Re: [PATCH] Add (minimal) BioPerl.

[Ludovic Courtès]

Ricardo Wurmus <address@hidden> skribis:

> Ludovic Courtès <address@hidden> writes:

[...]

>> There are two cases:
>>
>>   1. When using BioPerl as a library, users will also have Perl
>>      installed, so ‘guix package’ will report the right value for
>>      PERL5LIB.  No problem here.
>>
>>   2. When using just the executables, Perl might be missing from the
>>      profile.  ‘wrap-program’ looks best to me for that, even if there
>>      are many executables.
>
> Agreed.  Attached is a patch with an additional build phase that wraps
> all Perl scripts in $out/bin with the required PERL5LIB paths.
>
> Note: I'm using (getenv PERL5LIB) here for convenience, but that
> includes the native-input "perl-test-most" and the paths to its
> dependencies.  I don't know how to do this nicely in any other way,
> though, because I need not only the direct inputs to be in this list of
> paths, but also their propagated inputs.
>
> 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.

Thank you!

Ludo’.