diff options
62 files changed, 814 insertions, 32 deletions
diff --git a/dev-perl/Text-Graph/Manifest b/dev-perl/Text-Graph/Manifest new file mode 100644 index 000000000..edee5b777 --- /dev/null +++ b/dev-perl/Text-Graph/Manifest @@ -0,0 +1 @@ +DIST Text-Graph-0.83.tar.gz 11438 SHA256 51afb8aa4f267f39929801cf876a4e9ee28781504e4d2a05285f59506d4b6020 SHA512 bc0a9aa55eb8a611b0f094ed514ee5cabc4c6555bc62ee084876d70bfbc2b886303fd02e613ca68d639f4a1c5788b3744a2d5bb7d2d4678e46718e01d3dd8bc8 WHIRLPOOL cea259ebd8c6675d9f43e69337044282afbc4c73da805eb730b918cfcb19182da84d4ba64435230505403e04b728ee6f19737c2be49f9fcdfd6f969ed3186a53 diff --git a/dev-perl/Text-Graph/Text-Graph-0.83.ebuild b/dev-perl/Text-Graph/Text-Graph-0.83.ebuild new file mode 100644 index 000000000..b23a1a4d5 --- /dev/null +++ b/dev-perl/Text-Graph/Text-Graph-0.83.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MODULE_AUTHOR="GWADEJ" +MODULE_A_EXT="tar.gz" + +inherit perl-module + +DESCRIPTION="Perl module for generating simple text-based graphs" + +LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="dev-lang/perl" + +RDEPEND="${DEPEND}" diff --git a/dev-perl/Text-Graph/metadata.xml b/dev-perl/Text-Graph/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/dev-perl/Text-Graph/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/dev-perl/Text-RecordParser/Manifest b/dev-perl/Text-RecordParser/Manifest new file mode 100644 index 000000000..68fc44e1c --- /dev/null +++ b/dev-perl/Text-RecordParser/Manifest @@ -0,0 +1 @@ +DIST Text-RecordParser-1.6.5.tar.gz 83653 SHA256 da3b81414c63f8d9218d116745a88b948c46c98b187634f629892e54001bc35a SHA512 a05e2c7a1a26ff1776dc00dd1d5eb92b41e03177a1eee8aa0ffde9c03368f918e67d7d4f8eb54483704cf9f276a954a91cbd12ce04172bd1a6e0844d3b289258 WHIRLPOOL a9ec4539c2c4cdac33257770f6af6ce59095f39ef84b032020934b8dcee8f4f5caad375e9edfcec9d47d61edb8a841eae1162f5aff3839931a3e2428efe6f633 diff --git a/dev-perl/Text-RecordParser/Text-RecordParser-1.6.5.ebuild b/dev-perl/Text-RecordParser/Text-RecordParser-1.6.5.ebuild new file mode 100644 index 000000000..233c679fa --- /dev/null +++ b/dev-perl/Text-RecordParser/Text-RecordParser-1.6.5.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MODULE_AUTHOR="KCLARK" +inherit perl-module + +DESCRIPTION="Perl module to read record-oriented files" + +LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="dev-lang/perl" +DEPEND="${RDEPEND}" + +SRC_TEST="do" diff --git a/dev-perl/Text-RecordParser/metadata.xml b/dev-perl/Text-RecordParser/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/dev-perl/Text-RecordParser/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild index 4a52cfd40..9754ee5f0 100644 --- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild +++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild @@ -10,7 +10,7 @@ if [ "$PV" == "9999" ]; then inherit git-r3 fi -DESCRIPTION="Asssemble contigs/scaffolds using related reference sequence" +DESCRIPTION="Reference-assisted asssembly of contigs/scaffolds" HOMEPAGE="https://github.com/baoe/AlignGraph http://bioinformatics.oxfordjournals.org/content/30/12/i319.long" if [ "$PV" == "9999" ]; then diff --git a/sci-biology/Fastaq/Fastaq-9999.ebuild b/sci-biology/Fastaq/Fastaq-9999.ebuild new file mode 100644 index 000000000..9acd60e09 --- /dev/null +++ b/sci-biology/Fastaq/Fastaq-9999.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python3_3 python3_4 ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="Python3 script to manipulate FASTA/Q files plus API for developers" +HOMEPAGE="https://github.com/sanger-pathogens/Fastaq" +EGIT_REPO_URI="https://github.com/sanger-pathogens/Fastaq.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" diff --git a/sci-biology/Fastaq/metadata.xml b/sci-biology/Fastaq/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/Fastaq/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild index 5cb9ea210..1f7c89a6d 100644 --- a/sci-biology/MolBioLib/MolBioLib-5.ebuild +++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild @@ -10,7 +10,7 @@ SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.versi LICENSE="GPL-3" SLOT="0" -KEYWORDS="" +KEYWORDS="" # does not build IUSE="" # contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild index 4cc246b55..f9a6ee92c 100644 --- a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) inherit eutils toolchain-funcs -DESCRIPTION="De novo assembler for smaller genomes (bacteria to fungi)" +DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven coverage" HOMEPAGE="http://bioinf.spbau.ru/en/spades" SRC_URI="http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz http://spades.bioinf.spbau.ru/release3.5.0/manual.html" diff --git a/sci-biology/SSAKE/SSAKE-3.8.2.ebuild b/sci-biology/SSAKE/SSAKE-3.8.2.ebuild index bc1907871..a9ed70db2 100644 --- a/sci-biology/SSAKE/SSAKE-3.8.2.ebuild +++ b/sci-biology/SSAKE/SSAKE-3.8.