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

["Justin Lecher" <jlec@gentoo.org>]

commit:     b39edea7ff9a3cd0e7f0b5986b60fd27a46a20cd
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 14 17:17:02 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 14 17:17:16 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b39edea7

sci-biology/SnpEff: Bump to EAPI=6

* Clean multiverion code

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/SnpEff/SnpEff-4.1e.ebuild | 48 +++++++++++++++++++----------------
 sci-biology/SnpEff/metadata.xml       |  2 +-
 2 files changed, 27 insertions(+), 23 deletions(-)

diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
index 5e9434a..7ba4236 100644
--- a/sci-biology/SnpEff/SnpEff-4.1e.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
@@ -1,51 +1,55 @@
 # Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: $
+# $Id$
 
-EAPI=5
+EAPI=6
 
 inherit java-pkg-2 java-ant-2
 
-[ "$PV" == "9999" ] && inherit git-2
-
 DESCRIPTION="Annotate SNP changes and predict their effect"
 HOMEPAGE="http://snpeff.sourceforge.net"
-
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/pcingola/SnpEff.git"
-	#EGIT_BRANCH="v4.1B"
-	KEYWORDS=""
-else
-	SRC_URI="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip
-			http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
-	KEYWORDS="~amd64"
-	S="${WORKDIR}"
-fi
+SRC_URI="
+	http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip
+	http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
 
 LICENSE="LGPL-3"
 SLOT="0"
+KEYWORDS="~amd64"
 IUSE=""
 
 # https://github.com/pcingola/SnpEff/blob/master/README_release.txt
-DEPEND=">=virtual/jre-1.7:*
+DEPEND="
+	>=virtual/jre-1.7:*
 	dev-java/maven-bin:*
 	dev-java/antlr:*"
 RDEPEND="${DEPEND}
 	>=virtual/jdk-1.7:*"
 
+	S="${WORKDIR}"
+
 #src_compile(){
 #	mvn || die
 #}
 
 src_install(){
 	cd .. || die
-	mkdir -p "${D}"/usr/share
+	mkdir -p "${D}"/usr/share || die
 	# but portage does not install the .* files and subdirs, grr!
-	unzip "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip"
-	sed -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
-	sed -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
-	sed -e 's#$HOME/snpEff/#/usr/share/snpEff/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
-	sed -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	unzip \
+		"${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share \
+		|| die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip"
+	sed \
+		-e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+		-e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+		-e 's#$HOME/snpEff/#/usr/share/snpEff/#' \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+	-e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' \
+	-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
 }
 
 # now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/

diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/SnpEff/metadata.xml
+++ b/sci-biology/SnpEff/metadata.xml
@@ -5,7 +5,7 @@
     <email>mmokrejs@fold.natur.cuni.cz</email>
     <name>Martin Mokrejs</name>
   </maintainer>
-<maintainer type="project">
+  <maintainer type="project">
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>