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author | 2016-02-10 14:28:39 +0100 | |
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committer | 2016-02-10 14:28:39 +0100 | |
commit | 1a4dc5be8fd24487de1306cf68af5a7d507edb01 (patch) | |
tree | 6aa5ff451930c99d1a1f97ebd8aa54fd84712a56 | |
parent | sci-biology/eugene: version bump (diff) | |
download | sci-1a4dc5be8fd24487de1306cf68af5a7d507edb01.tar.gz sci-1a4dc5be8fd24487de1306cf68af5a7d507edb01.tar.bz2 sci-1a4dc5be8fd24487de1306cf68af5a7d507edb01.zip |
sci-biology/SnpEff: version bump
Package-Manager: portage-2.2.26
-rw-r--r-- | sci-biology/SnpEff/Manifest | 2 | ||||
-rw-r--r-- | sci-biology/SnpEff/SnpEff-4.1e.ebuild | 56 | ||||
-rw-r--r-- | sci-biology/SnpEff/metadata.xml | 9 |
3 files changed, 67 insertions, 0 deletions
diff --git a/sci-biology/SnpEff/Manifest b/sci-biology/SnpEff/Manifest new file mode 100644 index 000000000..f170dd6b4 --- /dev/null +++ b/sci-biology/SnpEff/Manifest @@ -0,0 +1,2 @@ +DIST SnpEff-4.1e.html 101225 SHA256 c0292d24c1c793e1e71f8c17c9e8fb1d05980f8f10b729ba24eaebea9f735eba SHA512 d1a83381cdc0d8ccc2d561654114785a18dd68ed195a1e9bd1d7ce48a419a6457c9c2274803ef6579418cef4b85d504bd6efdcbb5242b08e486f44208270ed47 WHIRLPOOL d91ce987b8492eb461144e5f8d2b870f3435775cda513ccaba2700c3a717a04501580263f75a7aee26662b73a5e0110c4d282970bb90c965850487471035435d +DIST snpEff_v4_1e_core.zip 48391193 SHA256 728573ab7d1cb00660a095d48bcea5a4a9459cdffc83806aa1667f03e2ff0272 SHA512 84dd8de4716de6168da074806618294aaf8002c418cac384123a0d315a7c0bd1345c5c878b9ac775d566533b7d172b1bfc45fcbf9899fb6b4b6b4fb1b29a7c50 WHIRLPOOL 955d457a7d537cdc83bfc5b6b0f696335269364a844ac1da091421e4d997a3e7a6c539ae2848d270fe175aa7bf0feac57b62da3f1fcec1105f4267c81b4d3fc6 diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild new file mode 100644 index 000000000..5e9434a4c --- /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 000000000..2bc893037 --- /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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> |