From a2848e731874cc8a47a101a8cbae060b6cac3795 Mon Sep 17 00:00:00 2001 From: Donnie Berkholz Date: Tue, 21 Feb 2006 20:27:27 +0000 Subject: New multiple sequence alignment package. Probably the best global aligner, although it runs slower. Takes 5-10 times longer than clustalw, but about half as long as t-coffee. (Portage version: 2.1_pre4-r1) --- sci-biology/probcons/ChangeLog | 12 ++++++ sci-biology/probcons/Manifest | 27 +++++++++++++ sci-biology/probcons/files/1.10-fix-cxxflags.patch | 21 +++++++++++ sci-biology/probcons/files/digest-probcons-1.10 | 3 ++ sci-biology/probcons/metadata.xml | 9 +++++ sci-biology/probcons/probcons-1.10.ebuild | 44 ++++++++++++++++++++++ 6 files changed, 116 insertions(+) create mode 100644 sci-biology/probcons/ChangeLog create mode 100644 sci-biology/probcons/Manifest create mode 100644 sci-biology/probcons/files/1.10-fix-cxxflags.patch create mode 100644 sci-biology/probcons/files/digest-probcons-1.10 create mode 100644 sci-biology/probcons/metadata.xml create mode 100644 sci-biology/probcons/probcons-1.10.ebuild (limited to 'sci-biology') diff --git a/sci-biology/probcons/ChangeLog b/sci-biology/probcons/ChangeLog new file mode 100644 index 000000000000..044374da44e0 --- /dev/null +++ b/sci-biology/probcons/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/probcons +# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/ChangeLog,v 1.1 2006/02/21 20:27:27 spyderous Exp $ + +*probcons-1.10 (21 Feb 2006) + + 21 Feb 2006; Donnie Berkholz ; + +files/1.10-fix-cxxflags.patch, +metadata.xml, +probcons-1.10.ebuild: + New multiple sequence alignment package. Probably the best global aligner, + although it runs slower. Takes 5-10 times longer than clustalw, but about + half as long as t-coffee. + diff --git a/sci-biology/probcons/Manifest b/sci-biology/probcons/Manifest new file mode 100644 index 000000000000..8f4dd746a9d1 --- /dev/null +++ b/sci-biology/probcons/Manifest @@ -0,0 +1,27 @@ +MD5 bcc20b9c5e249f07fb535f0744f816e2 files/1.10-fix-cxxflags.patch 845 +RMD160 1e04c84b35c245623619c6d5a7128a8ab1c880af files/1.10-fix-cxxflags.patch 845 +SHA256 73a298114996b5d879b9ec3253d104464cb456d19382668cdf75bfe9f93f11de files/1.10-fix-cxxflags.patch 845 +MD5 74eaf8b13786493ed6220c0c33e09b28 files/add-libint-error-message.patch 722 +RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 files/add-libint-error-message.patch 722 +SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390 files/add-libint-error-message.patch 722 +MD5 09ec4c47c33e46e812d1c8a09f00a91a files/digest-probcons-1.10 241 +RMD160 2d5910f5cca5eb03d3d6e7ca83954774d4080051 files/digest-probcons-1.10 241 +SHA256 6dcaf5dcb70c5db87bebfb7d61342cc1f56758d67fc2db674ae900bc685406ef files/digest-probcons-1.10 241 +MD5 dbaa3f7804f89cfbc6b41a8fceeec0ca files/digest-psi-3.2.3 232 +RMD160 36c9c50c4c7e2ef156f0f0334b2b330435968e9b files/digest-psi-3.2.3 232 +SHA256 e9a1506870d5bf1fdfb1aee4740fc584343f0e716afe52c19411d115adf0bc4c files/digest-psi-3.2.3 232 +MD5 285e67094e0841a79a32c9301c023b39 files/dont-build-libint.patch 355 +RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 files/dont-build-libint.patch 355 +SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18 files/dont-build-libint.patch 355 +MD5 9ec964134fe443be4a6d6760278bea87 files/try-more-compilers.patch 401 +RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f files/try-more-compilers.patch 401 +SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08 files/try-more-compilers.patch 401 +MD5 f73030c473338710e13e3dfe3ce59463 files/try-pthread-for-blas-lapack.patch 1489 +RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 files/try-pthread-for-blas-lapack.patch 1489 +SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5 files/try-pthread-for-blas-lapack.patch 1489 +MD5 6dc1efc685dfc6994c972eed20daf18c files/use-external-libint.patch 1359 +RMD160 560598e6d7c99d901d97dd6037480bd57c82433f files/use-external-libint.patch 1359 +SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 files/use-external-libint.patch 1359 +MD5 dfce50503ba4abc4c4d4845cef79faef probcons-1.10.ebuild 1238 +RMD160 6fe62998a1b18aa4700deb574d9edc2c99dd8025 probcons-1.10.ebuild 1238 +SHA256 abb10a9fea1636935526bb6cdaa195a4c17b3ba38e7554c460a746afff68b657 probcons-1.10.ebuild 1238 diff --git a/sci-biology/probcons/files/1.10-fix-cxxflags.patch b/sci-biology/probcons/files/1.10-fix-cxxflags.patch new file mode 100644 index 000000000000..bf76e77b36c1 --- /dev/null +++ b/sci-biology/probcons/files/1.10-fix-cxxflags.patch @@ -0,0 +1,21 @@ +diff -urN probcons.orig/Makefile probcons/Makefile +--- probcons.orig/Makefile 2006-02-21 12:14:37.000000000 -0800 ++++ probcons/Makefile 2006-02-21 12:15:15.000000000 -0800 +@@ -15,6 +15,8 @@ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10" + + # debug mode +@@ -25,7 +27,7 @@ + + # 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 diff --git a/sci-biology/probcons/files/digest-probcons-1.10 b/sci-biology/probcons/files/digest-probcons-1.10 new file mode 100644 index 000000000000..e49b2933d04c --- /dev/null +++ b/sci-biology/probcons/files/digest-probcons-1.10 @@ -0,0 +1,3 @@ +MD5 c7938b95732a85c35225bafd4b5b174f probcons_v1_10.tar.gz 43004 +RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 probcons_v1_10.tar.gz 43004 +SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518 probcons_v1_10.tar.gz 43004 diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml new file mode 100644 index 000000000000..211b8bd0f0a4 --- /dev/null +++ b/sci-biology/probcons/metadata.xml @@ -0,0 +1,9 @@ + + + +sci + +spyderous@gentoo.org +Donnie Berkholz + + diff --git a/sci-biology/probcons/probcons-1.10.ebuild b/sci-biology/probcons/probcons-1.10.ebuild new file mode 100644 index 000000000000..2128a8505739 --- /dev/null +++ b/sci-biology/probcons/probcons-1.10.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/probcons/probcons-1.10.ebuild,v 1.1 2006/02/21 20:27:27 spyderous Exp $ + +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/${MY_P}.tar.gz" +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +# Gnuplot is explicitly runtime-only, it's run using system() +RDEPEND="sci-visualization/gnuplot" +DEPEND="" +S="${WORKDIR}/${PN}" + +src_unpack() { + unpack ${A} + epatch ${FILESDIR}/${PV}-fix-cxxflags.patch +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + OPT_CXXFLAGS="${CXXFLAGS}" \ + || die "make failed" +} + +src_install() { + DESTTREE="/usr" dobin probcons project makegnuplot + # Overlap with imagemagick + DESTTREE="/usr" 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" +} -- cgit v1.2.3-65-gdbad