Version bump

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

3 files changed, 91 insertions, 2 deletions

diff --git a/sci-biology/beast-mcmc/ChangeLog b/sci-biology/beast-mcmc/ChangeLog
index 7fd908964e7a..484953414278 100644
--- a/sci-biology/beast-mcmc/ChangeLog
+++ b/sci-biology/beast-mcmc/ChangeLog
@@ -1,6 +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 1.2 2009/10/19 03:55:31 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/ChangeLog,v 1.3 2009/10/19 15:07:01 weaver Exp $
+
+*beast-mcmc-1.5.2 (19 Oct 2009)
+
+  19 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +beast-mcmc-1.5.2.ebuild:
+  Version bump
 
   18 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> beast-mcmc-9999.ebuild:
   Address upstream changes in live ebuild
diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest
index 466f081948b6..87484fd44f78 100644
--- a/sci-biology/beast-mcmc/Manifest
+++ b/sci-biology/beast-mcmc/Manifest
@@ -1,5 +1,7 @@
 DIST beast-mcmc-1.5.1.tar.bz2 32191300 RMD160 c9e9b5e5283e537a61c8656a093cb267dd2533dc SHA1 7750af1dcbfe65c949aabf5390ca36a6f45b3013 SHA256 f64bc0e6be372ef4ed7e3e287c99e5b9da2f7d961cd1c7eca9483ae70ab3ba5b
+DIST beast-mcmc-1.5.2.tar.bz2 38834702 RMD160 c4d954c604ae021afb6c1c19e041c5153ffad42b SHA1 fffd35a05b0cbcca74a491ef06cd7ea7e8c9d3c9 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1
 EBUILD beast-mcmc-1.5.1.ebuild 2917 RMD160 54c28423917fde18e23a78309aa4efcd55c9039c SHA1 575f4d65ab003d0700e76082fbab90aa393ed393 SHA256 106b6f5e544b9faf284082c5eba261097d29e0782c826218fa1dee398fb81126
+EBUILD beast-mcmc-1.5.2.ebuild 2919 RMD160 6a8f3e6cba0c36aec30e2bcd859f7d9cdc8e667d SHA1 e8ea8734d19934828659b048f99b1e967f4daa58 SHA256 44f00122a5707c5dae92fe346056f71b1183ac75ae106eb7d89e21a35fb66c9c
 EBUILD beast-mcmc-9999.ebuild 2869 RMD160 d00e3cb3826dce6ae8b1ed3db890597e0eec9249 SHA1 1555bb80c11a071d41af58e2bf4288422d6652c9 SHA256 ef97822c25a76d3ebd0e8902d6dc8960c6a2b1d258d83a6449889cb5d022a87e
-MISC ChangeLog 559 RMD160 cc8ae2c7c070e4ad6923ffa956e585c5c79a74cc SHA1 b1b6604215f06966e55ac6ee71c28c99e82457e4 SHA256 55191d7a85eee3ce65529dbb0b3a899827d8adbd5372433d33fee2ea7082baaf
+MISC ChangeLog 684 RMD160 eadf4b6cc547c997e2c06751c9c819191f760416 SHA1 b419b8882b9d70f055cc137409b1eade1ac384a2 SHA256 eab79e2ce760c62a8fd99b47ba6ec9b44dd18861099195e62c7cccc69d4a9eeb
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild
new file mode 100644
index 000000000000..99a7be94b578
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.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-1.5.2.ebuild,v 1.1 2009/10/19 15:07:01 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-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="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: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
+}