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

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>