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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
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.v${PV}.source.jar?raw=true -> ${PN}.v${PV}.source.jar"
LICENSE="Non-profit-OSL-3.0"
SLOT="0"
KEYWORDS="~amd64"
DEPEND="
>=virtual/jdk-1.5:*
"
RDEPEND=">=virtual/jre-1.5:*
sci-biology/bam-readcount
!sci-biology/VarScan-bin
"
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
}