From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] Add =?utf-8?B?cHl0aG9u4oCTcGxh?= =?utf-8?Q?stid=2C?= python-twobitreader. Date: Wed, 6 Apr 2016 15:11:49 -0400 Message-ID: <20160406191149.GD6333@jasmine> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45651) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ansrn-0004xE-8Y for guix-devel@gnu.org; Wed, 06 Apr 2016 15:11:52 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ansrl-0000Dp-SC for guix-devel@gnu.org; Wed, 06 Apr 2016 15:11:51 -0400 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:42236) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ansrl-0000Dk-OU for guix-devel@gnu.org; Wed, 06 Apr 2016 15:11:49 -0400 Content-Disposition: inline In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Ricardo Wurmus Cc: guix-devel On Wed, Apr 06, 2016 at 04:36:52PM +0200, Ricardo Wurmus wrote: > From ecb23f8eb2dbd83cbaa97972d6258ccb44c58194 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Wed, 6 Apr 2016 16:34:19 +0200 > Subject: [PATCH 1/2] gnu: Add python-twobitreader. > > * gnu/packages/bioinformatics.scm (python-twobitreader, > python2-twobitreader): New variables. LGTM! > --- > gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ > 1 file changed, 23 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 01e9060..d13303d 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -1038,6 +1038,29 @@ also includes an interface for tabix.") > (define-public python2-pysam > (package-with-python2 python-pysam)) > > +(define-public python-twobitreader > + (package > + (name "python-twobitreader") > + (version "3.1.2") > + (source (origin > + (method url-fetch) > + (uri (pypi-uri "twobitreader" version)) > + (sha256 > + (base32 > + "0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169")))) > + (build-system python-build-system) > + (native-inputs > + `(("python-sphinx" ,python-sphinx))) > + (home-page "https://github.com/benjschiller/twobitreader") > + (synopsis "Python library for reading .2bit files") > + (description > + "twobitreader is a Python library for reading .2bit files as used by the > +UCSC genome browser.") > + (license license:artistic2.0))) > + > +(define-public python2-twobitreader > + (package-with-python2 python-twobitreader)) > + > (define-public cd-hit > (package > (name "cd-hit") > -- > 2.1.0 > > From a2604f6d4b03727ebd7922ce373486b13ab31c00 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Wed, 6 Apr 2016 16:35:09 +0200 > Subject: [PATCH 2/2] gnu: Add python-plastid. > > * gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New > variables. > --- > gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ > 1 file changed, 35 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index d13303d..1896002 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -1061,6 +1061,41 @@ UCSC genome browser.") > (define-public python2-twobitreader > (package-with-python2 python-twobitreader)) > > +(define-public python-plastid > + (package > + (name "python-plastid") > + (version "0.4.5") > + (source (origin > + (method url-fetch) > + (uri (pypi-uri "plastid" version)) > + (sha256 > + (base32 > + "1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq")))) > + (build-system python-build-system) > + (arguments > + ;; Some test files are not included. > + `(#:tests? #f)) > + (propagated-inputs > + `(("python-numpy" ,python-numpy) > + ("python-scipy" ,python-scipy) > + ("python-pandas" ,python-pandas) > + ("python-pysam" ,python-pysam) > + ("python-matplotlib" ,python-matplotlib) > + ("python-biopython" ,python-biopython) > + ("python-twobitreader" ,python-twobitreader))) > + (native-inputs > + `(("python-cython" ,python-cython) > + ("python-nose" ,python-nose))) > + (home-page "https://github.com/joshuagryphon/plastid") > + (synopsis "Python library for genomic analysis") > + (description > + "plastid is a Python library for genomic analysis – in particular, > +high-throughput sequencing data – with an emphasis on simplicity.") > + (license license:bsd-3))) > + > +(define-public python2-plastid > + (package-with-python2 python-plastid)) > + > (define-public cd-hit > (package > (name "cd-hit") > -- > 2.1.0 >