Re: [PATCH] Add (minimal) BioPerl.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From e8cffdb9e7a2447657b3f700b2f0beb00ad0f98e Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Wed, 3 Jun 2015 17:44:20 +0200
>> Subject: [PATCH] gnu: Add BioPerl.
>>
>> * gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
>
> [...]
>
>> +(define-public bioperl-minimal
>> +  (package
>> +    (name "bioperl-minimal")
>
> So is it meant to be used as a Perl library, as a standalone executable,
> or both?

It's a library and a collection of perl executables using the library,
so I suppose "bioperl-minimal" would be appropriate?

>> +    (native-search-paths (list (search-path-specification
>> +                                (variable "PERL5LIB")
>> +                                (files '("lib/perl5/site_perl")))))
>
> Why is it needed?  At first sight it looks wrong because PERL5LIB is
> “owned” by Perl itself.
>
> If there’s an executable that needs to find the libs listed in
> ‘propagated-inputs’, the best way would be to use ‘wrap-program’, I
> think.

That's for the executables to find the library contained in this package
as well as the propagated Perl libraries.  There are *many* executables,
which made me shy away from wrapping each of them to be run with the
PERL5LIB variable set.

~~ Ricardo