diff options
Diffstat (limited to 'sci-biology/beast-mcmc/beast-mcmc-9999.ebuild')
-rw-r--r-- | sci-biology/beast-mcmc/beast-mcmc-9999.ebuild | 80 |
1 files changed, 0 insertions, 80 deletions
diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild deleted file mode 100644 index 824d891c6f2f..000000000000 --- a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -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 -} |