# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/gatk/gatk-1.6.ebuild,v 1.1 2012/09/30 17:17:21 weaver Exp $

EAPI=4

MY_HASH=93333f0

EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"

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

#inherit java-pkg-2 java-ant-2 git
inherit java-pkg-2 java-ant-2

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/tarball/${PV} -> ${P}.tar.gz"

LICENSE="as-is"
SLOT="0"
IUSE=""
KEYWORDS="~amd64"

COMMON_DEPS=""
DEPEND=">=virtual/jdk-1.6
	dev-vcs/git
	${COMMON_DEPS}"
RDEPEND=">=virtual/jre-1.6
	${COMMON_DEPS}"

S="${WORKDIR}/broadgsa-gatk-${MY_HASH}"

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

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