[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [PATCH] Add cufflinks.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] Add cufflinks. |
Date: |
Sat, 23 Jan 2016 09:14:41 +0100 |
User-agent: |
mu4e 0.9.13; emacs 24.5.1 |
Ludovic Courtès <address@hidden> writes:
> Ricardo Wurmus <address@hidden> skribis:
>
>> From e8186326701df11ee4bdb22d4717cf4b8c27dd50 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <address@hidden>
>> 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
[Prev in Thread] |
Current Thread |
[Next in Thread] |
- Re: [PATCH] Add cufflinks.,
Ricardo Wurmus <=