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -DESCRIPTION="Short-read trimmer, assembler, scaffolder in PERL using the 3'-most k-mers" +DESCRIPTION="Short-read trimmer, OLC assembler, scaffolder in PERL using the 3'-most k-mers" HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/ssake" SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/${PV}/ssake_v3-8-2.tar.gz" diff --git a/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild b/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild new file mode 100644 index 000000000..746863a9b --- /dev/null +++ b/sci-biology/Scaffolder-evaluation/Scaffolder-evaluation-9999.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 + +DESCRIPTION="Scripts to run genome assembly scaffolding tools and analyse output for accuracy" +HOMEPAGE="https://github.com/martinghunt/Scaffolder-evaluation + http://genomebiology.com/2014/15/3/R42" +EGIT_REPO_URI="https://github.com/martinghunt/Scaffolder-evaluation.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl + dev-lang/python + dev-lang/R + media-gfx/graphviz + sci-biology/mummer + sci-biology/bowtie + sci-biology/samtools + sci-biology/ncbi-tools + sci-biology/Fastaq" + +src_install(){ + dobin Analysis-scripts/* Wrapper-scripts/* + dodoc README.md +} diff --git a/sci-biology/Scaffolder-evaluation/metadata.xml b/sci-biology/Scaffolder-evaluation/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/Scaffolder-evaluation/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild index 71fc0b87e..2b56ae9a6 100644 --- a/sci-biology/arachne/arachne-46233.ebuild +++ b/sci-biology/arachne/arachne-46233.ebuild @@ -4,7 +4,7 @@ EAPI=5 -DESCRIPTION="Whole genome shotgun assembler for Sanger read lengths (overlap-layout-contig)" +DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)" HOMEPAGE="https://www.broadinstitute.org/crd/wiki http://genome.cshlp.org/content/12/1/177.abstract" SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz" diff --git a/sci-biology/assembly-stats/assembly-stats-9999.ebuild b/sci-biology/assembly-stats/assembly-stats-9999.ebuild new file mode 100644 index 000000000..895aa9a1f --- /dev/null +++ b/sci-biology/assembly-stats/assembly-stats-9999.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 cmake-utils + +DESCRIPTION="Assembly statistics (min, max, sum, N50, N90, count gaps and Ns)" +HOMEPAGE="https://github.com/martinghunt/assembly-stats" +EGIT_REPO_URI="https://github.com/martinghunt/assembly-stats.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=">=dev-cpp/gtest-1.7.0" +RDEPEND="${DEPEND}" + +# installs into /usr/local/bin +# should not even try to compile bundled gtest diff --git a/sci-biology/assembly-stats/metadata.xml b/sci-biology/assembly-stats/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/assembly-stats/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/bamtools/bamtools-2.4.0.ebuild b/sci-biology/bamtools/bamtools-2.4.0.ebuild index b2d7d623f..c27822c17 100644 --- a/sci-biology/bamtools/bamtools-2.4.0.ebuild +++ b/sci-biology/bamtools/bamtools-2.4.0.ebuild @@ -15,6 +15,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="static-libs" +# seems jsconcpp header filenames were prefixed 'json_' and the bundled version is about 0.10 DEPEND=" >=dev-libs/jsoncpp-0.5.0-r1 <dev-libs/jsoncpp-1 diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest new file mode 100644 index 000000000..532e6e077 --- /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-0.7.0_alpha.ebuild b/sci-biology/bfast/bfast-0.7.0_alpha.ebuild new file mode 100644 index 000000000..606057d6c --- /dev/null +++ b/sci-biology/bfast/bfast-0.7.0_alpha.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Blat-like Fast Accurate Search Tool (short read mapper)" +HOMEPAGE="https://sourceforge.net/projects/bfast" +SRC_URI="https://sourceforge.net/projects/bfast/files/bfast/0.7.0/bfast-0.7.0a.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl" + +S="${WORKDIR}"/bfast-0.7.0a diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/bfast/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/cap3-bin/cap3-bin-20071015.ebuild b/sci-biology/cap3-bin/cap3-bin-20071015.ebuild index 987b0e04f..7e53b9cfa 100644 --- a/sci-biology/cap3-bin/cap3-bin-20071015.ebuild +++ b/sci-biology/cap3-bin/cap3-bin-20071015.ebuild @@ -22,9 +22,9 @@ SRC_URI=" x86? