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
