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author | 2013-02-18 12:05:57 +0000 | |
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committer | 2013-02-18 12:05:57 +0000 | |
commit | c5aa7b1e26c6992666e48a49c4dcaa66d2ab656e (patch) | |
tree | def0685104f8b4ae72a69f1cf1586724ee7a939e /sci-biology/beast-mcmc | |
parent | QA: fix whitespaces in PATCHES array definition (diff) | |
download | historical-c5aa7b1e26c6992666e48a49c4dcaa66d2ab656e.tar.gz historical-c5aa7b1e26c6992666e48a49c4dcaa66d2ab656e.tar.bz2 historical-c5aa7b1e26c6992666e48a49c4dcaa66d2ab656e.zip |
sci-biology/beast-mcmc: Version Bump, fixes missing package, #374277
Package-Manager: portage-2.2.0_alpha163/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916
Diffstat (limited to 'sci-biology/beast-mcmc')
-rw-r--r-- | sci-biology/beast-mcmc/ChangeLog | 10 | ||||
-rw-r--r-- | sci-biology/beast-mcmc/Manifest | 22 | ||||
-rw-r--r-- | sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild | 86 | ||||
-rw-r--r-- | sci-biology/beast-mcmc/metadata.xml | 10 |
4 files changed, 116 insertions, 12 deletions
diff --git a/sci-biology/beast-mcmc/ChangeLog b/sci-biology/beast-mcmc/ChangeLog index 7990118817a7..c517c6648f80 100644 --- a/sci-biology/beast-mcmc/ChangeLog +++ b/sci-biology/beast-mcmc/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/beast-mcmc -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/ChangeLog,v 1.4 2010/03/21 01:21:23 weaver Exp $ +# 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 20 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -beast-mcmc-1.5.1.ebuild: Drop old version diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest index 4fc0aa320a47..bce2e7030ec0 100644 --- a/sci-biology/beast-mcmc/Manifest +++ b/sci-biology/beast-mcmc/Manifest @@ -1,5 +1,17 @@ -DIST beast-mcmc-1.5.2.tar.bz2 38834702 RMD160 c4d954c604ae021afb6c1c19e041c5153ffad42b SHA1 fffd35a05b0cbcca74a491ef06cd7ea7e8c9d3c9 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 -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 780 RMD160 56bc9dce0dcc75eb3112ae724911ae0288eb29c0 SHA1 5836db21e5d735a7bf09bcd7bc84413d2ae77b0f SHA256 58f2b2a964d980ac2169686441e650e80fd6177557422352bc45943a676b51a2 -MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA256 + +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 +MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.19 (GNU/Linux) + +iEYEAREIAAYFAlEiGSUACgkQgAnW8HDreRa2yQCfUgsntCv5EidAsPi6e6ddvyZL +hSEAoMavWET8d1oHCKnSJx6Umy5+KXyv +=EP8h +-----END PGP SIGNATURE----- diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild new file mode 100644 index 000000000000..69168b89db00 --- /dev/null +++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild @@ -0,0 +1,86 @@ +# 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) +} diff --git a/sci-biology/beast-mcmc/metadata.xml b/sci-biology/beast-mcmc/metadata.xml index 3302123e5718..fc7c76942a10 100644 --- a/sci-biology/beast-mcmc/metadata.xml +++ b/sci-biology/beast-mcmc/metadata.xml @@ -1,9 +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> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata> |