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* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-07-29 20:47 99% Martin Mokrejs
  0 siblings, 0 replies; 1+ results
From: Martin Mokrejs @ 2016-07-29 20:47 UTC (permalink / raw
  To: gentoo-commits

commit:     3bdd3d1c35c9e23cbc13e86dcb8c4b2321fd2620
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 29 20:47:12 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 29 20:47:12 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3bdd3d1c

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

Package-Manager: portage-2.3.0

 sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 47 +++++++++++++++++++++++
 sci-biology/ensembl-tools/metadata.xml            | 12 ++++++
 2 files changed, 59 insertions(+)

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 0000000..642caf8
--- /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
+}

diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/ensembl-tools/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>


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