diff options
35 files changed, 601 insertions, 53 deletions
diff --git a/sci-biology/MAKER/MAKER-9999.ebuild b/sci-biology/MAKER/MAKER-9999.ebuild deleted file mode 100644 index fa4733e5a..000000000 --- a/sci-biology/MAKER/MAKER-9999.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota" -HOMEPAGE="http://www.yandell-lab.org/software/maker.html" -SRC_URI="" - -RESTRICT="fetch" - -# for academia: GPL-v2 or Artistic-2 -# for commercial: ask -LICENSE="|| ( GPL-2 Artistic-2 )" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" diff --git a/sci-biology/abacas/ChangeLog b/sci-biology/abacas/ChangeLog new file mode 100644 index 000000000..9c7e05d33 --- /dev/null +++ b/sci-biology/abacas/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/abacas +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> abacas-1.3.1.ebuild: + sci-biology/abacas: clarify description + +*abacas-1.3.1 (31 Mar 2015) + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +abacas-1.3.1.ebuild, +metadata.xml: + sci-biology/abacas: new package diff --git a/sci-biology/abacas/Manifest b/sci-biology/abacas/Manifest new file mode 100644 index 000000000..f95aff4f7 --- /dev/null +++ b/sci-biology/abacas/Manifest @@ -0,0 +1 @@ +DIST abacas.1.3.1.pl 64936 SHA256 0afee209a4f879987b320e2f882bc0eab540a7a712a81a5f01b9795d2749310d SHA512 5b60f85439ab751e4b43eba827dc8b4a8ad7d3acbbdc1f13a0f83e227cf8eb4d94dd5a32c4e6e37aa4e263758973ada5ab8e476685c56b6856c06218b547f76f WHIRLPOOL 5b99ee3aab66f06ccd74f4393dff42f1525a8b2c2c7679dfde180bb2262dd4c9d2d3a45585ed39d10f38c6f53d3b3089be9c65ee1b22d90938fcc09c8da14500 diff --git a/sci-biology/abacas/abacas-1.3.1.ebuild b/sci-biology/abacas/abacas-1.3.1.ebuild new file mode 100644 index 000000000..e0cdf72ab --- /dev/null +++ b/sci-biology/abacas/abacas-1.3.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Order and orientate DNA contigs even via 6-frame protein alignments, design primers for gap closing" +HOMEPAGE="http://abacas.sourceforge.net" +SRC_URI="http://downloads.sourceforge.net/project/abacas/abacas.1.3.1.pl" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl + sci-biology/mummer" + +S="${WORKDIR}" + +src_prepare(){ + cp -p "${DISTDIR}"/abacas.1.3.1.pl abacas.pl || die + sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' -i abacas.pl || die +} +src_install(){ + dobin abacas.pl +} + +pkg_postinst(){ + einfo "To view the results use Artemis ACT (sci-biology/artemis)" +} diff --git a/sci-biology/MAKER/metadata.xml b/sci-biology/abacas/metadata.xml index 2bc893037..2bc893037 100644 --- a/sci-biology/MAKER/metadata.xml +++ b/sci-biology/abacas/metadata.xml diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog index 7d1df6d02..9bdce778d 100644 --- a/sci-biology/amos/ChangeLog +++ b/sci-biology/amos/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/amos -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*amos-3.1.0-r2 (31 Mar 2015) + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +amos-3.1.0-r2.ebuild, +files/amos-3.1.0-gcc-4.7.patch, + +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, amos-9999.ebuild: + sci-biology/amos: fix installation process and dependencies + 29 Dec 2013; Justin Lecher <jlec@gentoo.org> -amos-3.1.0-r1.ebuild, amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch, -files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest new file mode 100644 index 000000000..27ad50ff2 --- /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-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild new file mode 100644 index 000000000..b81479179 --- /dev/null +++ b/sci-biology/amos/amos-3.1.0-r2.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0-r1.ebuild,v 1.1 2013/12/29 00:24:16 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_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=" + dev-libs/boost + qt4? ( dev-qt/qtcore:4 )" +RDEPEND="${DEPEND} + dev-lang/perl + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/blat + sci-biology/mummer" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch +} + +# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/DotLib.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/AsmLib.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAreader.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosFoundation.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/Foundation.