commit: 194ebd83e325f228abacc2f5cff6c9dc7fef5dff Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jun 22 15:23:51 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jun 22 15:23:51 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=194ebd83
sci-biology/BBmap: version bump Package-Manager: portage-2.2.28 sci-biology/BBmap/BBmap-36.02.ebuild | 43 ++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild new file mode 100644 index 0000000..fa463a3 --- /dev/null +++ b/sci-biology/BBmap/BBmap-36.02.ebuild @@ -0,0 +1,43 @@ +# 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="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" +HOMEPAGE="http://sourceforge.net/projects/bbmap/"; +SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"; + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + sys-cluster/openmpi[java] + >=virtual/jdk-1.7:* + dev-java/ant-core" +RDEPEND="${DEPEND} + >=virtual/jre-1.7:*" + +S="${WORKDIR}"/bbmap + +src_prepare(){ + # fix the line in build.xml to point to mpi.jar location + # <property name="mpijar" location="/tmp/mpi.jar" ></property> + # see bug #542700 + sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml + sed -e 's#compiler="${jcompiler}" ##' -i build.xml +} + +src_compile(){ + ant dist || die +} + +src_install(){ + dobin *.sh + dodoc docs/readme.txt + java-pkg_dojar dist/lib/BBTools.jar +}
