Re: [PATCH] Add (minimal) BioPerl.

[Ricardo Wurmus]

Ludovic Courtès <address@hidden> writes:

>>>> +    (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.
>
> 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?

>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.
---
 gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc03062..5ea0609 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -226,6 +226,56 @@ pybedtools extends BEDTools by offering feature-level 
manipulations from with
 Python.")
     (license license:gpl2+)))
 
+(define-public bioperl-minimal
+  (package
+    (name "bioperl-minimal")
+    (version "1.6.924")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1"))))
+    (build-system perl-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after
+          'install 'wrap-programs
+          (lambda* (#:key outputs #:allow-other-keys)
+            ;; 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$"))
+              #t))))))
+    (inputs
+     `(("perl-module-build" ,perl-module-build)
+       ("perl-data-stag" ,perl-data-stag)
+       ("perl-libwww" ,perl-libwww)
+       ("perl-uri" ,perl-uri)))
+    (native-inputs
+     `(("perl-test-most" ,perl-test-most)))
+    (home-page "http://search.cpan.org/dist/BioPerl";)
+    (synopsis "Bioinformatics toolkit")
+    (description
+     "BioPerl is the product of a community effort to produce Perl code which
+is useful in biology.  Examples include Sequence objects, Alignment objects
+and database searching objects.  These objects not only do what they are
+advertised to do in the documentation, but they also interact - Alignment
+objects are made from the Sequence objects, Sequence objects have access to
+Annotation and SeqFeature objects and databases, Blast objects can be
+converted to Alignment objects, and so on.  This means that the objects
+provide a coordinated and extensible framework to do computational biology.")
+    (license (package-license perl))))
+
 (define-public python-biopython
   (package
     (name "python-biopython")
-- 
2.1.0