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 (file)
index 0000000..bec00b1
--- /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 <weaver@gentoo.org> +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 (file)
index 0000000..5356419
--- /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 (file)
index 0000000..3302123
--- /dev/null
+++ b/sci-biology/goby-cpp/metadata.xml
@@ -0,0 +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>
+</pkgmetadata>

diff --git a/sci-biology/goby/ChangeLog b/sci-biology/goby/ChangeLog
new file mode 100644 (file)
index 0000000..217521d
--- /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 <weaver@gentoo.org> +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 (file)
index 0000000..eb7303f
--- /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 (file)
index 0000000..4aa3c54
--- /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 (file)
index 0000000..85d36eb
--- /dev/null
+++ b/sci-biology/goby/metadata.xml
@@ -0,0 +1,12 @@
+<?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>
+       <use>
+               <flag name='cpp'>Compile C/C++ API</flag>
+       </use>
+</pkgmetadata>