diff options
| -rw-r--r-- | sci-biology/beast-mcmc/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild | 82 | ||||
| -rw-r--r-- | sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild (renamed from sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild) | 6 | ||||
| -rw-r--r-- | sci-biology/beast-mcmc/beast-mcmc-9999.ebuild | 6 |
4 files changed, 6 insertions, 89 deletions
diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest index 7fd843d7d423..56293f2fdd27 100644 --- a/sci-biology/beast-mcmc/Manifest +++ b/sci-biology/beast-mcmc/Manifest @@ -1,2 +1 @@ -DIST beast-mcmc-1.5.2.tar.bz2 38834702 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 SHA512 8549db6cb49d64eb3a97fa6478bdbabfecd44ccc6236c474a1961ec5d6fc8326072fb961035df70982a9f1c08a36572529a07b88e2d33a43fa0fd5c07df3a414 WHIRLPOOL 595f606640daa32c79373c9003ddbc1f80dcbbf01e9e9c18191328b80eb50b45ac70032027dd1efb0e256d78b88bfe1742151a16f6f333938099943a7b2cd16a DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5 diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild deleted file mode 100644 index e3566919c375..000000000000 --- a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# 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-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 - -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="~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|' "${S}"/scripts/* || die - cd lib - rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die - java-pkg_jar-from jdom-1.0 - java-pkg_jar-from colt - java-pkg_jar-from itext - java-pkg_jar-from jebl - java-pkg_jar-from matrix-toolkits-java - java-pkg_jar-from commons-math-1 - java-pkg-2_src_prepare -} - -src_compile() { - eant dist_all_BEAST -f build_BEAST_MCMC.xml \ - -Dgentoo.classpath=$(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 -} diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild index 5a66f595593c..8e59912e7175 100644 --- a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild +++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild @@ -7,7 +7,7 @@ EAPI=5 ESVN_REPO_URI="https://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" +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" @@ -30,7 +30,7 @@ IUSE="" # TODO: sys-cluster/mpijava COMMON_DEPS=" dev-java/colt:0 - dev-java/jdom:1.0 + dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 @@ -49,7 +49,7 @@ src_prepare() { 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 jdom java-pkg_jar-from colt java-pkg_jar-from itext # java-pkg_jar-from jebl diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild index 768799ce2195..7bb1f0faa1b3 100644 --- a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild +++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild @@ -7,7 +7,7 @@ EAPI="2" ESVN_REPO_URI="https://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" +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" @@ -26,7 +26,7 @@ IUSE="" # TODO: sys-cluster/mpijava COMMON_DEPS="dev-java/colt:0 - dev-java/jdom:1.0 + dev-java/jdom:0 dev-java/itext:0 dev-java/junit:4 dev-java/jebl:0 @@ -44,7 +44,7 @@ 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-1.0 + java-pkg_jar-from jdom java-pkg_jar-from colt java-pkg_jar-from itext java-pkg_jar-from jebl |