# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$

EAPI="6"

#JAVA_PKG_IUSE="doc source"
JAVA_PKG_IUSE=""

inherit git-r3 java-pkg-2

DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
HOMEPAGE="http://picard.sourceforge.net
	http://broadinstitute.github.io/picard"
EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"

LICENSE="MIT"
SLOT="0"
IUSE=""
KEYWORDS=""

CDEPEND="dev-java/snappy:1.1
	dev-java/cofoja:0
	dev-java/commons-jexl:2
	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,htsjdk"

src_prepare() {
	default
}

src_compile(){
	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
	# make jure SDK-1.8 is available, JRE-1.8 is not enough
	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
}

src_install() {
	cd build/libs || die
	java-pkg_dojar "${PN}".jar
	java-pkg_dojar "${PN}"-*-SNAPSHOT.jar

	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine

	#use source && java-pkg_dosrc "${S}"/src/java/*
	#use doc && java-pkg_dojavadoc "${S}"/javadoc
}