[PATCH] Add PePr.

[PATCH] Add PePr.

[Ricardo Wurmus]

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From 6aa9c0cb97350d5cccb43a78e69e2b8887347df0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 2 Oct 2015 16:37:03 +0200
Subject: [PATCH] gnu: Add PePr.

* gnu/packages/bioinformatics.scm (pepr): New variable.
---
 gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d0bf38b..8a81150 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3054,3 +3054,41 @@ Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
 identify genotyping errors, and to perform single-QTL and two-QTL,
 two-dimensional genome scans.")
   (license license:gpl3)))
+
+(define-public pepr
+  (package
+    (name "pepr")
+    (version "1.0.9")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://pypi.python.org/packages/source/P"
+                                  "/PePr/PePr-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2 ; python2 only
+       #:tests? #f ; no tests included
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-egg
+          (lambda _
+            (substitute* "setup.py"
+              (("from setuptools import setup")
+               "from distutils.core import setup"))
+            #t)))))
+    (propagated-inputs
+     `(("python2-numpy" ,python2-numpy)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-pysam" ,python2-pysam)))
+    (home-page "http://github.com/fhcrc/seqmagick")
+    (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
+    (description
+     "PePr is a ChIP-Seq peak calling or differential binding analysis tool
+that is primarily designed for data with biological replicates.  It uses a
+negative binomial distribution to model the read counts among the samples in
+the same group, and look for consistent differences between ChIP and control
+group or two ChIP groups run under different conditions.  PePr was published
+on Bioinformatics on Jun 2014.")
+    (license license:gpl3+)))
-- 
2.1.0

Re: [PATCH] Add PePr.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 6aa9c0cb97350d5cccb43a78e69e2b8887347df0 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 2 Oct 2015 16:37:03 +0200
> Subject: [PATCH] gnu: Add PePr.
>
> * gnu/packages/bioinformatics.scm (pepr): New variable.

[...]

> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'disable-egg
> +          (lambda _
> +            (substitute* "setup.py"
> +              (("from setuptools import setup")
> +               "from distutils.core import setup"))

It would be nice if we had a bug ID or something to refer to this issue:
we don’t want to duplicate the explanation everywhere, yet it’d be nice
to have a pointer to the explanation.  WDYT?

> +    (description
> +     "PePr is a ChIP-Seq peak calling or differential binding analysis tool
> +that is primarily designed for data with biological replicates.  It uses a
> +negative binomial distribution to model the read counts among the samples in
> +the same group, and look for consistent differences between ChIP and control
> +group or two ChIP groups run under different conditions.  PePr was published
> +on Bioinformatics on Jun 2014.")

I’d remove the last sentence.

Otherwise LGTM.

Thank you!

Ludo’.

Re: [PATCH] Add PePr.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From 6aa9c0cb97350d5cccb43a78e69e2b8887347df0 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Fri, 2 Oct 2015 16:37:03 +0200
>> Subject: [PATCH] gnu: Add PePr.
>>
>> * gnu/packages/bioinformatics.scm (pepr): New variable.
>
> [...]
>
>> +       (modify-phases %standard-phases
>> +         (add-after 'unpack 'disable-egg
>> +          (lambda _
>> +            (substitute* "setup.py"
>> +              (("from setuptools import setup")
>> +               "from distutils.core import setup"))
>
> It would be nice if we had a bug ID or something to refer to this issue:
> we don’t want to duplicate the explanation everywhere, yet it’d be nice
> to have a pointer to the explanation.  WDYT?

I added a comment with a link to an upstream bug report.

>> +    (description
>> +     "PePr is a ChIP-Seq peak calling or differential binding analysis tool
>> +that is primarily designed for data with biological replicates.  It uses a
>> +negative binomial distribution to model the read counts among the samples in
>> +the same group, and look for consistent differences between ChIP and control
>> +group or two ChIP groups run under different conditions.  PePr was published
>> +on Bioinformatics on Jun 2014.")
>
> I’d remove the last sentence.

Done.  Pushed as d1e3282.

Thanks!

~~ Ricardo