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# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
ESVN_REPO_URI="http://beast-mcmc.googlecode.com/svn/trunk/"
WANT_ANT_TASKS="ant-junit4"
EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
JAVA_ANT_REWRITE_CLASSPATH="true"
JAVA_ANT_ENCODING="latin1"
JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
#inherit java-pkg-2 java-ant-2 eutils subversion
inherit java-pkg-2 java-ant-2 eutils
MY_P=BEASTv${PV}
DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
HOMEPAGE="http://code.google.com/p/beast-mcmc/"
#SRC_URI=""
SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
# TODO: sys-cluster/mpijava
COMMON_DEPS="
dev-java/colt:0
dev-java/jdom:1.0
dev-java/itext:0
dev-java/junit:4
dev-java/jebl:0
dev-java/matrix-toolkits-java
dev-java/commons-math:2
dev-java/jdom-jaxen:1.0"
DEPEND=">=virtual/jdk-1.5
${COMMON_DEPS}"
RDEPEND=">=virtual/jre-1.5
${COMMON_DEPS}"
S="${WORKDIR}/beast_release_${PV//./_}"
src_prepare() {
sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/release/Linux/scripts/* || die
cd lib
rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die
#rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
java-pkg_jar-from jdom-1.0
java-pkg_jar-from colt
java-pkg_jar-from itext
# java-pkg_jar-from jebl
java-pkg_jar-from matrix-toolkits-java
java-pkg_jar-from commons-math-2
java-pkg-2_src_prepare
}
src_compile() {
eant dist_all_BEAST -f build_BEAST_MCMC.xml \
-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
eant dist -f build_pathogen.xml \
-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
}
src_install() {
java-pkg_dojar build/dist/*.jar dist/*.jar
java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
insinto /usr/share/${PN}
doins -r examples
dodoc NOTIFY doc/*.pdf
}
src_test() {
eant junit -f build.xml \
-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done)
}
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