Ludovic Courtès <l...@gnu.org> 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 <ricardo.wur...@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.
>
> [...]
>
>> + ;; 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?
>From 7a772f530dba93cfd405e9800e0f043e747a15cc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@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.
---
gnu/packages/bioinformatics.scm | 64 ++++++++++++++++++++++++++++++++++++++++-
1 file changed, 63 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..ef5c8eb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -52,7 +52,8 @@
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
- #:use-module (gnu packages zip))
+ #:use-module (gnu packages zip)
+ #:use-module (srfi srfi-1))
(define-public bamtools
(package
@@ -228,6 +229,67 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
Python.")
(license license:gpl2+)))
+(define-public bioperl-minimal
+ (let* ((inputs `(("perl-module-build" ,perl-module-build)
+ ("perl-data-stag" ,perl-data-stag)
+ ("perl-libwww" ,perl-libwww)
+ ("perl-uri" ,perl-uri)))
+ (transitive-inputs
+ (map (compose package-name cadr)
+ (delete-duplicates
+ (concatenate
+ (map (compose package-transitive-target-inputs cadr) inputs))))))
+ (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. As the PERL5LIB variable contains also
+ ;; the paths of native inputs, we pick the transitive target
+ ;; inputs from %build-inputs.
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin/"))
+ (path (string-join
+ (cons (string-append out "/lib/perl5/site_perl")
+ (map (lambda (name)
+ (assoc-ref %build-inputs name))
+ ',transitive-inputs))
+ ":")))
+ (for-each (lambda (file)
+ (wrap-program file
+ `("PERL5LIB" ":" prefix (,path))))
+ (find-files bin "\\.pl$"))
+ #t))))))
+ (inputs inputs)
+ (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
