From mboxrd@z Thu Jan  1 00:00:00 1970
From: Ricardo Wurmus <rekado@elephly.net>
Subject: Re: [PATCH] Add cufflinks.
Date: Sat, 23 Jan 2016 09:14:41 +0100
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To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludo@gnu.org>
Cc: guix-devel <guix-devel@gnu.org>


Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From e8186326701df11ee4bdb22d4717cf4b8c27dd50 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Wed, 16 Sep 2015 17:42:41 +0200
>> Subject: [PATCH] gnu: Add cufflinks.
>>
>> * gnu/packages/bioinformatics.scm (boost-1.55, cufflinks): New
>>   variables.
>
> [...]
>
>> +(define boost-1.55
>> +  (package (inherit boost)
>
> I would keep it next to ‘boost’.

Since the update to boost 1.60 this is no longer needed.

>> +          (lambda* (#:key inputs #:allow-other-keys)
>> +            ;; The includes for "eigen" are located in a subdirectory.
>> +            (setenv "CPATH" (string-append (assoc-ref inputs "eigen")
>> +                                           "/include/eigen3/" ":"
>> +                                           (or (getenv "CPATH") "")))
>
> It should be using ‘pkg-config eigen3 --cflags’, but pkg-config is
> missing.
>
> Could you check if adding pkg-config makes this hack unnecessary?
>
> Otherwise LGTM.

Cufflinks does not use pkg-config.  I have modified this to use
EIGEN_CPPFLAGS instead of the much broader CPATH:

+    (arguments
+     `(#:make-flags
+       (list
+        ;; The includes for "eigen" are located in a subdirectory.
+        (string-append "EIGEN_CPPFLAGS="
+                       "-I" (assoc-ref %build-inputs "eigen")
+                       "/include/eigen3/")

I have also cleaned up the package to use “modify-phases”, clarified the
description (“transcript” -> “RNA transcript”), and replaced the license
with “license:boost1.0”.

~~ Ricardo