commit: b39edea7ff9a3cd0e7f0b5986b60fd27a46a20cd Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Sun Feb 14 17:17:02 2016 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sun Feb 14 17:17:16 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b39edea7
sci-biology/SnpEff: Bump to EAPI=6 * Clean multiverion code Package-Manager: portage-2.2.27 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/SnpEff/SnpEff-4.1e.ebuild | 48 +++++++++++++++++++---------------- sci-biology/SnpEff/metadata.xml | 2 +- 2 files changed, 27 insertions(+), 23 deletions(-) diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild index 5e9434a..7ba4236 100644 --- a/sci-biology/SnpEff/SnpEff-4.1e.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild @@ -1,51 +1,55 @@ # Copyright 1999-2016 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# $Id$ -EAPI=5 +EAPI=6 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 +SRC_URI=" + http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip + http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html" LICENSE="LGPL-3" SLOT="0" +KEYWORDS="~amd64" IUSE="" # https://github.com/pcingola/SnpEff/blob/master/README_release.txt -DEPEND=">=virtual/jre-1.7:* +DEPEND=" + >=virtual/jre-1.7:* dev-java/maven-bin:* dev-java/antlr:*" RDEPEND="${DEPEND} >=virtual/jdk-1.7:*" + S="${WORKDIR}" + #src_compile(){ # mvn || die #} src_install(){ cd .. || die - mkdir -p "${D}"/usr/share + mkdir -p "${D}"/usr/share || die # but portage does not install the .* files and subdirs, grr! - unzip "${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 "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + unzip \ + "${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 "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed \ + -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' \ + -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed \ + -e 's#$HOME/snpEff/#/usr/share/snpEff/#' \ + -i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed \ + -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' \ + -i "${ED}"/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/ diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml index 1699e58..f68a1b6 100644 --- a/sci-biology/SnpEff/metadata.xml +++ b/sci-biology/SnpEff/metadata.xml @@ -5,7 +5,7 @@ <email>mmokr...@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biol...@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer>