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.tar ) amd64? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.tar )" -LICENSE="Artistic" +LICENSE="" # only for academic use SLOT="0" -KEYWORDS="~x86 ~amd64" +KEYWORDS="" IUSE="" S="${WORKDIR}/CAP3" diff --git a/sci-biology/cap3-bin/cap3-bin-20150210.ebuild b/sci-biology/cap3-bin/cap3-bin-20150210.ebuild index 72f7bca0b..40d88b617 100644 --- a/sci-biology/cap3-bin/cap3-bin-20150210.ebuild +++ b/sci-biology/cap3-bin/cap3-bin-20150210.ebuild @@ -19,9 +19,9 @@ SRC_URI=" x86? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.tar ) amd64? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar )" -LICENSE="Artistic" +LICENSE="" # only for academic use SLOT="0" -KEYWORDS="~x86 ~amd64" +KEYWORDS="" IUSE="" S="${WORKDIR}/CAP3" diff --git a/sci-biology/edena/edena-3.131028.ebuild b/sci-biology/edena/edena-3.131028.ebuild index 408b8757a..bdba5335e 100644 --- a/sci-biology/edena/edena-3.131028.ebuild +++ b/sci-biology/edena/edena-3.131028.ebuild @@ -6,7 +6,7 @@ EAPI=5 inherit toolchain-funcs -DESCRIPTION="De novo short read assembler" +DESCRIPTION="De novo short read OLC assembler (overlap-layout-consensus)" HOMEPAGE="http://www.genomic.ch/edena.php" SRC_URI="http://www.genomic.ch/edena/EdenaV"${PV}".tar.gz" diff --git a/sci-biology/gemini/gemini-9999.ebuild b/sci-biology/gemini/gemini-9999.ebuild new file mode 100644 index 000000000..90cdeaf30 --- /dev/null +++ b/sci-biology/gemini/gemini-9999.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit git-r3 distutils-r1 + +DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics" +HOMEPAGE="https://github.com/arq5x/gemini + http://gemini.readthedocs.org/en/latest" +EGIT_REPO_URI="https://github.com/arq5x/gemini.git" + +LICENSE="MIT" # see note below! +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +# GEMINI includes CADD scores (PMID: 24487276) for annotating variants. +# +# CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of +# Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) +# but are freely available for all academic, non-commercial applications. +# For commercial licensing information contact Jennifer McCullar diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/gemini/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/iCORN2/Manifest b/sci-biology/iCORN2/Manifest new file mode 100644 index 000000000..cfc925fa1 --- /dev/null +++ b/sci-biology/iCORN2/Manifest @@ -0,0 +1,2 @@ +DIST iCORN2_manual.html 6544 SHA256 db4b3accc794e4129a62d5113afaf920b62a5b9721569b28ee454f2766e32d99 SHA512 88899b09b331f8c68e9d6a5c938a6bdbda2df2f7993dd1786a96de463d1aa9e15419bc459a393e083e494bace50b48dd79ecb290c7910669151114ec8411b2a1 WHIRLPOOL 148169f2bc39d0b17898638d0f2a014266e7dab03999edc539cbb077398f90e46fc3a3a2ebee280cce60543150e1d45455742b8569e2b3e84f0e3ee1334b273e +DIST icorn2.V0.95.tgz 16295625 SHA256 fa3014ab249e542e80c3b5a9b0d14d0448b5467f02a3de14fc207779b5380c1d SHA512 397ceae5828e876eb93d2f3ed2e101929266228cf46624f954e0cc29f2df68650c4d443fc7f915fc9f7980b57b4af4305de307a0025b477aa2e2e5e28e2f2aa4 WHIRLPOOL ba9f4bb1b77a0ea4043776688ee1b4ffb08264ed6a6579bb6e92297e266d16b98829da16dd9891201c001d59b77327c517fcc3c938fb88d884524a2c7a79eb83 diff --git a/sci-biology/iCORN2/iCORN2-0.95.ebuild b/sci-biology/iCORN2/iCORN2-0.95.ebuild new file mode 100644 index 000000000..61613a44f --- /dev/null +++ b/sci-biology/iCORN2/iCORN2-0.95.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Iteratively map reads to a reference, fix mismatches and indels with GATK/picard" +HOMEPAGE="http://icorn.sourceforge.net/ + http://sourceforge.net/projects/icorn" +SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/ICORN2/icorn2.V${PV}.tgz + http://icorn.sourceforge.net/manual.html -> ${PN}_manual.html" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + sci-biology/snpomatic + || ( sci-biology/smalt sci-biology/smalt-bin ) + sci-biology/samtools:= + sci-biology/gatk + sci-biology/picard" +RDEPEND="${DEPEND} + dev-lang/perl + app-shells/tcsh" + +S="${WORKDIR}"/ICORN2 + +src_unpack(){ + default + # The bundled files GenomeAnalysisTK.jar from GATK + # contains bundled MarkDuplicates.jar from picard + # both .jar files were supposed to be in $ICORN2_HOME + rm -f *~ smalt || die +} + +src_prepare(){ + sed -e "s#java -jar \$ICORN2_HOME#java -jar /usr/share/${PN}/lib#" -i *.sh || die +} + +# the tarball is a terrible mess +src_install(){ + dobin *.pl *.sh + insinto /usr/share/"${PN}"/lib + doins GenomeAnalysisTK.jar MarkDuplicates.jar + insinto /usr/share/"${PN}"/LSF + doins LSF/* + dodoc README.txt + newdoc "${DISTDIR}"/"${PN}"_manual.html manual.html +} + +# http://icorn.sourceforge.net/documentation.html +# Define the shell variable ICORN_HOME, PILEUP_HOME and SNPOMATIC_HOME +pkg_postinst(){ + einfo "Ideally install Artemis ACT viewer or gap4 from staden package" +} diff --git a/sci-biology/iCORN2/metadata.xml b/sci-biology/iCORN2/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/iCORN2/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/megahit/megahit-9999.ebuild b/sci-biology/megahit/megahit-9999.ebuild new file mode 100644 index 000000000..def7fd6e0 --- /dev/null +++ b/sci-biology/megahit/megahit-9999.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 toolchain-funcs + +DESCRIPTION="Metagenome assembler using succinct de Bruijn graph approach with CUDA" +HOMEPAGE="https://github.com/voutcn/megahit + http://bioinformatics.oxfordjournals.org/content/31/10/1674.abstract" +EGIT_REPO_URI="https://github.com/voutcn/megahit.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="+openmp" + +DEPEND="" +RDEPEND="${DEPEND} + sys-libs/zlib" +# >=gcc-4.4 + +# use make use_gpu=1 to compile it and turn on --use-gpu to activate GPU acceleration when running megahit + +src_prepare(){ + default + sed -e "s#^CXXFLAGS = -g -O2#CXXFLAGS = ${CFLAGS}#" -i Makefile || die +} + +src_install(){ + dobin megahit megahit_toolkit megahit_sdbg_build megahit_asm_core + dodoc README.md +} diff --git a/sci-biology/megahit/metadata.xml b/sci-biology/megahit/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/megahit/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/oases/Manifest b/sci-biology/oases/Manifest new file mode 100644 index 000000000..27bb408c0 --- /dev/null +++ b/sci-biology/oases/Manifest @@ -0,0 +1,2 @@ +DIST OasesManual.pdf 113886 SHA256 e894e68ba5aaffa8cdcfcd56ed7411a352dae36e49e61d71c92408d9c57532b9 SHA512 c710a62cd1982060f723918f5f4de91adff12870d1682d0729035a3588ed37d26898c399c07b1b81b4b399c7ea1a14509784a6dbb9de6004bcadf6677cd5859f WHIRLPOOL b1146f6d0390ee6f03b08f1bd5df4ed6eb667d1d81431a16f3b2e9f8511a77a9187ada34b618903d97951faa55e1f0c687eca87058d78b3b0f02148f711171da +DIST oases_0.2.08.tgz 92037 SHA256 a90d469bd19d355edf6193dcf321f77216389d2831a849d4c151c1c0c771ab36 SHA512 e9a73a9227ce13995fcac7f456534a650099d8160d48d2d9831f3f05e482353c29dd76bbc74b0b451154eb5061ddb473649d21442941360f0e8c7623f6fe586c WHIRLPOOL dbb832c02b38a97b5a99134f8995ed47393900459d2fb6e2895fe823fe211d7d450800aa80d5d37ed2ff9b26641216b6ccb82c3faa5bea068adac935ddd33856 diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch new file mode 100644 index 000000000..58652b00e --- /dev/null +++ b/sci-biology/oases/files/Makefile.patch @@ -0,0 +1,15 @@ +--- Makefile.ori 2016-04-10 22:34:31.976222662 +0200 ++++ Makefile 2016-04-10 22:37:49.636225327 +0200 +@@ -1,8 +1,8 @@ +-CC = gcc +-CFLAGS = -Wall +-DEBUG = -g ++CC ?= gcc ++CFLAGS ?= -Wall ++DEBUG ?= -g + LIBS = -lm +-OPT = -O3 ++#OPT = -O3 + export MAXKMERLENGTH = 64 + export CATEGORIES = 2 + DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/oases/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild new file mode 100644 index 000000000..eff78420d --- /dev/null +++ b/sci-biology/oases/oases-0.2.08.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="De novo transcriptome assembler" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases" +SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz + http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf" +KEYWORDS="" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + >=sci-biology/velvet-1.2.08" + +S="${WORKDIR}"/oases_0.2.8 + +src_prepare(){ + epatch "${FILESDIR}"/Makefile.patch + sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die +} + +src_install(){ + dobin oases + dodoc README.md + dodoc "${DISTDIR}"/OasesManual.pdf +} diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild new file mode 100644 index 000000000..0c5439482 --- /dev/null +++ b/sci-biology/oases/oases-9999.