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosLib.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTArecord.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/ParseFasta.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/xfig.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAwriter.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAgrammar.pm +# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAiterator.pm + +# --with-jellyfish location of Jellyfish headers + +src_install() { + default + python_replicate_script "${ED}"/usr/bin/goBambus2 + # bambus needs TIGR::FASTAreader.pm and others + # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it + mkdir -p "${D}"/usr/share/"${PN}"/perl/AMOS || die + mv "${D}"/usr/lib64/AMOS/*.pm "${D}"/usr/share/"${PN}"/perl/AMOS || die + mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die + mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die + echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}" + doenvd "${S}/99${PN}" || die + # move also /usr/lib64/AMOS/AMOS.py to /usr/bin + mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die +} diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild index baecc2f9e..610c3d64c 100644 --- a/sci-biology/amos/amos-9999.ebuild +++ b/sci-biology/amos/amos-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -16,11 +16,32 @@ EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos" LICENSE="Artistic" SLOT="0" KEYWORDS="" -IUSE="" +IUSE="mpi qt4" DEPEND=" + mpi? ( virtual/mpi ) dev-libs/boost - dev-qt/qtcore:4" + qt4? ( dev-qt/qtcore:4 ) + sci-biology/blat + sci-biology/jellyfish" RDEPEND="${DEPEND} dev-perl/DBI + dev-perl/Statistics-Descriptive sci-biology/mummer" + +# --with-jellyfish location of Jellyfish headers + +src_install() { + default + python_replicate_script "${ED}"/usr/bin/goBambus2 + # bambus needs TIGR::FASTAreader.pm and others + # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it + mkdir -p "${D}/usr/share/${PN}/perl/AMOS" || die + mv "${D}"/usr/lib64/AMOS/*.pm "${D}/usr/share/${PN}/perl/AMOS" || die + mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die + mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die + echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}" + doenvd "${S}/99${PN}" || die + # move also /usr/lib64/AMOS/AMOS.py to /usr/bin + mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die +} 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 000000000..de2a41184 --- /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 000000000..97a8f59d0 --- /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/augustus/ChangeLog b/sci-biology/augustus/ChangeLog new file mode 100644 index 000000000..ee07f1637 --- /dev/null +++ b/sci-biology/augustus/ChangeLog @@ -0,0 +1,78 @@ +# ChangeLog for sci-biology/augustus +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $ + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 31 Jan 2013; Justin Lecher <jlec@gentoo.org> -augustus-2.3.1.ebuild, + -augustus-2.4.ebuild, -augustus-2.5.ebuild, metadata.xml: + Drop old, fixes multiple QA issues, #454822 + + 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for x86, wrt bug #454842 + + 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for amd64, wrt bug #454842 + +*augustus-2.5.5 (23 Jun 2011) + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> augustus-2.3.1.ebuild, + augustus-2.4.ebuild, augustus-2.5.ebuild, +augustus-2.5.5.ebuild, + +files/augustus-2.5.5-sane-build.patch: + Version Bump, respect LDFLAGS, #337655 + + 09 Mar 2011; Markos Chandras <hwoarang@gentoo.org> augustus-2.4.ebuild: + Stable on amd64 wrt bug #353573 + + 09 Mar 2011; Thomas Kahle <tomka@gentoo.org> augustus-2.4.ebuild: + x86 stable per bug 353573 + + 04 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + augustus-2.5.ebuild: + Respect LDFLAGS + +*augustus-2.5 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + +augustus-2.5.ebuild: + Version bump, update SRC_URI + +*augustus-2.4 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -augustus-2.1.ebuild, + -files/augustus-2.1-glibc-2.10.patch, +augustus-2.4.ebuild: + Version bump, drop old + + 09 Feb 2010; Pacho Ramos <pacho@gentoo.org> augustus-2.3.1.ebuild: + amd64 stable, bug 298767 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + