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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit java-pkg-2 java-ant-2
MY_PV=${PV/./_}
DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
HOMEPAGE="http://snpeff.sourceforge.net"
SRC_URI="
http://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip
http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
RDEPEND="
>=virtual/jre-1.7:*
dev-java/maven-bin:*
dev-java/antlr:*"
DEPEND="${RDEPEND}
>=virtual/jdk-1.7:*
dev-java/ant-core"
S="${WORKDIR}"
#src_compile(){
# mvn || die
#}
src_install(){
cd .. || die
mkdir -p "${ED}"/usr/share || die
# but portage does not install the .* files and subdirs, grr!
unzip \
"${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${ED}"/usr/share \
|| die "failed to unzip ${DISTDIR}/snpEff_v${MY_PV}_core.zip"
sed \
-e "s#$HOME/tools/picard/#${ED}/usr/share/picard/lib/#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
sed \
-e "s#$HOME/tools/gatk/#${ED}/usr/share/gatk/lib/#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
sed \
-e "s#$HOME/snpEff/#${ED}/usr/share/snpEff/#" \
-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
sed \
-e "s#$HOME/snpEff/snpEff.config#${ED}/usr/share/snpEff/snpEff.config#" \
-i "${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/
# 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.
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