[PATCH]: gnu: Add RSeQC.

[PATCH]: gnu: Add RSeQC.

[Ricardo Wurmus]

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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


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From e99a3cdb587afcf874495519c4dcf380295bd6f1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@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+             ;; remove dependency on outdated "distribute" module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

Re: [PATCH]: gnu: Add RSeQC.

[Ricardo Wurmus]

Ricardo Wurmus writes:

> 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.

The author has told me that the license is GPLv3; the website will be
updated accordingly.  I will change the license field as soon as the
change is publicly visible.

~~ Ricardo

Re: [PATCH]: gnu: Add RSeQC.

[Ricardo Wurmus]

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Ricardo Wurmus writes:

> The author has told me that the license is GPLv3; the website will be
> updated accordingly.  I will change the license field as soon as the
> change is publicly visible.

The license is now officially declared to be GPLv3:

    http://rseqc.sourceforge.net/#license

Attached is an updated patch.

~~ Ricardo


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From 88a5924c36ccd5317de0307ee4aa9b959ffeb9bd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@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 | 44 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5bd668e..905246a 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 +311,49 @@ 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.")
+    (license license:gpl3)))
+
 (define-public samtools
   (package
     (name "samtools")
-- 
2.1.0

Re: [PATCH]: gnu: Add RSeQC.

[Andreas Enge]

On Thu, Feb 19, 2015 at 11:29:47AM +0100, Ricardo Wurmus wrote:
> +    (license license:gpl3)))

From the text printed on the license page you give, it should be gpl3+.
Otherwise it looks good, pleas push!

Andreas

Re: [PATCH]: gnu: Add RSeQC.

[Ricardo Wurmus]

Andreas Enge writes:

> On Thu, Feb 19, 2015 at 11:29:47AM +0100, Ricardo Wurmus wrote:
>> +    (license license:gpl3)))
>
> From the text printed on the license page you give, it should be gpl3+.
> Otherwise it looks good, pleas push!

You are of course right!  Will push with that change.