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