commit: 10ed6d59cf94bab5ba74ce81ef0f36cdbbbb562c Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Apr 10 18:03:55 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Apr 10 18:03:55 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=10ed6d59
sci-biology/iCORN2: new package with bundled gatk and picard jar files Package-Manager: portage-2.2.28 sci-biology/iCORN2/iCORN2-0.95.ebuild | 57 +++++++++++++++++++++++++++++++++++ sci-biology/iCORN2/metadata.xml | 12 ++++++++ 2 files changed, 69 insertions(+) diff --git a/sci-biology/iCORN2/iCORN2-0.95.ebuild b/sci-biology/iCORN2/iCORN2-0.95.ebuild new file mode 100644 index 0000000..61613a4 --- /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 0000000..f68a1b6 --- /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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
