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authorJustin Lecher <jlec@gentoo.org>2013-02-18 12:05:57 +0000
committerJustin Lecher <jlec@gentoo.org>2013-02-18 12:05:57 +0000
commitc5aa7b1e26c6992666e48a49c4dcaa66d2ab656e (patch)
treedef0685104f8b4ae72a69f1cf1586724ee7a939e /sci-biology/beast-mcmc
parentQA: fix whitespaces in PATCHES array definition (diff)
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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/ChangeLog10
-rw-r--r--sci-biology/beast-mcmc/Manifest22
-rw-r--r--sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild86
-rw-r--r--sci-biology/beast-mcmc/metadata.xml10
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>