[gentoo-commits] proj/sci:master commit in: sci-biology/conrad/

[Martin Mokrejs]

commit:     53b862b685eda906c6becbbc09b10521a0919e57
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May  3 19:01:51 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May  3 19:01:51 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=53b862b6

sci-biology/conrad: new package, needs java spring

Package-Manager: portage-2.2.28

 sci-biology/conrad/conrad-1.ebuild | 51 ++++++++++++++++++++++++++++++++++++++
 sci-biology/conrad/metadata.xml    | 12 +++++++++
 2 files changed, 63 insertions(+)

diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
new file mode 100644
index 0000000..f9e19a1
--- /dev/null
+++ b/sci-biology/conrad/conrad-1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Gene predictor using ab initio and ad hoc evidence (RNA-Seq, BLAST) on gDNA"
+HOMEPAGE="http://www.broadinstitute.org/annotation/conrad
+	http://sourceforge.net/projects/conradcrf"
+SRC_URI="http://www.broadinstitute.org/annotation/conrad/conradSrcV1.zip"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND="
+	>=virtual/jre-1.5:*
+	dev-java/commons-logging
+	>=dev-java/commons-lang-2.1:*
+	dev-java/colt
+	dev-java/dom4j
+	"
+	# spring # see bug #97004
+	# LBFGS
+DEPEND="${RDEPEND}
+	>=virtual/jdk-1.5:*
+	dev-java/ant-core
+	>=dev-java/jfreechart-1.0.3
+	>=dev-java/jcommon-1.0.6
+	>=dev-java/commons-math-1.1
+	"
+S="${WORKDIR}"
+
+src_prepare(){
+	sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
+}
+
+src_compile(){
+	cd dev || die
+	ant compile || die
+}
+
+src_install() {
+	dobin bin/conrad.sh
+	java-pkg_dojar lib/conrad.jar
+	insinto /usr/share/conrad
+	dodoc -r docs models samples trainingFiles
+}

diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/conrad/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 type="person">
+    <email>mmokrejs@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>