In main tree

4 files changed, 0 insertions, 96 deletions

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 <weaver@gentoo.org> 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 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-</pkgmetadata>