Import from Science overlay and rewrite

(Portage version: 2.2_rc30/cvs/Linux x86_64)

4 files changed, 183 insertions, 0 deletions

diff --git a/sci-biology/beast-mcmc/ChangeLog b/sci-biology/beast-mcmc/ChangeLog
new file mode 100644
index 000000000000..7b23dc7a04bf
--- /dev/null
+++ b/sci-biology/beast-mcmc/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/beast-mcmc
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/ChangeLog,v 1.1 2009/10/02 21:47:11 weaver Exp $
+
+*beast-mcmc-9999 (02 Oct 2009)
+*beast-mcmc-1.5.1 (02 Oct 2009)
+
+  02 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+  +beast-mcmc-1.5.1.ebuild, +beast-mcmc-9999.ebuild:
+  Import from Science overlay and rewrite
+
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild
new file mode 100644
index 000000000000..cf908ae9abdc
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild,v 1.1 2009/10/02 21:47:11 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,commons-math-1,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="http://code.google.com/p/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:1
+	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 "$i:"; done) || die
+}
+
+src_install() {
+	java-pkg_dojar bin/dist/*.jar dist/*.jar
+
+	java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
+#	java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
+
+	insinto /usr/share/${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/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
new file mode 100644
index 000000000000..098b991c00ee
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild,v 1.1 2009/10/02 21:47:11 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,commons-math-1,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="http://code.google.com/p/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:1.0
+	dev-java/itext:0
+	dev-java/junit:4
+	dev-java/jebl:0
+	dev-java/matrix-toolkits-java
+	dev-java/commons-math:1
+	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 "$i:"; done) || die
+}
+
+src_install() {
+	java-pkg_dojar bin/dist/*.jar dist/*.jar
+
+	java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m'
+#	java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m'
+	java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m'
+
+	insinto /usr/share/${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
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/beast-mcmc/metadata.xml
@@ -0,0 +1,9 @@
+<?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>