# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2

EAPI=7

EANT_BUILD_TARGET="dist"
EANT_NEEDS_TOOLS="true"
JAVA_ANT_REWRITE_CLASSPATH="true"

inherit java-pkg-2 java-ant-2 vcs-snapshot

DESCRIPTION="The Genome Analysis Toolkit"
HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz"

LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"

RDEPEND=">=virtual/jre-1.6"
DEPEND="${RDEPEND}"

src_prepare() {
	java-pkg-2_src_prepare
	sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die
}

src_install() {
	java-pkg_dojar dist/*.jar
	java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar
	java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar
}