* [PATCH] Add PePr.
@ 2015-10-23 11:44 Ricardo Wurmus
2015-10-26 14:40 ` Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2015-10-23 11:44 UTC (permalink / raw)
To: guix-devel
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[-- Attachment #1: 0001-gnu-Add-PePr.patch --]
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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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] Add PePr.
2015-10-23 11:44 [PATCH] Add PePr Ricardo Wurmus
@ 2015-10-26 14:40 ` Ludovic Courtès
2016-03-01 10:51 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Ludovic Courtès @ 2015-10-26 14:40 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
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’.
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] Add PePr.
2015-10-26 14:40 ` Ludovic Courtès
@ 2016-03-01 10:51 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2016-03-01 10:51 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 3+ messages in thread
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2015-10-23 11:44 [PATCH] Add PePr Ricardo Wurmus
2015-10-26 14:40 ` Ludovic Courtès
2016-03-01 10:51 ` Ricardo Wurmus
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