Re: [PATCH] Add PePr.

[ludo@gnu.org (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’.