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
>From e99a3cdb587afcf874495519c4dcf380295bd6f1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
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+ ;; remove dependency on outdated "distribute" module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
