Re: [PATCH] Add PePr.

[Ricardo Wurmus]

Ludovic Courtès <address@hidden> writes:

> Ricardo Wurmus <address@hidden> skribis:
>
>> From 6aa9c0cb97350d5cccb43a78e69e2b8887347df0 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <address@hidden>
>> 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