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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
DESCRIPTION="Variant Effect Predictor (VEP), AssemblyMapper, IDMapper, RegionReporter tools"
HOMEPAGE="http://www.ensembl.org/info/docs/tools/vep/script
http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html"
SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip"
LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND="dev-perl/File-Copy-Recursive
dev-perl/Archive-Extract
dev-perl/Bio-DB-HTS
dev-perl/Bio-EnsEMBL"
#DEPEND="dev-perl/Perl-XS
RDEPEND="${DEPEND}"
S="${WORKDIR}/ensembl-tools-release-${PV}"
src_install(){
perl_set_version
pushd scripts/variant_effect_predictor || die
# BUG1: the INSTALL.pl does not exit upon error with non-zero exit code
# BUG2: it complains if ${VENDOR_LIB}/${PN} is not in PERL5LIB
# perl INSTALL.pl --AUTO=acf --NO_HTSLIB --PLUGINS all --DESTDIR ${VENDOR_LIB}/${PN} || die
newdoc README.txt variant_effect_predictor.txt
dobin variant_effect_predictor.pl gtf2vep.pl filter_vep.pl convert_cache.pl
insinto /usr/share/"${PN}"/examples
doins example_*
popd
pushd scripts/region_reporter || die
dobin *.pl
newdoc README.txt region_reporter.txt
popd
pushd scripts/assembly_converter
dobin *.pl
doins assemblymapper.in
newdoc README.txt assembly_converter.txt
popd
pushd scripts/id_history_converter
dobin *.pl
newdoc README.txt id_history_converter.txt
doins idmapper.in
popd
}
pkg_postinst(){
einfo "Probably you want to download some of the files from ftp://ftp.ensembl.org/pub/release-86/variation/VEP/"
}
# TODO The INSTALL.pl fetches https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/86/plugin_config.txt
# and calls eval on its contents
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