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit git-r3 + +inherit eutils + +DESCRIPTION="De novo transcriptome assembler" +HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="git://github.com/dzerbino/oases.git" + SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf" + KEYWORDS="" +else + SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz + http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf" + KEYWORDS="~amd64" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + >=sci-biology/velvet-1.2.08" + +src_prepare(){ + epatch "${FILESDIR}"/Makefile.patch +} + +src_install(){ + dobin oases + dodoc README.md + dodoc "${DISTDIR}"/OasesManual.pdf +} diff --git a/sci-biology/prinseq-lite/Manifest b/sci-biology/prinseq-lite/Manifest new file mode 100644 index 000000000..2565d2a25 --- /dev/null +++ b/sci-biology/prinseq-lite/Manifest @@ -0,0 +1 @@ +DIST prinseq-lite-0.20.4.tar.gz 494859 SHA256 9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f SHA512 f0f920de72e52cf94e22a12631e9a90fc926ceba93139d29772f6e0f60737a96b38af56adfc38f242d18d360bcd0ac4fadaa444414d17601eb281baab4b0e9b2 WHIRLPOOL cfbdecc8f0fe7f63a27178e119933781295765c503f4691fed438b059acfcb7f84a0e8d1aff611266f6adde28bd06e3acd37f2b064a4fa1e94e636484e4d6356 diff --git a/sci-biology/prinseq-lite/metadata.xml b/sci-biology/prinseq-lite/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/prinseq-lite/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild b/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild new file mode 100644 index 000000000..b7ae2fb76 --- /dev/null +++ b/sci-biology/prinseq-lite/prinseq-lite-0.20.4.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +DESCRIPTION="Describe, trim, reformat and convert to or form FASTA/FASTQ files" +HOMEPAGE="http://prinseq.sourceforge.net/" +SRC_URI="https://sourceforge.net/projects/prinseq/files/standalone/${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + virtual/perl-Getopt-Long + virtual/perl-File-Temp + dev-perl/Digest-MD5-File" +# Cwd +# Pod::Usage +# Fcntl qw(:flock SEEK_END) +# List::Util qw(sum min max) + +# prinseq-graphs.pl needs in addition +# https://sourceforge.net/projects/prinseq/files/README.txt +# JSON +# Cairo +# Statistics::PCA +# perl-core/MIME-Base64 + +src_install(){ + dobin *.pl + dodoc README +} diff --git a/sci-biology/pysamstats/Manifest b/sci-biology/pysamstats/Manifest new file mode 100644 index 000000000..e1d047535 --- /dev/null +++ b/sci-biology/pysamstats/Manifest @@ -0,0 +1 @@ +DIST pysamstats-0.24.2.tar.gz 269977 SHA256 abd484742977386c9df4f936c461e455d5dbe3e8a20c89353f2a4dd366eb370f SHA512 a22a929d2f4d762256563e270c781a37bfe7e7f0aa3ad263d4f0c82d09003ae644cce658d02480e8b6d6506898ef062a5a7ad1612f2bb6819fcb6fe02b00bcfe WHIRLPOOL aac9dce3d6388c46d691fc42727bc37c22e85d1b1528607580b0612c387d8eff1fd0be9e5b5fb886c6318c13f24d9b3e28cdaa9b95c887a4d872d376adef22f1 diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/pysamstats/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild new file mode 100644 index 000000000..39c5fe493 --- /dev/null +++ b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_4 ) + +inherit distutils-r1 + +DESCRIPTION="Calculate statistics against genome positions from a SAM, BAM or CRAM file" +HOMEPAGE="https://github.com/alimanfoo/pysamstats + https://pypi.python.org/pypi/pysamstats" +SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="dev-python/cython + >=sci-biology/pysam-0.8.4" +RDEPEND="${DEPEND}" diff --git a/sci-biology/reaper/Manifest b/sci-biology/reaper/Manifest new file mode 100644 index 000000000..ef6c1d644 --- /dev/null +++ b/sci-biology/reaper/Manifest @@ -0,0 +1 @@ +DIST reaper-15-348.tgz 143739 SHA256 1b25a9bbe97963ed08ee724d406145928de29f6d7a5bd4d5a5e1096f96f04fda SHA512 ac8186af07da26d5835e70dab878884daa4744ff3c5a13f5d8ec432881d579ca9b3585c89d232158d2b95af2533c9f79cb5185ab67819236d00d1cf9f576dbca WHIRLPOOL 79b6ab98e9e02b6ef01c35596fd68028f2342f81a319eecf5da5041fbe23421c8f571512aade6764b1f7626045f04357ff4889d60f57b2169e6a5cc30ab1bec8 diff --git a/sci-biology/reaper/metadata.xml b/sci-biology/reaper/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/reaper/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/reaper/reaper-15348.ebuild b/sci-biology/reaper/reaper-15348.ebuild new file mode 100644 index 000000000..854668d7c --- /dev/null +++ b/sci-biology/reaper/reaper-15348.