commit: 067729d439f3b5a98cbd371c0eba39cc8b7ed00f Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 14:18:08 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 14:18:08 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=067729d4
sci-biology/ensemble-tools: remove pack, latest update 2013 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - sci-biology/ensembl-tools/ensembl-tools-86.ebuild | 59 ----------------------- sci-biology/ensembl-tools/metadata.xml | 15 ------ 3 files changed, 75 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/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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">Ensembl/ensembl-tools</remote-id> - </upstream> -</pkgmetadata>
