commit: 1a4dc5be8fd24487de1306cf68af5a7d507edb01 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Feb 10 13:28:39 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Feb 10 13:28:39 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a4dc5be
sci-biology/SnpEff: version bump Package-Manager: portage-2.2.26 sci-biology/SnpEff/SnpEff-4.1e.ebuild | 56 +++++++++++++++++++++++++++++++++++ sci-biology/SnpEff/metadata.xml | 9 ++++++ 2 files changed, 65 insertions(+) diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild new file mode 100644 index 0000000..5e9434a --- /dev/null +++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="Annotate SNP changes and predict their effect" +HOMEPAGE="http://snpeff.sourceforge.net"; + +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/pcingola/SnpEff.git"; + #EGIT_BRANCH="v4.1B" + KEYWORDS="" +else + SRC_URI="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip + http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html" + KEYWORDS="~amd64" + S="${WORKDIR}" +fi + +LICENSE="LGPL-3" +SLOT="0" +IUSE="" + +# https://github.com/pcingola/SnpEff/blob/master/README_release.txt +DEPEND=">=virtual/jre-1.7:* + dev-java/maven-bin:* + dev-java/antlr:*" +RDEPEND="${DEPEND} + >=virtual/jdk-1.7:*" + +#src_compile(){ +# mvn || die +#} + +src_install(){ + cd .. || die + mkdir -p "${D}"/usr/share + # but portage does not install the .* files and subdirs, grr! + unzip "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip" + sed -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed -e 's#$HOME/snpEff/#/usr/share/snpEff/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die +} + +# now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/ +# it also automagically fetches them but into /tmp/ unlike $CWD +# +# java -Xmx4g path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.75 path/to/snps.vcf +# +# It is best to just unpack the tarball locally and not use portage at all. diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/SnpEff/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>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
