp/makefile +@@ -2,12 +2,12 @@ + .SUFFIXES : .dy + + +-CC = cc ++CC ?= gcc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` ++CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags` + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm ++LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0 + $(CC) $(CFLAGS) $(INCFLAGS) $? + + test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o +- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) ++ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) + + INCFLAGS = -I../base/ -I../dynlibsrc/ + DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch new file mode 100644 index 000000000000..42af0c7e849b --- /dev/null +++ b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch @@ -0,0 +1,302 @@ +diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c +index 5889e7d..bc95629 100644 +--- a/src/HMMer2/sqio.c ++++ b/src/HMMer2/sqio.c +@@ -213,7 +213,7 @@ readline(FILE *f, char *s) + } + } + +-/* Function: getline() ++/* Function: get_line() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ readline(FILE *f, char *s) + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++get_line(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V) + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ get_line(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V) + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ get_line(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V) + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V) + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ get_line(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V) + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V) + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ get_line(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V) + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ get_line(V); + } + + +@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V) + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V) + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ get_line(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V) + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ get_line(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ get_line(V); + } + + static int +@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V) + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ get_line(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V) + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + static int +@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V) + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) get_line(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ get_line(V); + } + + +@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V) + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V) + } + + do { +- getline(V); ++ get_line(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V) + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V) + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ get_line(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V) + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ get_line(V); + } + + static void +@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V) + + do { + done = feof(V->f); +- getline(V); ++ get_line(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V) + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V) + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V) + while (1) + { + /* sequence line */ +- getline(V); ++ get_line(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ get_line(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V) + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ get_line(V); + } + + +@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env) + + /* Load the first line. + */ +- getline(dbfp); ++ get_line(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset) + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ get_line(sqfp); + } + + +@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp) + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ get_line(sqfp); + } + } + +@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo) + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ get_line(V); + } while (! feof(V->f)); + break; + diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch new file mode 100644 index 000000000000..827ce4cdfa7a --- /dev/null +++ b/sci-biology/wise/files/wise-api.tex.patch @@ -0,0 +1,38 @@ +--- api.tex.old 2005-03-06 11:31:59.862760952 -0500 ++++ api.tex 2005-03-06 11:42:31.375756384 -0500 +@@ -204,7 +204,7 @@ + \item Build two Sequence objects, from a file or strings (\ref{object_Sequence}) + \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins + \item Read in the comparison matrix using CompMat (\ref{object_CompMat}) +-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap}) ++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap}) + \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay}) + \end{itemize} + +@@ -213,7 +213,7 @@ + \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence}) + \item Make a protein database from the single protein object (\ref{object_ProteinDB}) + \item Make a protein database from a single fasta