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authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/goby
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proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/goby')
-rw-r--r--sci-biology/goby/Manifest4
-rw-r--r--sci-biology/goby/goby-1.9.7.3.ebuild57
-rw-r--r--sci-biology/goby/goby-1.9.8.1.ebuild57
-rw-r--r--sci-biology/goby/metadata.xml8
4 files changed, 126 insertions, 0 deletions
diff --git a/sci-biology/goby/Manifest b/sci-biology/goby/Manifest
new file mode 100644
index 000000000000..9e3b65fbcbaa
--- /dev/null
+++ b/sci-biology/goby/Manifest
@@ -0,0 +1,4 @@
+DIST goby_1.9.7.3-deps.zip 19959489 SHA256 3932c61f001fc1d06ef298043d5206041e47175fa28d755efd01148de35b567a
+DIST goby_1.9.7.3-src.zip 15642000 SHA256 fe32a6720fcc0858811e40b744c9bcfffbb6cf277be50102446ff8798fd9ab24
+DIST goby_1.9.8.1-deps.zip 20820943 SHA256 eb11916408a7978a1e90967783b8167b96c6d0dd60ae58cf1dab915a519d1bbb
+DIST goby_1.9.8.1-src.zip 15748880 SHA256 e2489a815a38bd10b1ec59b4e262a023f97994d9953f97bcc6571cadd05919c3
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..20622d49ffa7
--- /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
+# $Id$
+
+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/goby-1.9.8.1.ebuild b/sci-biology/goby/goby-1.9.8.1.ebuild
new file mode 100644
index 000000000000..5039b96941b3
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.8.1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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..3bc02ac6b32e
--- /dev/null
+++ b/sci-biology/goby/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <use>
+ <flag name="cpp">Compile C/C++ API</flag>
+ </use>
+</pkgmetadata>