From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/beast-mcmc/Manifest | 6 ++ sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild | 85 +++++++++++++++++++++++ sci-biology/beast-mcmc/beast-mcmc-9999.ebuild | 80 +++++++++++++++++++++ sci-biology/beast-mcmc/metadata.xml | 11 +++ 4 files changed, 182 insertions(+) create mode 100644 sci-biology/beast-mcmc/Manifest create mode 100644 sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild create mode 100644 sci-biology/beast-mcmc/beast-mcmc-9999.ebuild create mode 100644 sci-biology/beast-mcmc/metadata.xml (limited to 'sci-biology/beast-mcmc') 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 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + + beast-dev/beast-mcmc + + -- cgit v1.2.3