augustus-2.3.1.ebuild: + stable x86, bug 298767 + +*augustus-2.3.1 (16 Nov 2009) + + 16 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +augustus-2.3.1.ebuild: + Version bump + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> augustus-2.1.ebuild: + amd64/x86 stable, bug #290924 + + 09 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> augustus-2.1.ebuild, + +files/augustus-2.1-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #276719. + +*augustus-2.1 (19 Mar 2009) + + 19 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> + -files/augustus-2.0.3-cflags.patch, -files/augustus-2.0.3-gcc4.3.patch, + -augustus-2.0.3.ebuild, +augustus-2.1.ebuild: + Version bump + +*augustus-2.0.3 (04 Jan 2009) + + 04 Jan 2009; weaver <weaver@gentoo.org> + +files/augustus-2.0.3-cflags.patch, +files/augustus-2.0.3-gcc4.3.patch, + +metadata.xml, +augustus-2.0.3.ebuild: + Initial commit, ebuild written by me diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest new file mode 100644 index 000000000..1a68ffa25 --- /dev/null +++ b/sci-biology/augustus/Manifest @@ -0,0 +1 @@ +DIST augustus-3.0.3.tar.gz 81617475 SHA256 557364b86483c67ee11d05c074e12157ced7e4f4fe779889cd54c2c22579bf2d SHA512 8d573e800551aa8011e5663705b08a3ab4bc04acfb05041dd53738f40c8aec2ecb5794b9173a07f3ff0380413a9b6867f03cd3e7001b704eef2ebcab656452ab WHIRLPOOL d57dff333f0786b19278e971303a13d5d77c5e01d803c8e488505d6c1efa24068a0052ef5f7f9b8d1b5f9e954f0b9b64124a90acdc3896776ef23b01166920e7 diff --git a/sci-biology/augustus/augustus-3.0.3.ebuild b/sci-biology/augustus/augustus-3.0.3.ebuild new file mode 100644 index 000000000..da2db427c --- /dev/null +++ b/sci-biology/augustus/augustus-3.0.3.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.5.5.ebuild,v 1.3 2013/01/31 18:42:11 ago Exp $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://augustus.gobics.de/" +SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/${P}.tar.gz" + +LICENSE="GPL-3" +# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT +# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT +# LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +DEPEND=" + sci-libs/gsl + dev-libs/boost + sys-libs/zlib + sys-devel/flex" +RDEPEND="${DEPEND}" + +src_prepare() { + # TODO: do we need anything from the 2.5.5 patch? + # 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/metadata.xml b/sci-biology/augustus/metadata.xml new file mode 100644 index 000000000..f17a827e3 --- /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/bambus/ChangeLog b/sci-biology/bambus/ChangeLog new file mode 100644 index 000000000..9140d875d --- /dev/null +++ b/sci-biology/bambus/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/bambus +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild: + sci-biology/bambus: fix installation process and use current perl-module files + from amos package instead diff --git a/sci-biology/bambus/Manifest b/sci-biology/bambus/Manifest index 1625f9a2b..117e5e97f 100644 --- a/sci-biology/bambus/Manifest +++ b/sci-biology/bambus/Manifest @@ -1 +1,2 @@ -DIST bambus-2.33.tar.gz 504535 SHA256 bc8e3c712719bccb00357001713e56f58aac57ae452fd73148eeccff291eefdc +DIST bambus-2.33.tar.gz 504535 SHA256 bc8e3c712719bccb00357001713e56f58aac57ae452fd73148eeccff291eefdc SHA512 b31360439938bd88a19694af0addceafa658e144c2d6dcc156f7b5a3a2df0e806d55f4e4e7cd31dbbdd9464201506da61b3d0b288ba34138770d3023ab40795a WHIRLPOOL de070bc2b8972b2563446dc2f2b130310110926dc8e7e8f08477992b7f43aa5636a65ce66f21781fdb3a0751e49f5072f0080204b07d7ea866631c81b2902d62 +DIST scaffolding_MIRA_BAMBUS.pdf 181237 SHA256 1a86233ab1cfaef6b23a09267129fd3eeec0a81a4d90995d69c3c72da5cca68c SHA512 fcdf458917b09613dea2769921dee625528b08fbb92c5bc0d8b32bb0f29f6b8d163e4b0a2fdf6c338ba4a872cd29cffd7d0a7aeb8beb6c9afc76d0cc812bbc29 WHIRLPOOL 780bf5d38357377477becae03feee14c8f2603cd337716c12b9011785897830edf48a35423003b57e0bc1dc550a9921800d0ff64c49f44ca01c928bf3df36bbf diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild index 2c05ad171..71ecb4b1b 100644 --- a/sci-biology/bambus/bambus-2.33.ebuild +++ b/sci-biology/bambus/bambus-2.33.ebuild @@ -1,15 +1,17 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit eutils DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle" HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS + http://sourceforge.net/projects/amos/files/bambus