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-rw-r--r--profiles/package.mask1
-rw-r--r--sci-biology/ensembl-tools/Manifest1
-rw-r--r--sci-biology/ensembl-tools/ensembl-tools-86.ebuild59
-rw-r--r--sci-biology/ensembl-tools/metadata.xml15
4 files changed, 0 insertions, 76 deletions
diff --git a/profiles/package.mask b/profiles/package.mask
index 01dfb9327..3bb2f9f5c 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -54,4 +54,3 @@ sci-biology/cortex_var
sci-biology/cross_genome
sci-biology/dawg
sci-biology/EBARDenovo
-sci-biology/ensembl-tools
diff --git a/sci-biology/ensembl-tools/Manifest b/sci-biology/ensembl-tools/Manifest
deleted file mode 100644
index c96d69a89..000000000
--- a/sci-biology/ensembl-tools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ensembl-tools-86.zip 193004 SHA256 55ce1578e6a927a21997342a07df9e4dbc1eddaf2fc5c99a0e72c04f1029811c SHA512 c897e0062d15b1c3f7e3b9f137c30ba2e65dc9b44da792250f4754c4c5570fe49990d4e206d605578fd9334b898fa9bfafc85c9f81d8f9e3b15b8663706d05c6 WHIRLPOOL 88e42734974422f429e0820c081275f4767ce7ff5622151a2ccd3e9f3dfde2f72a5a23a1d337f0cfb4dd3195db52312694eabe870acfd48b8dca03078db9b8df
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
diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml
deleted file mode 100644
index 7cd2955fb..000000000
--- a/sci-biology/ensembl-tools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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>
- <upstream>
- <remote-id type="github">Ensembl/ensembl-tools</remote-id>
- </upstream>
-</pkgmetadata>