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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)"
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 -> ${P}.zip"
LICENSE="Apache-2.0"
SLOT="0"
KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry
IUSE=""
DEPEND="dev-perl/File-Copy-Recursive
dev-perl/Archive-Extract"
#DEPEND="dev-perl/Perl-XS
# dev-perl/Bio-DB-HTS"
RDEPEND="${DEPEND}"
S="${WORKDIR}/ensembl-tools-release-${PV}"
src_install(){
perl_set_version
insinto ${VENDOR_LIB}/${PN}
cd scripts/variant_effect_predictor || die
# FIXME: INSTALL.pl does not exit upon error
./INSTALL.pl --DESTDIR="${DESTDIR}"/"${EPREFIX}" --AUTO=ac || die
newdoc README.txt variant_effect_predictor.txt
cd ../../scripts/region_reporter || die
dobin *.pl
newdoc README.txt region_reporter.txt
cd ../../scripts/assembly_converter
dobin *.pl
insinto /usr/share/"${PN}"/examples
doins assemblymapper.in
#insinto ${VENDOR_LIB}/${PN}
#doins *.pm
newdoc README.txt assembly_converter.txt
insinto /usr/share/"${PN}"/examples
doins assemblymapper.in
cd ../../scripts/id_history_converter
dobin *.pl
newdoc README.txt id_history_converter.txt
insinto /usr/share/"${PN}"/examples
doins idmapper.in
}
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