http://www.tigr.org/software/bambus" -SRC_URI="http://sourceforge.net/projects/amos/files/bambus/2.33/bambus-2.33.tar.gz" +SRC_URI="http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz + http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" LICENSE="Artistic" SLOT="0" @@ -26,28 +28,32 @@ RDEPEND="${DEPEND} src_prepare() { # epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch - sed -i 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' Makefile || die - sed -i 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' doc/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/IO/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/DotLib/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/grommit/Makefile || die - sed -i 's:^CC:#CC:' Makefile || die - sed -i 's:^CXX:#CXX:' Makefile || die - sed -i 's:^LD:#LD:' Makefile || die - sed -i 's:^AR:#AR:' Makefile || die - sed -i 's:^export:#export:' Makefile || die - sed -i 's:-Wl::' src/grommit/Makefile || die - sed -i 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/ -shared -fPIC:' src/grommit/Makefile || die - sed -i 's:make all:make all DESTDIR=$(DESTDIR):' Makefile || die - sed -i 's:make install:make install DESTDIR=$(DESTDIR):' Makefile || die - sed -i 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)) -shared -fPIC:' src/grommit/Makefile || die - sed -i 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS):' src/grommit/Makefile || die - sed -i 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' src/goBambus.pl || die + sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die + sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i doc/Makefile || die + sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/IO/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/DotLib/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/grommit/Makefile || die + sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die + sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die + sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die + sed -e 's:^AR\t=:#AR=:' -i Makefile || die + sed -e 's:^export:#export:' -i Makefile || die + sed -e 's:-Wl::' -i src/grommit/Makefile || die + # sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die + sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die + sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die + sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die + sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present" - einfo "in sci-biology/tigr-foundation-libs. It sees bambus-2.33/src/TIGR_Foundation_CC/ contains" + einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains" einfo "the following 3 files getopt.cc getopt.hh getopt1.cc which were possibly copied" einfo "over from some old GNU libc and maybe could be completely dropped?" einfo "Affected would be:" @@ -59,7 +65,7 @@ src_prepare() { #sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs" cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/" epatch "${FILESDIR}"/TigrFoundation-all-patches.patch || die - sed -i "s:/export/usr/local:${D}/usr:g" Makefile || die + sed -e "s:/export/usr/local:${D}/usr:g" -i Makefile || die } src_compile() { @@ -99,6 +105,7 @@ src_install() { rmdir "${D}"/usr/doc || die dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl" + dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf } pkg_postinst(){ diff --git a/sci-biology/exonerate-gff3/ChangeLog b/sci-biology/exonerate-gff3/ChangeLog new file mode 100644 index 000000000..fc492c85e --- /dev/null +++ b/sci-biology/exonerate-gff3/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/exonerate-gff3 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*exonerate-gff3-2.2.0-r1 (30 Mar 2015) + + 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +exonerate-gff3-2.2.0-r1.ebuild, +files/exonerate-gff3-2.2.0-asneeded.patch, + +metadata.xml: + sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 + format output support + diff --git a/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild new file mode 100644 index 000000000..fd2472821 --- /dev/null +++ b/sci-biology/exonerate-gff3/exonerate-gff3-2.2.0-r1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/exonerate/exonerate-2.2.0-r1.ebuild,v 1.5 2013/01/25 16:24:50 jlec Exp $ + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils toolchain-funcs git-r3 + +DESCRIPTION="exonerate-2.2.0 with patches to add GFF3 formatted output" +HOMEPAGE="https://github.com/hotdogee/exonerate-gff3" +EGIT_REPO_URI="https://github.com/hotdogee/exonerate-gff3.