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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-05-03 21:01:51 +0200 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-05-03 21:01:51 +0200 |
| commit | 53b862b685eda906c6becbbc09b10521a0919e57 (patch) | |
| tree | 347c888617b3e35f5340801c5e92380e6c6bde6d /sci-biology | |
| parent | sci-biology/full_lengther_next: version bump (diff) | |
| download | sci-53b862b685eda906c6becbbc09b10521a0919e57.tar.gz sci-53b862b685eda906c6becbbc09b10521a0919e57.tar.bz2 sci-53b862b685eda906c6becbbc09b10521a0919e57.zip | |
sci-biology/conrad: new package, needs java spring
Package-Manager: portage-2.2.28
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/conrad/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/conrad/conrad-1.ebuild | 51 | ||||
| -rw-r--r-- | sci-biology/conrad/metadata.xml | 12 |
3 files changed, 64 insertions, 0 deletions
diff --git a/sci-biology/conrad/Manifest b/sci-biology/conrad/Manifest new file mode 100644 index 000000000..dbda934f8 --- /dev/null +++ b/sci-biology/conrad/Manifest @@ -0,0 +1 @@ +DIST conradSrcV1.zip 13315561 SHA256 fa978d5694d588f1047160f4cab2f8c8cdb613cda8c39a26f482e18e7e7dd742 SHA512 9a6cec2ecb601297e1055e2501c518156f6a4f8a3e30b77e8d2b83d347641f7f590595acdd3aa773296296b74826a3ad382bc538f90bcb439c5b135f83fb6b25 WHIRLPOOL 44712ed80c2e44628543373fe8791692ed8d8492983e3d9c1d70e59a77595a7b7cad2de93ec5a9163a621531739a4eeb9713e19be500d90c4dd631b5aa754461 diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild new file mode 100644 index 000000000..f9e19a18f --- /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 000000000..f68a1b6fa --- /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@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> |