From 5e2fcfa47bb951d319e95d9340bc724aeb045002 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Mokrej=C5=A1?= <mmokrejs@fold.natur.cuni.cz>
Date: Wed, 7 Dec 2016 13:52:28 +0100
Subject: 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(-)

(limited to 'sci-biology/ensembl-tools')

diff --git a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
index 95e9525e8..793f51e7a 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
-- 
cgit v1.2.3