sci-biology/ensembl-tools: note dependency not yet in science overlay

Package-Manager: portage-2.3.2

1 files changed, 54 insertions, 0 deletions

diff --git a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
new file mode 100644
index 000000000..cee11494b
--- /dev/null
+++ b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
@@ -0,0 +1,54 @@
+# 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 -> ${P}.zip"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry
+IUSE=""
+
+DEPEND="dev-perl/File-Copy-Recursive
+	dev-perl/Archive-Extract
+	dev-perl/Bio-DB-HTS"
+# BUG: needs Bio::EnsEMBL::Registry from http://www.ensembl.org/info/docs/api/api_installation.html
+#	dev-perl/Bio-EnsEMBL" # 
+#DEPEND="dev-perl/Perl-XS
+RDEPEND="${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
+}