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="utils test threads" + +REQUIRED_USE="test? ( utils )" + +# block with sci-biology/exonerate , maybe the best would be to change SRC_URI in sci-biology/exonerate +DEPEND=" + !sci-biology/exonerate + 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) + $(use_enable threads pthreads) + --enable-largefile + --enable-glib2 + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + doman doc/man/man1/*.1 +} diff --git a/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch new file mode 100644 index 000000000..3268055cd --- /dev/null +++ b/sci-biology/exonerate-gff3/files/exonerate-gff3-2.2.0-asneeded.patch @@ -0,0 +1,15 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- configure.in ++++ configure.in +@@ -289,7 +289,7 @@ + if test "$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-gff3/metadata.xml b/sci-biology/exonerate-gff3/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/exonerate-gff3/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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog index cf2f8f7be..d3ea5cd21 100644 --- a/sci-biology/jellyfish/ChangeLog +++ b/sci-biology/jellyfish/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + jellyfish-2.1.3.ebuild: + sci-biology/jellyfish: fix /usr/lib64/pkgconfig/jellyfish-2.0.pc + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + jellyfish-2.1.3.ebuild: + sci-biology/jellyfish: fix installation of header *.hpp files into + /usr/include/jellyfish-2.1.3/jellyfish/ broken somewhere in upstream's code + 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> jellyfish-2.1.3.ebuild: added a comment on old version diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild index 51f683c81..c217e42e2 100644 --- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild +++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild @@ -4,7 +4,7 @@ EAPI=5 -DESCRIPTION="k-mer counter withing reads for assemblies" +DESCRIPTION="k-mer counter within reads for assemblies" HOMEPAGE="http://www.genome.umd.edu/jellyfish.html" SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf" @@ -18,3 +18,11 @@ IUSE="" DEPEND="" RDEPEND="${DEPEND}" + +src_install(){ + default + sed -e 's#jellyfish-2.1.3#jellyfish#' -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die + mkdir -p "${D}/usr/include/${PN}" || die + mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die + rm -rf "${D}/usr/include/${P}" +} diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog index 93a1fa976..72b81bfd1 100644 --- a/sci-biology/kmergenie/ChangeLog +++ b/sci-biology/kmergenie/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*kmergenie-1.6971 (30 Mar 2015) + + 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +kmergenie-1.6971.ebuild, -kmergenie-1.6950.ebuild: + sci-biology/kmergenie: version bump + 18 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> kmergenie-1.6950.ebuild: install the real binary, add dependency of external python module; the DEPEND diff --git a/sci-biology/kmergenie/Manifest b/sci-biology/kmergenie/Manifest index 3fba4587a..4f45385ab 100644 --- a/sci-biology/kmergenie/Manifest +++ b/sci-biology/kmergenie/Manifest @@ -1 +1 @@ -DIST kmergenie-1.6950.tar.gz 423073 SHA256 5ca272253098886571a6044bf613e701775bd66b61e76d0260101e74c036b5da SHA512 2f12bd8cb3f374d25df278d244a546cc83f24b78e39d486ee8f1a731157c6c2b4d614c614c6bf1577e148a482c7eac5e11d3c36cdcf357ea29beb0ed4fa9e4bb WHIRLPOOL 2f1af8fda1c4d15e7e6bf3ec1bb4f342ca20455a319282987a197a1475afc73f97dc34049903328134250387b97ec56f9a9ccb59c697d4091f210821ea827119 +DIST kmergenie-1.6971.tar.gz 422649 SHA256 a0a39046321f2e8cc32ca6e3538ed827ef61d568c799610d268725cffcd16ba6 SHA512 43dad36b461444023c0f730bd8097f2481e958e58db9fbe32ce6e38414438a946d3e648ec719bda63215661457ff1d3ce805631203f2ef69e3ffb8aa2075325d WHIRLPOOL 2d113ffac7d50a68335e3fc1a444700d944d854427c2ba808d7464f80c4f49a299df496b23ec0ced71f770c7a19a6831af8a94033b55d707e6b91cbab941e4d5 diff --git a/sci-biology/kmergenie/kmergenie-1.6950.ebuild b/sci-biology/kmergenie/kmergenie-1.6971.ebuild