From: Andrey Kislyuk Date: Sun, 25 Sep 2011 21:50:28 +0000 (+0000) Subject: New package, ebuild written by me X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=08eeb588c73c87cdd85573821e201db21c6a1373;p=gentoo.git New package, ebuild written by me Package-Manager: portage-2.2.0_alpha45/cvs/Linux x86_64 --- diff --git a/sci-biology/goby-cpp/ChangeLog b/sci-biology/goby-cpp/ChangeLog new file mode 100644 index 000000000000..bec00b1eede4 --- /dev/null +++ b/sci-biology/goby-cpp/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/goby-cpp +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby-cpp/ChangeLog,v 1.1 2011/09/25 21:45:36 weaver Exp $ + +*goby-cpp-1.9.7.3 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk +goby-cpp-1.9.7.3.ebuild, + +metadata.xml: + New package, ebuild written by me + diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild new file mode 100644 index 000000000000..5356419cbd6c --- /dev/null +++ b/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby-cpp/goby-cpp-1.9.7.3.ebuild,v 1.1 2011/09/25 21:45:36 weaver Exp $ + +EAPI=4 + +inherit autotools + +DESCRIPTION="A DNA sequencing data management framework - C/C++ API" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip" + +LICENSE="GPL-3" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND=">=dev-libs/protobuf-2.4.1 + >=dev-libs/libpcre-8.12" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/goby_${PV}/cpp" + +src_prepare() { + eautoreconf +} diff --git a/sci-biology/goby-cpp/metadata.xml b/sci-biology/goby-cpp/metadata.xml new file mode 100644 index 000000000000..3302123e5718 --- /dev/null +++ b/sci-biology/goby-cpp/metadata.xml @@ -0,0 +1,9 @@ + + + + + weaver@gentoo.org + Andrey Kislyuk + + sci-biology + diff --git a/sci-biology/goby/ChangeLog b/sci-biology/goby/ChangeLog new file mode 100644 index 000000000000..217521d6dc03 --- /dev/null +++ b/sci-biology/goby/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/goby +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/ChangeLog,v 1.1 2011/09/25 21:50:28 weaver Exp $ + +*goby-1.9.7.3 (25 Sep 2011) + + 25 Sep 2011; Andrey Kislyuk +goby-1.9.7.3.ebuild, + +metadata.xml: + New package, ebuild written by me + diff --git a/sci-biology/goby/Manifest b/sci-biology/goby/Manifest new file mode 100644 index 000000000000..eb7303f8541f --- /dev/null +++ b/sci-biology/goby/Manifest @@ -0,0 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +DIST goby_1.9.7.3-deps.zip 19959489 RMD160 f105e632eaac0863b4073bbca5d135014bf81fa9 SHA1 64a06bda9eedabd75cc86c50368660d9d67a7319 SHA256 3932c61f001fc1d06ef298043d5206041e47175fa28d755efd01148de35b567a +DIST goby_1.9.7.3-src.zip 15642000 RMD160 d8329dc566b62fdcb36b988406f8d357857f3b10 SHA1 63cadf1dbe5603948f765bb6af2788cbb5edd93e SHA256 fe32a6720fcc0858811e40b744c9bcfffbb6cf277be50102446ff8798fd9ab24 +EBUILD goby-1.9.7.3.ebuild 1642 RMD160 ac14eedf89adf2f4625a5eac98b3b17ca76023ed SHA1 3f7c84bd642834bdcac7ba5859be183555151ee7 SHA256 c00a9ed4bd9a7a9723474335fc810bcd7b6097267f609eb5cc685f50e2906ba0 +MISC ChangeLog 360 RMD160 459145eb924a4fc6f417f919de2d8a8134b7422c SHA1 db9f53660c6fe931b73c9c87d2075a6dfa9030b9 SHA256 e8282abbe76d3ef941fb206e6a3d21db83711fb4a42a4fd6a32710c9ad8e94fa +MISC metadata.xml 318 RMD160 c2c725d13f90803cc98059763f8e446e14e6bef7 SHA1 040c908da940371f7064350526e9ff5ab49aa01a SHA256 3479df13467f79899e26e35091ecafa15ec58532c555bf5341f5b03c9c1c9e8d +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v1.4.11 (GNU/Linux) + +iEYEARECAAYFAk5/oioACgkQ8xSwyhbn2OaBkACdEh54vS7bKbQpO8apg6aUq5DR +l3IAnRSiH0RT71OdOQ0Y3abC8wszmwko +=XNwY +-----END PGP SIGNATURE----- diff --git a/sci-biology/goby/goby-1.9.7.3.ebuild b/sci-biology/goby/goby-1.9.7.3.ebuild new file mode 100644 index 000000000000..4aa3c54939da --- /dev/null +++ b/sci-biology/goby/goby-1.9.7.3.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/goby-1.9.7.3.ebuild,v 1.1 2011/09/25 21:50:28 weaver Exp $ + +EAPI=4 + +ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby" +EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2" +EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar" + +JAVA_ANT_REWRITE_CLASSPATH="true" + +#inherit java-pkg-2 java-ant-2 subversion +inherit java-pkg-2 java-ant-2 + +MY_P="${PN}_${PV}" + +DESCRIPTION="A DNA sequencing data management framework" +HOMEPAGE="http://campagnelab.org/software/goby/" +SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip + http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="+cpp" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPS="dev-java/commons-logging + dev-java/commons-lang:2.1 + dev-java/commons-io:1 + dev-libs/protobuf[java] + dev-java/fastutil:5.0 + dev-java/log4j + dev-java/jsap + dev-java/commons-configuration + dev-java/commons-math:2" +DEPEND=">=virtual/jdk-1.6 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.6 + ${COMMON_DEPS} + cpp? ( ~sci-biology/goby-cpp-${PV} )" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + sed -i '/sge/ d' build.xml || die + java-pkg-2_src_prepare +} + +src_install() { + java-pkg_dojar goby*.jar + java-pkg_dolauncher goby --jar goby.jar + + insinto /usr/share/${PN} + doins -r python + dodoc CHANGES.txt +} diff --git a/sci-biology/goby/metadata.xml b/sci-biology/goby/metadata.xml new file mode 100644 index 000000000000..85d36ebbded8 --- /dev/null +++ b/sci-biology/goby/metadata.xml @@ -0,0 +1,12 @@ + + + + + weaver@gentoo.org + Andrey Kislyuk + + sci-biology + + Compile C/C++ API + +