[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [PATCH] Add PePr.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] Add PePr. |
Date: |
Tue, 1 Mar 2016 11:51:45 +0100 |
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
[Prev in Thread] |
Current Thread |
[Next in Thread] |
- Re: [PATCH] Add PePr.,
Ricardo Wurmus <=