From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 3/3]: Add pybedtools. Date: Fri, 20 Feb 2015 17:48:35 +0100 Message-ID: References: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58169) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YOqkv-0007vN-2Z for guix-devel@gnu.org; Fri, 20 Feb 2015 11:48:46 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YOqkr-00074h-QF for guix-devel@gnu.org; Fri, 20 Feb 2015 11:48:45 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:57266) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YOqkr-00074d-FI for guix-devel@gnu.org; Fri, 20 Feb 2015 11:48:41 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id ED10E380835 for ; Fri, 20 Feb 2015 17:48:40 +0100 (CET) Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id xuE2TnE28LJV for ; Fri, 20 Feb 2015 17:48:35 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Fri, 20 Feb 2015 17:48:35 +0100 (CET) In-Reply-To: Content-Disposition: inline; filename="0003-gnu-Add-pybedtools.patch" 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: Guix-devel >From 26054dc29fa3132e58b2a71e20f37cfc3446a68d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 Feb 2015 17:43:08 +0100 Subject: [PATCH 3/3] gnu: Add pybedtools. * gnu/packages/bioinformatics.scm (python2-pybedtools): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b64dab7..092a6e3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -33,6 +33,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages tbb) #:use-module (gnu packages vim) + #:use-module (gnu packages web) #:use-module (gnu packages zip)) (define-public bedops @@ -141,6 +142,39 @@ intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.") (license license:gpl2))) +(define-public python2-pybedtools + (package + (name "python2-pybedtools") + (version "0.6.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-" + version ".tar.gz")) + (sha256 + (base32 + "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an")))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; no Python 3 support + (inputs + `(("python-cython" ,python2-cython) + ("python-matplotlib" ,python2-matplotlib) + ("python-setuptools" ,python2-setuptools))) + (propagated-inputs + `(("bedtools" ,bedtools) + ("samtools" ,samtools))) + (native-inputs + `(("python-pyyaml" ,python2-pyyaml) + ("python-nose" ,python2-nose))) + (home-page "https://pythonhosted.org/pybedtools/") + (synopsis "Python wrapper for BEDtools programs") + (description + "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs, +which are widely used for genomic interval manipulation or \"genome algebra\". +pybedtools extends BEDTools by offering feature-level manipulations from with +Python.") + (license license:gpl2+))) + (define-public bowtie (package (name "bowtie") -- 2.1.0