[gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     e5cf10b0eb4504480f9e6a26e4b11de229e3e37a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec  7 10:00:10 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec  7 10:00:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5cf10b0

sci-biology/SnpEff: version bump, may be moved to our main repo

Package-Manager: portage-2.3.2

 .../SnpEff/{SnpEff-4.2.ebuild => SnpEff-4.3g.ebuild}       | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/sci-biology/SnpEff/SnpEff-4.2.ebuild b/sci-biology/SnpEff/SnpEff-4.3g.ebuild
similarity index 81%
rename from sci-biology/SnpEff/SnpEff-4.2.ebuild
rename to sci-biology/SnpEff/SnpEff-4.3g.ebuild
index 7cdd51c..f817588 100644
--- a/sci-biology/SnpEff/SnpEff-4.2.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.3g.ebuild
@@ -2,19 +2,21 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 inherit java-pkg-2 java-ant-2
 
-DESCRIPTION="Annotate SNP changes and predict their effect"
+MY_PV=${PV/./_}
+
+DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
 HOMEPAGE="http://snpeff.sourceforge.net"
 SRC_URI="
-	http://sourceforge.net/projects/snpeff/files/snpEff_v4_2_core.zip
+	http://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip
 	http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
 
 LICENSE="LGPL-3"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 # https://github.com/pcingola/SnpEff/blob/master/README_release.txt
@@ -37,8 +39,8 @@ src_install(){
 	mkdir -p "${D}"/usr/share || die
 	# but portage does not install the .* files and subdirs, grr!
 	unzip \
-		"${DISTDIR}"/snpEff_v4_2_core.zip -d "${D}"/usr/share \
-		|| die "failed to unzip ${DISTDIR}/snpEff_v4_2_core.zip"
+		"${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${D}"/usr/share \
+		|| die "failed to unzip ${DISTDIR}/snpEff_v${MY_PV}_core.zip"
 	sed \
 		-e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \
 		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die