From mboxrd@z Thu Jan  1 00:00:00 1970
From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=)
Subject: Re: [PATCH] Add PePr.
Date: Mon, 26 Oct 2015 15:40:21 +0100
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In-Reply-To: <idjbnbpyfli.fsf@bimsb-sys02.mdc-berlin.net> (Ricardo Wurmus's
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To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: guix-devel <guix-devel@gnu.org>

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?

> +    (description
> +     "PePr is a ChIP-Seq peak calling or differential binding analysis t=
ool
> +that is primarily designed for data with biological replicates.  It uses=
 a
> +negative binomial distribution to model the read counts among the sample=
s in
> +the same group, and look for consistent differences between ChIP and con=
trol
> +group or two ChIP groups run under different conditions.  PePr was publi=
shed
> +on Bioinformatics on Jun 2014.")

I=E2=80=99d remove the last sentence.

Otherwise LGTM.

Thank you!

Ludo=E2=80=99.