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

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

commit:     da001fc52d309509f4bc99d41b8b147672e8ac33
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 20 18:51:04 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 20 18:51:04 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da001fc5

sci-biology/VarScan: version bump

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/VarScan/VarScan-2.4.3.ebuild | 35 ++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/sci-biology/VarScan/VarScan-2.4.3.ebuild b/sci-biology/VarScan/VarScan-2.4.3.ebuild
new file mode 100644
index 000000000..3ef29a10c
--- /dev/null
+++ b/sci-biology/VarScan/VarScan-2.4.3.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)"
+HOMEPAGE="http://varscan.sourceforge.net/"
+
+# binary
+#https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.jar
+SRC_URI="https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.source.jar?raw=true -> ${PN}.v${PV}.source.jar"
+
+LICENSE="Non-profit-OSL-3.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+	>=virtual/jdk-1.5:*
+	!sci-biology/VarScan-bin"
+RDEPEND=">=virtual/jre-1.5:*"
+
+S="${WORKDIR}"/net/sf/varscan
+
+src_compile(){
+	javac *.java
+}
+
+src_install(){
+	java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar
+	java-pkg_dolauncher VarScan
+}