diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
---|---|---|
committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/mothur |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/mothur')
-rw-r--r-- | sci-biology/mothur/Manifest | 7 | ||||
-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 | 8 | ||||
-rw-r--r-- | sci-biology/mothur/mothur-1.27.0-r1.ebuild | 43 |
5 files changed, 203 insertions, 0 deletions
diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest new file mode 100644 index 000000000000..c6d74e207412 --- /dev/null +++ b/sci-biology/mothur/Manifest @@ -0,0 +1,7 @@ +AUX mothur-1.27.0-makefile.patch 1196 SHA256 970d789187d58081bda269a863d965c1601ee18e09c39aa6dcaba2ef0aa89f5a SHA512 8a78ddbc926d4e116deed440fda8431ccbca3299ac182fc84850259187dc130cc43fb6f23845d055d998293fa43f94cbe35930242c5f6aa049f8275ad3e42adf WHIRLPOOL c0ae488479f430f212ff2158b74aa61ef9547b865be1db7ca3b546edf48907aa9aead69acfbc02c35b7d675209ac8f7d267a8f9a98ff167a0f73d0fc2efdd6ea +AUX mothur-1.27.0-overflows.patch 4894 SHA256 7b1f25400aa8f78ef55bcbd7d613eb877ce2774fc2e9492b6f9c544266661b5b SHA512 aa392b2060cecc38006a7ac50aaa8e4249a020029234ac2abdc33441b12a09faabb0335144ff4d888e55a1da1838a45347981f49f6658f3546a54a30b5e2133a WHIRLPOOL 7f0f8089b938c6a30ee13e217e21a4628ca56490aba36e7b6b14657ec70f3ba043243c80088be6b3e3d145835d4c3e3e3ee68d073f6556383a06e018f0cd716f +DIST mothur-1.27.0.zip 7095054 SHA256 7521d0dfc849dc9ef707bf83032e471966914b9833247c49e5d30b8d9281a6c7 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 WHIRLPOOL 32e5c9c2be6e593b2dbc64be38c49b4dec3ea048cd3c972cf948136b394608a2dc168be58b7fb500a17fc6a152b7777fcd09b3f9fb3bf60c7dd92d043a4bf361 +EBUILD mothur-1.27.0-r1.ebuild 881 SHA256 f485ea8a591e1fe7f1f121dda9b0dd8c58d301e86f947f8fe5cf98eb07ee2b8b SHA512 6f2fcb2d296ef3ef33786b579106f14ee0dfe05a50b53f5e0225c477598da1171cbd88e84f0fc7df5a973c221319a2fa23fb5cbddb339e7ede4e54b34b223be2 WHIRLPOOL 3a0a4e95ca0a7cc73e035f975d369b07ca5a5f75beea46f195856ee66cd64ac066606c4212f6676ecaac5b25182e4ce3fb2c3e3db90175de446165acc2522bdd +MISC ChangeLog 2910 SHA256 d1271431f72a4b8d1d9fd37fdb2cafa07b05167a80f67859740b2b547e540307 SHA512 f52727a3fb8ac2b61d833e4484aa7b597c4e1ee521d816403a98d86a2256968034ef4034cd61f1221d5745d5ca5aca9a4b398d56848d262084be99473f8c1a7d WHIRLPOOL d35766e69fb50bba2451c957fbfc80bbb972a7a1b393b623c1adad29623992c5c37d29c620a2816d68f2d9b7f6aa5a465110eacec6043686f012877719825588 +MISC ChangeLog-2015 2717 SHA256 0951ac13aa91ee601c257ec73a3b8261d0ab456853edb2af7c88abb96a4c7c23 SHA512 1f1cc58996af9e116ccedaaf6609b3227208939d13b027ef70f0694edf906b759fac42d57a37a5537b1ce2b8fd67a40a5dfc37e0dd0158fa6301e91a48481163 WHIRLPOOL 955bd00c7dc0a234fde17e2e82b203fbff7182b8d0eb4abc933a67b0d9a3d281c59a5bcd0034a8c171cc565d683c3b5ab2625c5845c8fd5637a0174a50008e48 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 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..959160fe46b1 --- /dev/null +++ b/sci-biology/mothur/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 type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</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..d12d3c9b4399 --- /dev/null +++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +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} +} |