summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorPatrice Clement <monsieurp@gentoo.org>2016-04-15 14:31:52 +0000
committerPatrice Clement <monsieurp@gentoo.org>2016-04-15 14:32:56 +0000
commitbe04d3b23ea359ae22bffd3db2da101a7094a131 (patch)
tree47fb53cf3addc68b5a7ab120dd1b07489c77f2df /sci-biology
parentdev-python/superlance: new package, version 0.11 (diff)
downloadgentoo-be04d3b23ea359ae22bffd3db2da101a7094a131.tar.gz
gentoo-be04d3b23ea359ae22bffd3db2da101a7094a131.tar.bz2
gentoo-be04d3b23ea359ae22bffd3db2da101a7094a131.zip
sci-biology/goby: Bump fastutil dependency SLOT to 0.
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/goby/goby-1.9.7.3-r1.ebuild57
-rw-r--r--sci-biology/goby/goby-1.9.8.1-r1.ebuild57
2 files changed, 114 insertions, 0 deletions
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
+}
diff --git a/sci-biology/goby/goby-1.9.8.1-r1.ebuild b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
new file mode 100644
index 000000000000..ee1702ec5244
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.8.1-r1.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,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
+}