From 9ac94339acf22ce7fcfb3f0602ca6319902de970 Mon Sep 17 00:00:00 2001 From: Andrey Kislyuk Date: Fri, 2 Oct 2009 12:41:23 -0400 Subject: In main tree --- sci-biology/beast-mcmc/ChangeLog | 7 --- sci-biology/beast-mcmc/Manifest | 3 -- sci-biology/beast-mcmc/beast-mcmc-9999.ebuild | 77 --------------------------- sci-biology/beast-mcmc/metadata.xml | 9 ---- 4 files changed, 96 deletions(-) delete mode 100644 sci-biology/beast-mcmc/ChangeLog delete mode 100644 sci-biology/beast-mcmc/Manifest delete mode 100644 sci-biology/beast-mcmc/beast-mcmc-9999.ebuild delete mode 100644 sci-biology/beast-mcmc/metadata.xml diff --git a/sci-biology/beast-mcmc/ChangeLog b/sci-biology/beast-mcmc/ChangeLog deleted file mode 100644 index bd1d04f2a..000000000 --- a/sci-biology/beast-mcmc/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/beast-mcmc -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 24 Apr 2009; Andrey Kislyuk ChangeLog: - New package, ebuild written by me - diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest deleted file mode 100644 index c0847d294..000000000 --- a/sci-biology/beast-mcmc/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -EBUILD beast-mcmc-9999.ebuild 2761 RMD160 4548a35631a3cf4f75d44b87ff8423bb818fc422 SHA1 e8c6ee1499a7caf16d58d3ab5bd86c9f5e00c4a4 SHA256 e82673e76f1b3a1609062172ea38c58f456d778cfd21d6abe65b7ffc4639ced1 -MISC ChangeLog 221 RMD160 97f5c0cb57502ac0869a799273c987f5e5f1009d SHA1 1ee219d1d57927a737d7c07f8fcbd3ec7f4cc66a SHA256 8df60b3ccbb9bfada51f0396899426eba494b2caee9d9caffeb4efa698c6dcee -MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 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 80df0a71e..000000000 --- a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-9999.ebuild,v 1.2 2009/04/08 20:45:57 weaver Exp $ - -EAPI="2" - -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" -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="http://code.google.com/p/beast-mcmc/" -#SRC_URI="http://beast-mcmc.googlecode.com/files/BEASTv${PV}.tgz" -SRC_URI="" - -LICENSE="LGPL" -SLOT="0" -KEYWORDS="" -IUSE="" - -# TODO: sys-cluster/mpijava, dev-java/commons-math -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" -DEPEND=">=virtual/jdk-1.5 - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.5 - ${COMMON_DEPS}" - -src_prepare() { - sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die - cd lib - rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar || die -# rm -v commons-math-*.jar - java-pkg_jar-from jdom-1.0 - java-pkg_jar-from colt - java-pkg_jar-from itext - java-pkg_jar-from jebl - java-pkg_jar-from matrix-toolkits-java - java-pkg-2_src_prepare -} - -src_compile() { - eant dist_all_BEAST -f build_BEAST_MCMC.xml \ - -Dgentoo.classpath=$(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 "$i:"; done) || die -} - -src_install() { - java-pkg_dojar bin/dist/*.jar dist/*.jar - - java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' -# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' - - insinto /usr/share/${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/metadata.xml b/sci-biology/beast-mcmc/metadata.xml deleted file mode 100644 index 3302123e5..000000000 --- a/sci-biology/beast-mcmc/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - - weaver@gentoo.org - Andrey Kislyuk - - sci-biology - -- cgit v1.2.3-65-gdbad