From be04d3b23ea359ae22bffd3db2da101a7094a131 Mon Sep 17 00:00:00 2001
From: Patrice Clement <monsieurp@gentoo.org>
Date: Fri, 15 Apr 2016 14:31:52 +0000
Subject: sci-biology/goby: Bump fastutil dependency SLOT to 0.

---
 sci-biology/goby/goby-1.9.7.3-r1.ebuild | 57 +++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 sci-biology/goby/goby-1.9.7.3-r1.ebuild

(limited to 'sci-biology/goby/goby-1.9.7.3-r1.ebuild')

diff --git a/sci-biology/goby/goby-1.9.7.3-r1.ebuild b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
new file mode 100644
index 000000000000..7b59b99146e4
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.7.3-r1.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,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: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
+}
-- 
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