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authorlayman <layman@localhost>2015-08-14 22:06:49 +0100
committerlayman <layman@localhost>2015-08-14 22:08:47 +0100
commitc18359435de9e9cb23bcfaefd6ff9ad502ab2f92 (patch)
treeb6912834d4e6ce39394b28f20f0d589a498fe43c
parentapp-admin/eselect: Update Patch (diff)
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sci-biology/tophat: tophat-2.1.0 version bump
Package-Manager: portage-2.2.20-prefix
-rw-r--r--sci-biology/tophat/ChangeLog5
-rw-r--r--sci-biology/tophat/Manifest1
-rw-r--r--sci-biology/tophat/tophat-2.1.0.ebuild43
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
+}