+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2

+# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/ChangeLog,v 1.5 2013/02/18 12:05:56 jlec Exp $

+

+*beast-mcmc-1.7.5 (18 Feb 2013)

+

+ 18 Feb 2013; Justin Lecher <jlec@gentoo.org> +beast-mcmc-1.7.5.ebuild,

+ metadata.xml:

+ Version Bump, fixes missing package, #374277

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+DIST beast-mcmc-1.5.2.tar.bz2 38834702 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 SHA512 8549db6cb49d64eb3a97fa6478bdbabfecd44ccc6236c474a1961ec5d6fc8326072fb961035df70982a9f1c08a36572529a07b88e2d33a43fa0fd5c07df3a414 WHIRLPOOL 595f606640daa32c79373c9003ddbc1f80dcbbf01e9e9c18191328b80eb50b45ac70032027dd1efb0e256d78b88bfe1742151a16f6f333938099943a7b2cd16a

+DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5

+EBUILD beast-mcmc-1.5.2.ebuild 2919 SHA256 44f00122a5707c5dae92fe346056f71b1183ac75ae106eb7d89e21a35fb66c9c SHA512 d89b69570a908768a65033c7fa162aa11547073f2909640b92d7d9f451bd2b451c534a2c9fd77c5c0be93efe8bf5b4f1142bc1a4b2206e54904d82975ee7d3bf WHIRLPOOL 59cf70050d3c27d3319893be712256a62ea4c15730ea04c0a1f396b34cb170d54c7d3eb529e19cc6924ec6b9a9780c39112e096ca5244d420c9bdef713694af8

+EBUILD beast-mcmc-1.7.5.ebuild 3030 SHA256 0efcaa87d6d9bd9c9d2129a4d00e6486587048a2fb32b0ecd6ce20c680a8f911 SHA512 c4302121ca41ae351d461169355c8891f25ffd24c95c58f31bd1d32d5732a5c2da06f2a4db07e4f4f24d77ab6aea434d660a2947807b37fc5280696fef7ea295 WHIRLPOOL a67e07b5a91d8ed2a9588c43ab9ca67a81753f299f46c8d6c2e82cfa9809d288e9947e633af9d6ad63bb82b91dcf20867ddd54d1ebe4a8cf20bdb93e91d2863e

+EBUILD beast-mcmc-9999.ebuild 2869 SHA256 ef97822c25a76d3ebd0e8902d6dc8960c6a2b1d258d83a6449889cb5d022a87e SHA512 721d89db46ac3fc7c3ce2c76150f94268ee775e22aa7f2c59ad0505d8419d546210a7cbf1bb2238a5b2245f26a428b3c88e725672e35b30b2b1851df4fa6a106 WHIRLPOOL 7099ce46dd003a07da377ce9a5f35b3ace6c1412604ef35c03d29176c80ee94ea3758a8bf54d8ca9ce8212debbcdfd20f0daad502910c8bd38b110856436d6e5

+MISC ChangeLog 948 SHA256 ae229c2c4983a5cd570db87deb202aa24e1b0d160e8549940162666f84a37ce2 SHA512 ada12574cf1df32ef3f5be009dd80a67a987cc00f6b156c76deaa1375b8614d253e7762627712e82bcfac82367d4ddcab06a855e84fe83b27cb92f5c11d51458 WHIRLPOOL c9e214886a2a3c493f55d9db1dc7fdf3b16876549e46732b5339dfd000495f8282986c1886326fccc6605cd4456c16c22fe4561a2200bdc3bec3acb0eaacf25e

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+# Copyright 1999-2013 Gentoo Foundation

+# Distributed under the terms of the GNU General Public License v2

+# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild,v 1.1 2013/02/18 12:05:56 jlec Exp $

+

+EAPI=5

+

+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

+

+MY_P=BEASTv${PV}

+

+DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"

+HOMEPAGE="http://code.google.com/p/beast-mcmc/"

+#SRC_URI=""

+SRC_URI="http://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: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}"/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-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-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)

+}

+ <maintainer>

+ <email>weaver@gentoo.org</email>

+ <name>Andrey Kislyuk</name>

+ </maintainer>

+ <herd>sci-biology</herd>