From mboxrd@z Thu Jan  1 00:00:00 1970
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: Re: [PATCH] Add PePr.
Date: Tue, 1 Mar 2016 11:51:45 +0100
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To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludo@gnu.org>
Cc: guix-devel <guix-devel@gnu.org>


Ludovic Court=C3=A8s <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=E2=80=99t want to duplicate the explanation everywhere, yet it=E2=
=80=99d 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 analysi=
s tool
>> +that is primarily designed for data with biological replicates.  It u=
ses a
>> +negative binomial distribution to model the read counts among the sam=
ples in
>> +the same group, and look for consistent differences between ChIP and =
control
>> +group or two ChIP groups run under different conditions.  PePr was pu=
blished
>> +on Bioinformatics on Jun 2014.")
>
> I=E2=80=99d remove the last sentence.

Done.  Pushed as d1e3282.

Thanks!

~~ Ricardo