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- # Copyright 1999-2013 Gentoo Foundation
- # Distributed under the terms of the GNU General Public License v2
- EAPI="5"
- JAVA_PKG_IUSE="doc source test"
- WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
- inherit java-pkg-2 java-ant-2
- DESCRIPTION="Java-based command-line utilities that manipulate SAM files"
- HOMEPAGE="http://picard.sourceforge.net/"
- SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
- LICENSE="Apache-2.0"
- SLOT="0"
- IUSE=""
- KEYWORDS="~amd64 ~x86"
- CDEPEND="dev-java/snappy:1.0
- dev-java/cofoja:0
- dev-java/commons-jexl:2
- dev-java/ant-core:0"
- DEPEND=">=virtual/jdk-1.6
- dev-java/ant-apache-bcel:0
- test? (
- dev-java/testng:0
- dev-lang/R
- )
- ${CDEPEND}"
- RDEPEND=">=virtual/jre-1.6
- ${CDEPEND}"
- EANT_BUILD_TARGET="all"
- EANT_TEST_TARGET="test"
- EANT_NEEDS_TOOLS="true"
- JAVA_ANT_REWRITE_CLASSPATH="true"
- EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
- EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
- java_prepare() {
- mkdir "${S}"/lib || die
- epatch "${FILESDIR}"/${PV}-gentoo.patch
- mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
- }
- src_install() {
- cd dist || die
- for i in *-${PV}.jar; do
- java-pkg_newjar $i ${i/-${PV}/}
- rm $i || die
- done
- java-pkg_dojar *.jar
- for i in *.jar; do
- java-pkg_dolauncher ${i/.jar/} --jar $i;
- done
- use source && java-pkg_dosrc "${S}"/src/java/*
- use doc && java-pkg_dojavadoc "${S}"/javadoc
- }
- src_test() {
- java-pkg-2_src_test
- }
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