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| author |   Justin <jlec@gentoo.org> | 2015-08-15 07:56:44 +0200 |
|---|---|---|
| committer | Justin <jlec@gentoo.org> | 2015-08-15 07:56:44 +0200 |
| commit | 7672a9f4962e4ae9c80622ef78df9bd145780aab (patch) | |
| tree | b6912834d4e6ce39394b28f20f0d589a498fe43c | |
| parent | app-admin/eselect: Update Patch (diff) | |
| parent | sci-biology/tophat: tophat-2.1.0 version bump (diff) | |
| download | sci-7672a9f4962e4ae9c80622ef78df9bd145780aab.tar.gz sci-7672a9f4962e4ae9c80622ef78df9bd145780aab.tar.bz2 sci-7672a9f4962e4ae9c80622ef78df9bd145780aab.zip | |
Merge pull request #461 from mschubert/tophat_2.1.0
sci-biology/tophat: tophat-2.1.0 version bump
| -rw-r--r-- | sci-biology/tophat/ChangeLog | 5 | ||||
| -rw-r--r-- | sci-biology/tophat/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/tophat/tophat-2.1.0.ebuild | 43 |
3 files changed, 49 insertions, 0 deletions
diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog index 84e8313d9..93ca57b5b 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 <mschu.dev@gmail.com> +tophat-2.1.0.ebuild: + sci-biology/tophat: tophat-2.1.0 version bump + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild: added PYTHON_USEDEP diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest index 0361b69de..fd00473d3 100644 --- a/sci-biology/tophat/Manifest +++ b/sci-biology/tophat/Manifest @@ -1,3 +1,4 @@ DIST tophat-2.0.12.tar.gz 1767329 SHA256 ce97d9f3c6d6c0dd256744498b5209a9260ca3118a8e5210d9404fae890a4d74 SHA512 c2eae628cb1d0a19793708df710a10e04663e3dae12725f93faf17d1784360239a82a7fd9cee6e3d9b7156fe74b9612b71a97de540c9ba0ff9a61005a14c4b3b WHIRLPOOL a2582c7ec91fd589e0e8854b65250eaafe567241fad0023b788359e1d67b3cbf024ddf3a3543974bf43e13b13420ea37186a85d1b55059ea1cfd87915e4d39c0 DIST tophat-2.0.13.tar.gz 1998819 SHA256 acbe8f1a47131053d4b766df117c9f83458fdc5df6a500d7488e4c6cef51e512 SHA512 1fd38f4e866997f82209892111c976d29dc9e1055ba8fc65ee3ea2436a4d9673a73985dcac73519c7f8abc719bda20366aa84a36e8dea4a9b7d135c1b94afb89 WHIRLPOOL bf4dc17c5d508194c85dc73c73d66a390e95484db14ca282c5be5ca6ab55e2c7edfd9861ff6f0daba4344089a25e47372ceaf2d4ea269d27dc6808f4e0b637b0 DIST tophat-2.0.14.tar.gz 2013476 SHA256 547c5c9d127cbf7d61bc73c4251ff98a07d57e59b3718666a18b58acfb8fcfbf SHA512 fcdf7c8ad298284acabeac3bc96c7f08e74927d3c6e38fa93914a0bba470ba495cc5920ef0c22efcd652788e484162c0632c6d3574f3d90ba15fe8690feb0ec8 WHIRLPOOL ca2bcc89553160480b5594cfb755701d3b72ee8c8c7629b8b6091a9849bd910423a699dd7750f7ee654fa15c216538bfa0786ecdc14855eb73e39a30029ca00e +DIST tophat-2.1.0.tar.gz 4300174 SHA256 eceb56527c23c970f51cb3ff4f4c2a2d28d110cfa8f2f0a333d1b58152c35274 SHA512 c1c9e3006ab7777811fdfe61611143117af0819ba8eaa0ca359e76352a6d2c03c8616195bc7aca79fedbc1cd1a15e6d242ef5f006500bdee7e35b11787afcea6 WHIRLPOOL 8c0336d0b3b2675df1c6e2f9d8da6ed08f30626e957e41655042eb8c7dae8d892c233f17fd235da327a3bfba45ba1a8715558f6a65d9d4adeaa870049cc01940 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 000000000..0e4b31ee9 --- /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 +} |