reinit the tree, so we can have metadata

4 files changed, 182 insertions, 0 deletions

diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest
new file mode 100644
index 000000000000..42dfe1981f0b
--- /dev/null
+++ b/sci-biology/beast-mcmc/Manifest
@@ -0,0 +1,6 @@
+DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5
+EBUILD beast-mcmc-1.7.5-r1.ebuild 2906 SHA256 9f36131b95bf15763235e913fe720760f217e6c789b352cdf0cee32d82ca870f SHA512 1bc83f37bd0bfd2477bcf31e7206d1d4337c24123870a407aac2b2ac69ea65d52958930dd2d5c9c961b862f3e7935356809aefbadc8938b7798125b4ebec7ac0 WHIRLPOOL ba33e77030a822941599a9311e079ddd669407201f8065f467ca3eef06c1b5f4da435dd45505eef9037c2946efb6313ff94569bd3e2e7f5f79cca9bfa44ceedd
+EBUILD beast-mcmc-9999.ebuild 2743 SHA256 72a683da9d25129601f93d486b7539c9d9d01afaac322742147199ef169b1629 SHA512 d2860b91189860b027ca7f10026e99df5e5d447912445061fa09aa770d10ef33ed972107355df15d5e7c6f034baefbb8798efecca3e7132852183c2c9bcc0ed1 WHIRLPOOL 0f4f4b25cd91735ab935f43f1b76d57fb51afbb4104190577c0c60d55c9255b611362e4cba4f08f4ed385bb0c21371cd6382ea1eb1b3509361ada3bf0da28eb7
+MISC ChangeLog 3648 SHA256 c343a586829fd9422063e1891e6cca19e48755007d9b789357e146266ad1dd1f SHA512 36ddb6176cf1663861d3aa4409cfe3b51a7ac296baaeb5cccf56f4cecd80569665fb8542999a4afb5290b09f8a05ae887f5487b8a781da67253273b38bb7d420 WHIRLPOOL fee385b5fd2f98bc1f8e3949d0b627c057da506172e4955691a0bab92257f4e107adfeb0374f2b2fdc116e97bb906c088a25efcebc3f7c069bc8005f56bb2000
+MISC ChangeLog-2015 1088 SHA256 22102992e5ea52840e6ebd312fac6ae891fa3c243d27b81eec35ed4df7dcb568 SHA512 8d69f4a97c447bbff89a6c4941851c89843bb5735a167292a605e127f23adbf9d01d8a7d4245bc7d1f567c685573957049b1e2137640933a15a050811b3d66a1 WHIRLPOOL a059171d64e19668d5aecc1b7c3ea0c715a4034d0416bf347ba9d9a4e744c037a3d3038949c47b5c44d680ef01de49fd819980859a4668cd60b15cb104a2209a
+MISC metadata.xml 356 SHA256 caaf423fe7d400f1973478f9248fd0d546026a4f9c2c65f20e9098b9ef2cc3d3 SHA512 fa6d4dc538ef266e20cfb717dd6c7982c9b88e7b5ab3fcd11074ab41be660ae2f8a0bf55bc5abbb1a669ad64c3e46c1dd47cc8761e7e4b5767cff7d2da661dec WHIRLPOOL d87c7cbd33ebaaa4784ebef3a12ab510cc9b9b923cb1ecd2b1df2045711cd373009ffac6550ba75dde66c7095ed0326b36d6cb749a1e09efb4a638ac6009076c
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild
new file mode 100644
index 000000000000..7bbc7e087de8
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
+
+WANT_ANT_TASKS="ant-junit4"
+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"
+
+#inherit java-pkg-2 java-ant-2 eutils subversion
+inherit java-pkg-2 java-ant-2 eutils
+
+MY_P=BEASTv${PV}
+
+DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
+HOMEPAGE="https://github.com/beast-dev/beast-mcmc"
+#SRC_URI=""
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+# TODO: sys-cluster/mpijava
+COMMON_DEPS="
+	dev-java/colt:0
+	dev-java/jdom: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|' "${S}"/release/Linux/scripts/* || die
+	cd lib
+	rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die
+	#rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
+	java-pkg_jar-from jdom
+	java-pkg_jar-from colt
+	java-pkg_jar-from itext
+#	java-pkg_jar-from jebl
+	java-pkg_jar-from matrix-toolkits-java
+	java-pkg_jar-from commons-math-2
+	java-pkg-2_src_prepare
+}
+
+src_compile() {
+	eant dist_all_BEAST -f build_BEAST_MCMC.xml \
+		-Dgentoo.classpath=$(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
+	dodoc NOTIFY doc/*.pdf
+}
+
+src_test() {
+	eant junit -f build.xml \
+		-Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done)
+}
diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
new file mode 100644
index 000000000000..824d891c6f2f
--- /dev/null
+++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="2"
+
+ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
+
+WANT_ANT_TASKS="ant-junit4"
+EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+JAVA_ANT_ENCODING="latin1"
+JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
+
+inherit java-pkg-2 java-ant-2 eutils subversion
+
+DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
+HOMEPAGE="https://github.com/beast-dev/beast-mcmc"
+SRC_URI=""
+#SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# TODO: sys-cluster/mpijava
+COMMON_DEPS="dev-java/colt:0
+	dev-java/jdom: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|' "${S}"/scripts/* || die
+	cd lib
+	rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
+	java-pkg_jar-from jdom
+	java-pkg_jar-from colt
+	java-pkg_jar-from itext
+	java-pkg_jar-from jebl
+	java-pkg_jar-from matrix-toolkits-java
+	java-pkg_jar-from commons-math-1
+	java-pkg-2_src_prepare
+}
+
+src_compile() {
+	eant dist_all_BEAST -f build_BEAST_MCMC.xml \
+		-Dgentoo.classpath=$(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/metadata.xml b/sci-biology/beast-mcmc/metadata.xml
new file mode 100644
index 000000000000..18e746ab76ff
--- /dev/null
+++ b/sci-biology/beast-mcmc/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="github">beast-dev/beast-mcmc</remote-id>
+  </upstream>
+</pkgmetadata>