# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/goby-1.9.7.3.ebuild,v 1.1 2011/09/25 21:50:28 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 }