Re: [PATCH] Add (minimal) BioPerl.

[Ludovic Courtès]

Ricardo Wurmus <address@hidden> skribis:

> Hi,
>
> Ricardo Wurmus <address@hidden> writes:
>
>> Ludovic Courtès <address@hidden> writes:
>>
>>>> Is there a better way to make sure that all (direct and transient)
>>>> runtime dependencies can be found through the PERL5LIB variable?
>>>
>>> Good question.  The #:inputs parameter of build phases contains all the
>>> inputs (native, normal, and propagated) when not cross-compiling, so
>>> that doesn’t help.
>>>
>>> Currently you would have to enumerate the subset of the inputs that you
>>> want to use in ‘wrap-program’ as done in the ‘clusterssh’ recipe, for
>>> instance.  That’s tedious but still preferable, esp. if that reduces the
>>> size of the package’s closure.
>>>
>>>> From a7f69eb16e91ca94e5894b234a98a7f14e78fd64 Mon Sep 17 00:00:00 2001
>>>> From: Ricardo Wurmus <address@hidden>
>>>> Date: Wed, 3 Jun 2015 17:44:20 +0200
>>>> Subject: [PATCH] gnu: Add BioPerl.
>>>>
>>>> * gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
>>>
>>> [...]
>>>
>>>> +            ;; Make sure all executables in "bin" find the required Perl
>>>> +            ;; modules at runtime.
>>>> +            (let* ((out (assoc-ref outputs "out"))
>>>> +                   (bin (string-append out "/bin/"))
>>>> +                   (path (string-append out "/lib/perl5/site_perl:"
>>>> +                                        (getenv "PERL5LIB"))))
>>>> +              (for-each (lambda (file)
>>>> +                          (wrap-program file
>>>> +                            `("PERL5LIB" ":" prefix (,path))))
>>>> +                        (find-files bin "\\.pl$"))
>>>
>>> So either leave a “FIXME” saying that this is closing over a superset of
>>> what’s actually needed at run time, or enumerate the inputs.
>>>
>>> Otherwise LGTM.
>>
>> Attached is a new patch in which only the paths of the transitive target
>> inputs (+ the output perl site_perl directory) are wrapped around the
>> executables.  The resulting path is a lot shorter than the PERL5LIB path
>> at build time and judging from my quick tests the executables do not
>> complain about missing Perl modules.
>>
>> WDYT?
>
> I think that this patch is better than the previous versions in which
> all programmes were wrapped in whatever “PERL5LIB” contained at
> build-time.  If there are no objections, I’ll push the last commit to
> add ‘bioperl-minimal’.

Sure, please go ahead.

Thanks,
Ludo’.