| # Copyright 1999-2013 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| 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 |
| } |