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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/goby-1.9.8.1.ebuild,v 1.1 2012/01/05 23:00:11 weaver Exp $
EAPI=4
ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2"
EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
JAVA_ANT_REWRITE_CLASSPATH="true"
#inherit java-pkg-2 java-ant-2 subversion
inherit java-pkg-2 java-ant-2
MY_P="${PN}_${PV}"
DESCRIPTION="A DNA sequencing data management framework"
HOMEPAGE="http://campagnelab.org/software/goby/"
SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
LICENSE="GPL-3 LGPL-3"
SLOT="0"
IUSE="+cpp"
KEYWORDS="~amd64 ~x86"
COMMON_DEPS="dev-java/commons-logging
dev-java/commons-lang:2.1
dev-java/commons-io:1
dev-libs/protobuf[java]
dev-java/fastutil:5.0
dev-java/log4j
dev-java/jsap
dev-java/commons-configuration
dev-java/commons-math:2"
DEPEND=">=virtual/jdk-1.6
${COMMON_DEPS}"
RDEPEND=">=virtual/jre-1.6
${COMMON_DEPS}
cpp? ( ~sci-biology/goby-cpp-${PV} )"
S="${WORKDIR}/${MY_P}"
src_prepare() {
sed -i '/sge/ d' build.xml || die
java-pkg-2_src_prepare
}
src_install() {
java-pkg_dojar goby*.jar
java-pkg_dolauncher goby --jar goby.jar
insinto /usr/share/${PN}
doins -r python
dodoc CHANGES.txt
}
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