sci-biology/ensembl-tools: new package, needs more fixes, upstream contacted

Package-Manager: portage-2.3.0

1 files changed, 47 insertions, 0 deletions

diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
new file mode 100644
index 000000000..642caf8eb
--- /dev/null
+++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
@@ -0,0 +1,47 @@
+# 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://grch37.ensembl.org/info/docs/tools/vep/script/index.html"
+SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry
+IUSE=""
+
+DEPEND=""
+#DEPEND="dev-perl/Perl-XS
+#	dev-perl/Bio-DB-HTS"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ensembl-tools-release-${PV}"
+
+src_install(){
+	perl_set_version
+	insinto ${VENDOR_LIB}/${PN}
+	cd scripts/variant_effect_predictor || die
+	perl INSTALL.pl --DESTDIR="${EPREFIX}"/"${DESTDIR}" --AUTO ac
+	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 ${VENDOR_LIB}/${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
+}