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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
JAVA_PKG_IUSE="doc source"
inherit java-pkg-2 java-ant-2
DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
HOMEPAGE="http://picard.sourceforge.net
http://broadinstitute.github.io/picard"
SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
CDEPEND="dev-java/snappy:1.1
dev-java/cofoja:0
dev-java/commons-jexl:2
dev-java/ant-core:0
dev-java/htsjdk:0"
DEPEND=">=virtual/jdk-1.8
${CDEPEND}"
RDEPEND=">=virtual/jre-1.8
${CDEPEND}"
EANT_BUILD_TARGET="all"
EANT_NEEDS_TOOLS="true"
JAVA_ANT_REWRITE_CLASSPATH="true"
EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
java_prepare() {
default
rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die
epatch "${FILESDIR}"/${PV}-build.xml.patch
}
src_install() {
cd dist || die
java-pkg_dojar ${PN}.jar
java-pkg_dojar ${PN}-lib.jar
java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
use source && java-pkg_dosrc "${S}"/src/java/*
use doc && java-pkg_dojavadoc "${S}"/javadoc
}
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