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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