index 46f37dabd..46f37dabd 100644 --- a/sci-biology/kmergenie/kmergenie-1.6950.ebuild +++ b/sci-biology/kmergenie/kmergenie-1.6971.ebuild diff --git a/sci-biology/MAKER/ChangeLog b/sci-biology/maker/ChangeLog index d954ed6f5..d954ed6f5 100644 --- a/sci-biology/MAKER/ChangeLog +++ b/sci-biology/maker/ChangeLog diff --git a/sci-biology/maker/Manifest b/sci-biology/maker/Manifest new file mode 100644 index 000000000..8b2a8d085 --- /dev/null +++ b/sci-biology/maker/Manifest @@ -0,0 +1 @@ +DIST maker-2.31.8.tgz 13607357 SHA256 a99c7e433638979808ea3f4bcd2b6b69f4474bd898807aba4520debd58717420 SHA512 1533888c4960a74395f4bfdd26a4f86ba33d93764b1e40094fcd2d8e7e355495464619820b0c805061f467c20d979ddf17bdb2979a7f17117c1a721032ee538d WHIRLPOOL 2df90ae76891160ed08fc3a703d3d8a982e737fa23c3f65d197bd900816588a2e8d8ec364e1122af4be289f01b5c704414487eb19ece8a8fedd9c9aac11e40e2 diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild new file mode 100644 index 000000000..6bc8ff57a --- /dev/null +++ b/sci-biology/maker/maker-2.31.8.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils perl-module + +DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota" +HOMEPAGE="http://www.yandell-lab.org/software/maker.html" +SRC_URI="maker-"${PV}".tgz" + +RESTRICT="fetch" + +# for academia: GPL-v2 or Artistic-2 +# for commercial: ask +LICENSE="|| ( GPL-2 Artistic-2 )" +SLOT="0" +KEYWORDS="" +IUSE="" + +# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/ +# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm +# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm +# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm +DEPEND="virtual/mpi + dev-perl/DBI + dev-perl/DBD-SQLite + dev-perl/File-Which + dev-perl/Bit-Vector + dev-perl/Inline-C + dev-perl/IO-All + dev-perl/libwww-perl + dev-perl/DBD-Pg + virtual/perl-Module-Build + >=sci-biology/bioperl-1.6 + sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ ) + sci-biology/snap + sci-biology/repeatmasker + sci-biology/exonerate + sci-biology/augustus" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/maker/src + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "maker-"${PV}".tgz and place it into ${DISTDIR}" +} + +src_compile(){ + perl Build.PL || die + ./Build install || die +} diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/maker/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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snap/ChangeLog b/sci-biology/snap/ChangeLog new file mode 100644 index 000000000..68ed8bc29 --- /dev/null +++ b/sci-biology/snap/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/snap +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*snap-20131129 (30 Mar 2015) + + 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +snap-20131129.ebuild: + sci-biology/snap: new package diff --git a/sci-biology/snap/Manifest b/sci-biology/snap/Manifest new file mode 100644 index 000000000..3d7ad61cf --- /dev/null +++ b/sci-biology/snap/Manifest @@ -0,0 +1 @@ +DIST snap-2013-11-29.tar.gz 703047 SHA256 e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a SHA512 162c39701d72fe6bb6e9941178593c9c0aeffb6fb197f7a456cdaea63d0beb4b2f03919f3659151250d571eeafffd4aee275224bb8cbf22ee1a48a92f4866d7a WHIRLPOOL 5207fbd779a1f53ae5b08a02811868067a4abd0052e8adea732c59af79e04bcda90270ee83e62883664c3e242dfc63561a83e9f4f8f3c12e53ecc265038f4b91 diff --git a/sci-biology/snap/metadata.xml b/sci-biology/snap/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/snap/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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snap/snap-20131129.ebuild b/sci-biology/snap/snap-20131129.ebuild new file mode 100644 index 000000000..6592102b9 --- /dev/null +++ b/sci-biology/snap/snap-20131129.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="HMM-based prokaryotic and eukaryotic gene prediction tool" +HOMEPAGE="http://korflab.ucdavis.edu/software.html" +SRC_URI="http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/snap + +src_prepare(){ + sed -e "s#CC=\"gcc.*#CC=$(tc-getCC)#" -i Zoe/Makefile || die + sed -e "s#CC=\"gcc.*#CC=$(tc-getCC)#" -i Makefile || die +} + +src_install(){ + echo "ZOE=/usr/share/snap/HMM" > 99snap || die + doenvd 99snap + insinto /usr/share/snap/HMM + doins HMM/[a-zA-Z]*.hmm + dobin snap fathom forge *.pl + dodoc 00README +} |