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +MY_PV="15-348" + +DESCRIPTION="Demultiplex, trim 3'-adapter/polyA and filter short read DNA sequences" +HOMEPAGE="http://www.ebi.ac.uk/~stijn/reaper" +SRC_URI="http://www.ebi.ac.uk/~stijn/reaper/src/${PN}-${MY_PV}.tgz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sys-libs/zlib" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/"${PN}"-"${MY_PV}"/src + +src_prepare(){ + sed -e 's/ -O3 / ${CFLAGS} /' -i Makefile || die +} + +src_compile(){ + emake +} + +src_install(){ + dobin reaper tally minion swan + dodoc ../doc/*.html +} diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild index 18e3e697e..7a64c7e70 100644 --- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild +++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2016 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -22,8 +22,8 @@ RDEPEND=" sci-biology/rmblast >=sci-biology/trf-4.0.4 sci-biology/repeatmasker-libraries - sci-biology/phrap" -# dev-perl/Text-Soundex see bug #566740 + sci-biology/phrap + dev-perl/Text-Soundex" S="${WORKDIR}/RepeatMasker" diff --git a/sci-biology/sailfish/Manifest b/sci-biology/sailfish/Manifest index 022dbb249..7f7524587 100644 --- a/sci-biology/sailfish/Manifest +++ b/sci-biology/sailfish/Manifest @@ -1 +1 @@ -DIST sailfish-0.9.1.tar.gz 1616817 SHA256 c3e74bb95501618ba34883395ac84f07504e038200936b5c03cab269ab60f1de SHA512 3765ddb7ba64d34757cb71e0a7255759f7c6e53ee1d45ac744ed12f98f9025e9a05d9b49a681c6e90b265d2e08b6591444b575d0933b2737d01f417602f5010e WHIRLPOOL 7614e9d6bb72718ee63648ef698484b378d0945f2da44dc560f0a5f5bea5336dfe358fbd801e9254cbc2d4fdf0bbd3a4ea82adae4e90e3cdcda26d93295a381d +DIST sailfish-0.9.2.tar.gz 1617759 SHA256 4872c5241864ae12a3aa5e519cf6d2d38d0e510bfcfd420c8d05249f7ee83f82 SHA512 3bf62810c62f9284246f1095fb6f0e042ef9883867c3040d51e80e6370f40b286290f7d5620e2667e6301022777948edc4fdb7693b4fb1e31843f2d3c676f8a6 WHIRLPOOL c3d425551dd4e5cd5724572df7b3e2b7a6e1f90c26aa7fc3ff17dd181e21c4d1cb9e9c38870222eb9805ce9b6f11372799c39cb78ba85bf81607bc580262b511 diff --git a/sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch index 7ac3d0882..7ac3d0882 100644 --- a/sci-biology/sailfish/files/sailfish-0.9.1-no-boost-static.patch +++ b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch diff --git a/sci-biology/sailfish/sailfish-0.9.1.ebuild b/sci-biology/sailfish/sailfish-0.9.2.ebuild index 8a1b1c087..6350ef6a3 100644 --- a/sci-biology/sailfish/sailfish-0.9.1.ebuild +++ b/sci-biology/sailfish/sailfish-0.9.2.ebuild @@ -10,17 +10,27 @@ DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/" SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" -LICENSE="GPL-3" +LICENSE="GPL-3+" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -PATCHES=( "${FILESDIR}"/${PN}-0.9.1-no-boost-static.patch ) +PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch ) DEPEND="dev-libs/boost:0 dev-libs/jemalloc dev-cpp/tbb" RDEPEND="${DEPEND}" +# a C++-11 compliant compiler is needs, aka >=gcc-4.7 + +# TODO: disable +# [ 7%] Performing download step (verify and extract) for 'libdivsufsort' +#i +# contains bundled RapMap +# contains bundled libdivsufsort-master +# contains bundled libgff +# contains bundled jellyfish-2.2.3 +# contains bundled sparsehash-sparsehash-2.0.2 src_install() { cmake-utils_src_install diff --git a/sci-biology/sga/sga-9999.ebuild b/sci-biology/sga/sga-9999.ebuild index a2d4897ee..e21c072ca 100644 --- a/sci-biology/sga/sga-9999.ebuild +++ b/sci-biology/sga/sga-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2016 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -6,7 +6,7 @@ EAPI=5 inherit eutils git-r3 -DESCRIPTION="String Graph Assembler for short-read assemblies" +DESCRIPTION="String Graph OLC Assembler for short reads (overlap-layout-consensus)" HOMEPAGE="https://github.com/jts/sga" EGIT_REPO_URI="git://github.com/jts/sga" @@ -18,11 +18,12 @@ IUSE="jemalloc python" DEPEND="dev-cpp/sparsehash sci-biology/bamtools sys-libs/zlib - jemalloc? ( dev-libs/jemalloc ) + jemalloc? ( dev-libs/jemalloc )" +RDEPEND="${DEPEND} python? ( sci-biology/pysam sci-biology/ruffus )" -RDEPEND="${DEPEND}" +# http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/install/sga.htm src_configure(){ cd src || die ./autogen.sh || die diff --git a/sci-biology/smalt/smalt-0.7.6.ebuild b/sci-biology/smalt/smalt-0.7.6.ebuild index 25d01048e..9fd8f0ec1 100644 --- a/sci-biology/smalt/smalt-0.7.6.ebuild +++ b/sci-biology/smalt/smalt-0.7.6.ebuild @@ -13,7 +13,7 @@ SRC_URI="http://sourceforge.net/projects/${PN}/files/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" IUSE="" S="${WORKDIR}"/${MY_P} @@ -24,6 +24,6 @@ src_install(){ doins misc/*.py dodoc README NEWS } -# is the tarball with source code lacking the manual? +# is the tarball with source code lacking the manual? Upstream contacted. # dodoc NEWS ${MY_PN}_manual.pdf # doman ${MY_PN}.1 diff --git a/sci-biology/snpomatic/metadata.xml b/sci-biology/snpomatic/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/snpomatic/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snpomatic/snpomatic-9999.ebuild b/sci-biology/snpomatic/snpomatic-9999.ebuild new file mode 100644 index 000000000..1d134f1d2 --- /dev/null +++ b/sci-biology/snpomatic/snpomatic-9999.