diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 64 |
1 files changed, 63 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a50a85f2d..d7e4da6fe8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -51,7 +51,8 @@ #: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 aragorn (package @@ -276,6 +277,67 @@ 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") |