commit: 5e2fcfa47bb951d319e95d9340bc724aeb045002 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Dec 7 12:52:28 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Dec 7 12:52:28 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5e2fcfa4
sci-biology/ensembl-tools: mimic upstream's INSTALL.pl so we can install on Gentoo Seems the code fetching VEP plugins will need more reverse-engineering unless this can be completed during run-time (do not know). Package-Manager: portage-2.3.2 sci-biology/ensembl-tools/ensembl-tools-86.ebuild | 37 ++++++++++++++--------- 1 file changed, 22 insertions(+), 15 deletions(-) diff --git a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild index 95e9525..793f51e 100644 --- a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild +++ b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild @@ -7,14 +7,14 @@ EAPI=5 PERL_EXPORT_PHASE_FUNCTIONS=no inherit perl-module -DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)" +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 -> ${P}.zip" LICENSE="Apache-2.0" SLOT="0" -KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry +KEYWORDS="" IUSE="" DEPEND="dev-perl/File-Copy-Recursive @@ -28,26 +28,33 @@ S="${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 + 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 - cd ../../scripts/region_reporter || die + dobin variant_effect_predictor.pl gtf2vep.pl filter_vep.pl convert_cache.pl + insinto /usr/share/"${PN}"/examples + doins example_* + popd + pushd scripts/region_reporter || die dobin *.pl newdoc README.txt region_reporter.txt - cd ../../scripts/assembly_converter + popd + pushd scripts/assembly_converter dobin *.pl - insinto /usr/share/"${PN}"/examples doins assemblymapper.in - #insinto ${VENDOR_LIB}/${PN} - #doins *.pm newdoc README.txt assembly_converter.txt - insinto /usr/share/"${PN}"/examples - doins assemblymapper.in - cd ../../scripts/id_history_converter + popd + pushd scripts/id_history_converter dobin *.pl newdoc README.txt id_history_converter.txt - insinto /usr/share/"${PN}"/examples 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
