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Diffstat (limited to 'sci-biology/ensembl-tools/ensembl-tools-86.ebuild')
-rw-r--r--sci-biology/ensembl-tools/ensembl-tools-86.ebuild59
1 files changed, 0 insertions, 59 deletions
diff --git a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
deleted file mode 100644
index 4c838f717..000000000
--- a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# 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