file (\ref{object_ProteinDB}) +-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap}) ++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap}) + \item Show the Hscore object using a show function (\ref{object_Hscore}) + \item Retrieve individual protein objects from the database by taking out the + DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object +@@ -232,7 +232,7 @@ + \item Read in a codon table (\ref{object_CodonTable}) + \item Make a random DNA model (\ref{object_RandomModelDNA}) + \item Make an algorithm type (\ref{module_gwrap}) +-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap}) ++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap}) + \item Run the actual algorithm (\ref{module_gwrap}) + \item show the alignment using genedisplay (\ref{module_gwrap}) + \end{itemize} +@@ -5055,7 +5055,7 @@ + Member functions of RandomModel + + \section{sequence\_codon} +-\label{module_sequence\_codon} ++\label{module_sequence_codon} + This module only contains factory methods + + \subsection{sequence\_codon factory methods} diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env new file mode 100644 index 000000000000..3f781c80833b --- /dev/null +++ b/sci-biology/wise/files/wise-env @@ -0,0 +1 @@ +WISECONFIGDIR="/usr/share/wise/wisecfg" diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/wise/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild new file mode 100644 index 000000000000..f68686842689 --- /dev/null +++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +DESCRIPTION="Intelligent algorithms for DNA searches" +HOMEPAGE="http://www.ebi.ac.uk/Wise2/" +SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha amd64 ia64 ~sparc x86" +IUSE="doc static-libs" + +RDEPEND="~sci-biology/hmmer-2.3.2" +DEPEND=" + ${RDEPEND} + app-shells/tcsh + dev-lang/perl + virtual/latex-base" + +S="${WORKDIR}"/${PN}$(delete_version_separator 3) + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-glibc-2.10.patch \ + "${FILESDIR}"/${P}-cflags.patch + cd "${S}"/docs || die + cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die + cat wise2api.tex temp.tex apiend.tex > api.tex || die + epatch "${FILESDIR}"/${PN}-api.tex.patch +} + +src_compile() { + emake \ + -C src \ + CC="$(tc-getCC)" \ + all + if use doc; then + cd "${S}"/docs || die + for i in api appendix dynamite wise2 wise3arch; do + latex ${i} || die + latex ${i} || die + dvips ${i}.dvi -o || die + done + fi +} + +src_test() { + cd "${S}"/src || die + WISECONFIGDIR="${S}/wisecfg" emake test +} + +src_install() { + dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb + use static-libs && \ + dolib.a \ + "${S}"/src/base/libwisebase.a \ + "${S}"/src/dynlibsrc/libdyna.a \ + "${S}"/src/models/libmodel.a + + insinto /usr/share/${PN} + doins -r "${S}"/wisecfg + + if use doc; then + insinto /usr/share/doc/${PF} + doins "${S}"/docs/*.ps + fi + newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file" +} diff --git a/sci-biology/yass/Manifest b/sci-biology/yass/Manifest new file mode 100644 index 000000000000..d2e3a2dba99c --- /dev/null +++ b/sci-biology/yass/Manifest @@ -0,0 +1 @@ +DIST yass-1.14.tar.gz 235530 SHA256 f23da1c16cf98317ad11c085feede9790401e888a95d486b550f0c081d4c9018 diff --git a/sci-biology/yass/files/1.14-as-needed.patch b/sci-biology/yass/files/1.14-as-needed.patch new file mode 100644 index 000000000000..e57503801c7a --- /dev/null +++ b/sci-biology/yass/files/1.14-as-needed.patch @@ -0,0 +1,207 @@ +diff --git a/configure.ac b/configure.ac +index 68453ef..3ecfd21 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -28,13 +28,11 @@ AC_CHECK_FUNCS([floor memset clock pow sqrt strchr strdup strtol strtoul]) + dnl 1) threads options + + dnl abc) : with-threads option +-AC_ARG_WITH( +- threads, +- [ --with-threads compile with all threads], +- [threads="yes"], +- [threads="no"]) ++AC_ARG_ENABLE( ++ [threads], ++ AS_HELP_STRING([--enable-threads], [compile with all threads])) + +-if test "$threads" = "yes"; then ++AS_IF([test "x$enable_threads" = "xyes"], [ + AC_MSG_RESULT(detected cpu parameter: threads); + + dnl pthread library here ? (UNIX system) +@@ -46,167 +44,25 @@ if test "$threads" = "yes"; then + AC_MSG_RESULT(yes) + AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) + CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN -DTHREAD_FORWARD_REVERSE -DTHREAD_QUERY_CHUNK " +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + else + AC_MSG_RESULT(no : disabling \"--with-threads\" parameter) + fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 2; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-threads\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +- +- +- +-dnl a) : with-thread-fr option +-AC_ARG_WITH( +- thread-fr, +- [ --with-thread-fr compile with two separate threads for Forward and Reverse sequence], +- [thread_forward_reverse="yes"], +- [thread_forward_reverse="no"]) +- +-if test "$thread_forward_reverse" = "yes"; then +- AC_MSG_RESULT(detected cpu parameter: thread-fr); +- +- dnl pthread library here ? (UNIX system) +- AC_MSG_CHECKING(for pthread lib) +- AC_CHECK_LIB(pthread, pthread_create, +- [have_pthread="yes"], +- [have_pthread="no"]) +- if test "$have_pthread" = "yes"; then +- AC_MSG_RESULT(yes) +- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) +- CFLAGS=" $CFLAGS -DTHREAD_FORWARD_REVERSE " +- LDFLAGS="$LDFLAGS -lpthread" +- else +- AC_MSG_RESULT(no : disabling \"--with-thread-fr\" parameter) +- fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-thread-fr\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +- +- +- +-dnl b) : with-thread-aa option +-AC_ARG_WITH( +- thread-aa, +- [ --with-thread-aa compile with two separate threads for Assemble and Align steps], +- [thread_assemble_align="yes"], +- [thread_assemble_align="no"]) +- +-if test "$thread_assemble_align" = "yes"; then +- AC_MSG_RESULT(detected cpu parameter: thread-aa); +- +- dnl pthread library here ? (UNIX system) +- AC_MSG_CHECKING(for pthread lib) +- AC_CHECK_LIB(pthread, pthread_create, +- [have_pthread="yes"], +- [have_pthread="no"]) +- if test "$have_pthread" = "yes"; then +- AC_MSG_RESULT(yes) +- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) +- CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN " +- LDFLAGS="$LDFLAGS -lpthread" +- else +- AC_MSG_RESULT(no : disabling \"--with-thread-aa\" parameter) +- fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-thread-aa\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +-dnl c) : with-thread-qc option +-AC_ARG_WITH( +- thread-qc, +- [ --with-thread-qc compile with threads for the query chunks], +- [thread_query_chunk="yes"], +- [thread_query_chunk="no"]) +- +-if test "$thread_query_chunk" = "yes"; then +- AC_MSG_RESULT(detected cpu parameter: thread-qc); +- +- dnl pthread library here ? (UNIX system) +- AC_MSG_CHECKING(for pthread lib) +- AC_CHECK_LIB(pthread, pthread_create, +- [have_pthread="yes"], +- [have_pthread="no"]) +- if test "$have_pthread" = "yes"; then +- AC_MSG_RESULT(yes) +- AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) +- CFLAGS=" $CFLAGS -DTHREAD_QUERY_CHUNK " +- LDFLAGS="$LDFLAGS -lpthread" +- else +- AC_MSG_RESULT(no : disabling \"--with-thread-qc\" parameter) +- fi +- +-else +- if test -s /proc/cpuinfo; then +- AC_MSG_CHECKING(for multi-processor) +- dnl Multithread advice +- if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then +- AC_MSG_RESULT(yes) +- AC_MSG_RESULT(- try \"configure --with-thread-qc\") +- else +- AC_MSG_RESULT(no) +- fi; +- fi; +-fi +- +- +- ++]) + + dnl 2) : low-memory option +-AC_ARG_WITH( +- low-memory, +- [ --with-low-memory use less memory, but can miss some repeats], +- [low_memory="yes"], +- [low_memory="no"]) ++AC_ARG_ENABLE( ++ [lowmemory], ++ AS_HELP_STRING([--enable-lowmemory], [use less memory, but can miss some repeats])) + +-if test "$low_memory" = "yes"; then ++AS_IF([test "x$enable_lowmemory" = "xyes"], [ + AC_MSG_RESULT(detected memory parameter: low memory); + CFLAGS=" $CFLAGS -DLOW_MEMORY " +-else +- AC_MSG_RESULT(detected memory parameter : plain memory) +-fi +- +- +-CFLAGS="$CFLAGS -O3 -Wall -ansi -pedantic -funroll-loops -pipe -fomit-frame-pointer " +-LDFLAGS="$LDFLAGS -lm" ++]) + + AC_SUBST(CFLAGS) + AC_SUBST(LDFLAGS) ++ + AM_WITH_DMALLOC + AM_INIT_AUTOMAKE + AC_CONFIG_FILES([Makefile +diff --git a/src/Makefile.am b/src/Makefile.am +index e456f94..8d90ca9 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -6,3 +6,4 @@ + bin_PROGRAMS = yass + yass_SOURCES = align.c assemble.c avl.c display.c global_var.c hash.c kword.c list.c main.c prdyn.c proba.c red_black.c regroup.c threads.c tuple.c util.c \ + align.h assemble.h avl.h display.h global_var.h hash.h kword.h list.h prdyn.h proba.h red_black.h regroup.h threads.h tuple.h util.h ++yass_LDADD = -lm diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml new file mode 100644 index 000000000000..e4a717e691b2 --- /dev/null +++ b/sci-biology/yass/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <use> + <flag name="dmalloc">Enable debugging with the dmalloc library</flag> + <flag name="lowmem">Build for environments with low amounts of memory</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/yass/yass-1.14-r1.ebuild b/sci-biology/yass/yass-1.14-r1.ebuild new file mode 100644 index 000000000000..6476a839c935 --- /dev/null +++ b/sci-biology/yass/yass-1.14-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +inherit autotools eutils + +DESCRIPTION="Genomic similarity search with multiple transition constrained spaced seeds" +HOMEPAGE="http://bioinfo.lifl.fr/yass/" +SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="dmalloc lowmem threads" +KEYWORDS="~amd64 ~x86" + +DEPEND="dmalloc? ( dev-libs/dmalloc )" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-as-needed.patch + eautoreconf +} + +src_configure() { + econf \ + $(use_enable threads) \ + $(use_enable lowmem lowmemory) \ + $(use_with dmalloc) +} + +src_install() { + emake DESTDIR="${D}" install || die + dodoc AUTHORS README NEWS || die +} diff --git a/sci-biology/yass/yass-1.14.ebuild b/sci-biology/yass/yass-1.14.ebuild new file mode 100644 index 000000000000..c0d6242a201d --- /dev/null +++ b/sci-biology/yass/yass-1.14.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="2" + +DESCRIPTION="Genomic similarity search with multiple transition constrained spaced seeds" +HOMEPAGE="http://bioinfo.lifl.fr/yass/" +SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="" + +src_install() { + einstall || die + dodoc AUTHORS README NEWS +} |