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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/mothur | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/mothur')
-rw-r--r-- | sci-biology/mothur/Manifest | 2 | ||||
-rw-r--r-- | sci-biology/mothur/files/mothur-1.27.0-makefile.patch | 52 | ||||
-rw-r--r-- | sci-biology/mothur/files/mothur-1.27.0-overflows.patch | 93 | ||||
-rw-r--r-- | sci-biology/mothur/metadata.xml | 5 | ||||
-rw-r--r-- | sci-biology/mothur/mothur-1.27.0-r1.ebuild | 44 | ||||
-rw-r--r-- | sci-biology/mothur/mothur-1.6.0.ebuild | 33 |
6 files changed, 229 insertions, 0 deletions
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} +} |