commit: c18359435de9e9cb23bcfaefd6ff9ad502ab2f92 Author: layman <layman <AT> localhost> AuthorDate: Fri Aug 14 21:06:49 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Fri Aug 14 21:08:47 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1835943
sci-biology/tophat: tophat-2.1.0 version bump Package-Manager: portage-2.2.20-prefix sci-biology/tophat/ChangeLog | 5 ++++ sci-biology/tophat/tophat-2.1.0.ebuild | 43 ++++++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog index 84e8313..93ca57b 100644 --- a/sci-biology/tophat/ChangeLog +++ b/sci-biology/tophat/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.14 2015/04/07 14:35:24 jlec Exp $ +*tophat-2.1.0 (14 Aug 2015) + + 14 Aug 2015; Michael Schubert <[email protected]> +tophat-2.1.0.ebuild: + sci-biology/tophat: tophat-2.1.0 version bump + 02 May 2015; Martin Mokrejs <[email protected]> tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild: added PYTHON_USEDEP diff --git a/sci-biology/tophat/tophat-2.1.0.ebuild b/sci-biology/tophat/tophat-2.1.0.ebuild new file mode 100644 index 0000000..0e4b31e --- /dev/null +++ b/sci-biology/tophat/tophat-2.1.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.9.ebuild,v 1.1 2014/03/06 09:46:50 jlec Exp $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +AUTOTOOLS_IN_SOURCE_BUILD=yes +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2" +HOMEPAGE="http://ccb.jhu.edu/software/tophat"; +SRC_URI="https://github.com/infphilo/tophat/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +DEPEND="dev-libs/boost" +# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency +# boost and seqan is needed for tophat_reporter + +# tophat.py calls +# samtools_0.1.18 view -h - +# samtools_0.1.18 sort +# samtools_0.1.18 merge -f -h -u -Q --sam-header +RDEPEND="${DEPEND} + >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )" + +src_configure() { + local myeconfargs=( + $(use_enable debug) + ) + autotools-utils_src_configure + + echo "../src/libtophat.a: libtophat.a" >> src/Makefile + echo "../src/libgc.a: libgc.a" >> src/Makefile + echo "samtools_0.1.18:" >> src/Makefile + echo -e "\tcp samtools-0.1.18/\$@ \$@" >> src/Makefile +}
