From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH]: gnu: Add RSeQC. Date: Wed, 18 Feb 2015 15:12:13 +0100 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:39466) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YO5NE-0005Bc-Hf for guix-devel@gnu.org; Wed, 18 Feb 2015 09:13:09 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YO5NB-00069n-7S for guix-devel@gnu.org; Wed, 18 Feb 2015 09:13:08 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:52658) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YO5NA-00068L-RB for guix-devel@gnu.org; Wed, 18 Feb 2015 09:13:05 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 580E8380665 for ; Wed, 18 Feb 2015 15:13:03 +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 boWuokFjoL4l for ; Wed, 18 Feb 2015 15:12:57 +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 ; Wed, 18 Feb 2015 15:12:57 +0100 (CET) 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 --=-=-= Content-Type: text/plain Attached is a patch to add RSeQC to the bioinformatics module. It only works with Python 2.7. I removed the bundled copy of pysam to be able to use our python-pysam package instead. The license isn't very clear. The Google Code website[1] lists the license as "GPLv3", but nowhere in the source is the license version specified. "PKG-INFO" declares "License :: GPL", whereas "./doc/COPYING" contains the MIT license. It's all pretty messy, so I contacted one of the authors to ask for clarification. Apart from the license issues (which need to be solved before adding RSeQC), does this patch look okay? ~~ Ricardo ___________ [1]: http://code.google.com/p/rseqc --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename="0001-gnu-Add-RSeQC.patch" >From e99a3cdb587afcf874495519c4dcf380295bd6f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 18 Feb 2015 15:00:04 +0100 Subject: [PATCH] gnu: Add RSeQC. * gnu/packages/bioinformatics.scm (rseqc): New variable. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5bd668e..cf7e674 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22,6 +22,7 @@ #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages base) @@ -310,6 +311,52 @@ several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.") (license license:gpl3+))) +(define-public rseqc + (package + (name "rseqc") + (version "2.6.1") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/rseqc/" + version "/RSeQC-" version ".tar.gz")) + (sha256 + (base32 "09rf0x9d6apjja5l01cgprj7vigpw6kiqhy34ibwwlxil0db0ri4")) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled copy of pysam + (delete-file-recursively "lib/pysam") + (substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") "") + ;; do not use bundled copy of pysam + (("^have_pysam = False") "have_pysam = True")))))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) + (inputs + `(("python-cython" ,python2-cython) + ("python-pysam" ,python2-pysam) + ("python-numpy" ,python2-numpy) + ("python-setuptools" ,python2-setuptools) + ("zlib" ,zlib))) + (native-inputs + `(("python-nose" ,python2-nose))) + (home-page "http://rseqc.sourceforge.net/") + (synopsis "RNA-seq quality control package") + (description + "RSeQC provides a number of modules that can comprehensively evaluate +high throughput sequence data, especially RNA-seq data. Some basic modules +inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, +while RNA-seq specific modules evaluate sequencing saturation, mapped reads +distribution, coverage uniformity, strand specificity, etc.") + ;; The license version is only mentioned on the Google Code website; there + ;; are no license headers. I have contacted one of the authors to ask for + ;; clarification. + (license license:gpl3))) + (define-public samtools (package (name "samtools") -- 2.1.0 --=-=-=--