81 lines
2.7 KiB
Bash
81 lines
2.7 KiB
Bash
# Copyright 1999-2009 Gentoo Foundation
|
|
# Distributed under the terms of the GNU General Public License v2
|
|
# $Id$
|
|
|
|
EAPI="2"
|
|
|
|
ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
|
|
|
|
WANT_ANT_TASKS="ant-junit4"
|
|
EANT_GENTOO_CLASSPATH="colt,jdom,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
|
|
|
|
DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
|
|
HOMEPAGE="https://github.com/beast-dev/beast-mcmc"
|
|
SRC_URI=""
|
|
#SRC_URI="mirror://gentoo/${P}.tar.bz2"
|
|
|
|
LICENSE="LGPL-3"
|
|
SLOT="0"
|
|
KEYWORDS=""
|
|
IUSE=""
|
|
|
|
# TODO: sys-cluster/mpijava
|
|
COMMON_DEPS="dev-java/colt:0
|
|
dev-java/jdom: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|' "${S}"/scripts/* || die
|
|
cd lib
|
|
rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
|
|
java-pkg_jar-from jdom
|
|
java-pkg_jar-from colt
|
|
java-pkg_jar-from itext
|
|
java-pkg_jar-from jebl
|
|
java-pkg_jar-from matrix-toolkits-java
|
|
java-pkg_jar-from commons-math-1
|
|
java-pkg-2_src_prepare
|
|
}
|
|
|
|
src_compile() {
|
|
eant dist_all_BEAST -f build_BEAST_MCMC.xml \
|
|
-Dgentoo.classpath=$(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 || die
|
|
dodoc NOTIFY doc/*.pdf
|
|
}
|
|
|
|
src_test() {
|
|
eant junit -f build_BEAST_MCMC.xml \
|
|
-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die
|
|
}
|