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit git-r3 + +DESCRIPTION="Stringent short-read aligner supporting filters and various output formats" +HOMEPAGE="https://github.com/magnusmanske/snpomatic" +# http://snpomatic.sourceforge.net/snpomatic_manual.pdf +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/magnusmanske/snpomatic.git" + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e 's/^CXX=/#CXX=/;s/^CXXFLAGS=/#CXXFLAGS=/' -i Makefile || die +} + +src_install(){ + dobin findknownsnps + dodoc doc/Manual.doc +} diff --git a/sci-biology/somatic-sniper/Manifest b/sci-biology/somatic-sniper/Manifest new file mode 100644 index 000000000..a7055a373 --- /dev/null +++ b/sci-biology/somatic-sniper/Manifest @@ -0,0 +1 @@ +DIST somatic-sniper-1.0.4.tar.gz 1985061 SHA256 7f82e6e0bf2831b87d558617e749287241e654e3d1b068fd6aa2892b25763db2 SHA512 ce6093ba5d853f6ed597cf7c707a52dce7121c7b0b5f6c18ecf3c9850ae41c1df062465390085411669f528c2a85c106a8cb60c0bc39b8d3e3a6ebd644800445 WHIRLPOOL 8204644cfa657b291938aaaa2df50962de5ad534767893e41e01da43a51b42cc7bc5aea883a72ae7e2e22034069df9a63b7a18fec49fa8e41b0d86e632fd81e6 diff --git a/sci-biology/somatic-sniper/metadata.xml b/sci-biology/somatic-sniper/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/somatic-sniper/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild new file mode 100644 index 000000000..e4629b62c --- /dev/null +++ b/sci-biology/somatic-sniper/somatic-sniper-1.0.4.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Compare BAM files from normal and tumor samples and report somatic SNPs" +HOMEPAGE="http://gmt.genome.wustl.edu" +SRC_URI="https://github.com/genome/somatic-sniper/archive/v${PV}.tar.gz -> ${P}.tar.gz" +# git clone git://github.com/genome/somatic-sniper.git + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + sys-libs/zlib + sys-libs/ncurses:* + sci-biology/samtools:0.1-legacy" +RDEPEND="${DEPEND}" + +# contains bundled copy of samtools-0.1.6 but links using a static version +# cd /var/tmp/portage/sci-biology/somatic-sniper-1.0.4/work/somatic-sniper-1.0.4_build/build/src/exe/bam-somaticsniper && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-somaticsniper.dir/link.txt --verbose=1 +# /usr/bin/x86_64-pc-linux-gnu-gcc -Wall -Wl,-O1 -Wl,--as-needed CMakeFiles/bam-somaticsniper.dir/main.c.o -o ../../../../bin/bam-somaticsniper -rdynamic -lpthread -lpthread ../../lib/sniper/libsniper.a -lpthread -lm ../../../../vendor/samtools/libbam.a -lz + +# contains build-common from git tree diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest index c6e18e680..65fc9cd9f 100644 --- a/sci-biology/trinityrnaseq/Manifest +++ b/sci-biology/trinityrnaseq/Manifest @@ -1,2 +1,3 @@ DIST trinityrnaseq-2.0.6.tar.gz 158619106 SHA256 e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1 SHA512 459461db38e42d0b77b9cb84b1ecc4ccb03bbe0fe6e970915d5df58e8c98368a07fab7a157679b0d4247b729b49966b1f3927abee11059e5e3a3406e8e598d45 WHIRLPOOL 040926ab4d1a157c340cf5886bc4cf2846e8756d84c39a1f8673b5ba59dd57b39f075b0fc915deff05dd50655b0e8f0c1b8fe3b6ceb0e0a4b2aec618bef58470 DIST trinityrnaseq-2.1.1.tar.gz 137541420 SHA256 012ccb42e1eab8a5b14c4e78becf3e7e69964d76c17fcca8110db6ffe63d3e0b SHA512 36b67211902871c6dbba31a074c4e92d2e925c57fe54bf59418874282e283693d2d9b4e14333385a7adcef3edbf928bc1001df105b56412841662c45a9a74f3f WHIRLPOOL 73869a3f2dbc72011723429d6ac3acb3fde8c7ccfe4122510afbea9fdfc732a457c8f5d16573190448c4e0d2c5dcc437e2f9cfe96f4239368c95b2da79fd52bd +DIST trinityrnaseq-2.2.0.tar.gz 174159736 SHA256 f34603e56ac76a81447dd230b31248d5890ecffee8ef264104d4f1fa7fe46c9e SHA512 87ba299df990d066ae6aa8a870c3a27647da0d78cf0a48c5084967865d4e278ce383b3f6e54541d4626654f0638f12c739aaed04ed770bc99ed84b94c2e6e5c3 WHIRLPOOL 027ccd958288991c4871cfa6b370d14bc2bf586bc1ffc3247795aaf305368caac373343682f11cde6d72a65422c95718b89fee65ac77c04a21c7c3aaa4c8112d diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild index 0e93c19c8..88c104fc4 100644 --- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild @@ -23,7 +23,7 @@ DEPEND="" RDEPEND="${DEPEND} sci-biology/parafly =sci-biology/jellyfish-2.1.4 - sci-biology/samtools + sci-biology/samtools:0.1-legacy >=sci-biology/GAL-0.2.1 dev-perl/IO-All" # ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed @@ -44,7 +44,7 @@ src_install(){ dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md # insinto /usr/share/"${PN}"/util - rm -f trinity-plugins/GAL_0.2.1 util/fasta_tool + rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool doins -r util/* # dobin Inchworm/bin/* diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild index b383de4c2..4a51bdfec 100644 --- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild @@ -23,7 +23,7 @@ RDEPEND="${DEPEND} sci-biology/parafly =sci-biology/jellyfish-2.1.4 >=sci-libs/htslib-1.2.1 - <=sci-biology/samtools-1.1 + sci-biology/samtools:0.1-legacy >=sci-biology/trimmomatic-0.32 >=sci-biology/GAL-0.2.1 dev-perl/IO-All" @@ -53,7 +53,7 @@ src_install(){ dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md # insinto /usr/share/"${PN}"/util - rm -f trinity-plugins/GAL_0.2.1 util/fasta_tool + rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool doins -r util/* # dobin Inchworm/bin/* diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild new file mode 100644 index 000000000..4a51bdfec --- /dev/null +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2016 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 + +# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ... + +DESCRIPTION="Transcriptome assembler for RNA-seq reads" +HOMEPAGE="http://trinityrnaseq.github.io/" +SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/parafly + =sci-biology/jellyfish-2.1.4 + >=sci-libs/htslib-1.2.1 + sci-biology/samtools:0.1-legacy + >=sci-biology/trimmomatic-0.32 + >=sci-biology/GAL-0.2.1 + dev-perl/IO-All" +# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed +# version of bundled jellyfish is 2.1.4 +# version of bundled samtools is 0.1.19 +# version of bundled htslib is 1.2.1 +# version of bundled GAL is 0.2.1 +# version of bundled trimmomatic is 0.32 + +# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases + +src_prepare(){ + epatch "${FILESDIR}"/disable_some_plugins.patch +} + +#src_compile(){ +# emake all +# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly +#} + +src_install(){ + perl_set_version + dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool + # should become a new package depending on dev-perl/IO-All + dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool + dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md + # + insinto /usr/share/"${PN}"/util + rm -rf trinity-plugins/GAL_0.2.1 util/fasta_tool + doins -r util/* + # + dobin Inchworm/bin/* + cd Chrysalis || die + dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl + cd "${S}" || die + insinto "${VENDOR_LIB}/${PN}" + doins util/misc/PerlLib/*.pm PerlLib/*.pm + insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib + doins PerlLib/KmerGraphLib/*.pm + insinto "${VENDOR_LIB}/${PN}"/CDNA + doins PerlLib/CDNA/*.pm + insinto "${VENDOR_LIB}/${PN}"/HPC + doins PerlLib/HPC/*.pm + insinto "${VENDOR_LIB}/${PN}"/Simulate + doins PerlLib/Simulate/*.pm + insinto "${VENDOR_LIB}/${PN}"/CanvasXpress + doins PerlLib/CanvasXpress/*.pm + chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}" +} diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild index e1b558561..35f7f5870 100644 --- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild +++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2016 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -10,7 +10,7 @@ inherit eutils python-single-r1 toolchain-funcs MY_PV="${PV/_}" # convert from _rc2 to rc2 -DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler (Celera Assembler and CABOG)" +DESCRIPTION="De novo whole-genome shotgun DNA sequence OLC assembler (Celera Assembler, CABOG)" HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2" diff --git a/sci-libs/pmx/pmx-9999.ebuild b/sci-libs/pmx/pmx-9999.ebuild index 3ecdda817..e2e80f99c 100644 --- a/sci-libs/pmx/pmx-9999.ebuild +++ b/sci-libs/pmx/pmx-9999.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2016 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI=5 +EAPI=6 PYTHON_COMPAT=( python2_7 ) inherit eutils distutils-r1 git-r3 DESCRIPTION="Python library to read PDB, GRO or Gromacs XTC files" -HOMEPAGE="http://code.google.com/p/pmx" -EGIT_REPO_URI="https://code.google.com/p/${PN}.git" +HOMEPAGE="https://github.com/dseeliger/pmx" +EGIT_REPO_URI="https://github.com/dseeliger/${PN}.git" LICENSE="LGPL-3" SLOT="0" |