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gnu: bioperl-minimal: Avoid top-level cross-module references. 

This could lead to circular reference breakage.

* gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level
references to perl-* variables and their transitive inputs to
'arguments' and 'inputs'.
master
Ludovic Courtès 2021-07-01 17:11:16 +02:00
parent b17ee44212
commit ebb8e44a4a
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GPG Key ID: 090B11993D9AEBB5
1 changed files with 55 additions and 54 deletions
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@ -1147,15 +1147,6 @@ alignments and perform the following operations:
(license license:expat))) (license license:expat)))
(define-public bioperl-minimal (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 (package
(name "bioperl-minimal") (name "bioperl-minimal")
(version "1.7.0") (version "1.7.0")
@ -1174,6 +1165,12 @@ alignments and perform the following operations:
"0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783")))) "0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
(build-system perl-build-system) (build-system perl-build-system)
(arguments (arguments
(let ((transitive-inputs
(map (compose package-name cadr)
(delete-duplicates
(concatenate
(map (compose package-transitive-target-inputs cadr)
(package-inputs this-package)))))))
`(#:phases `(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after (add-after
@ -1195,8 +1192,12 @@ alignments and perform the following operations:
(wrap-program file (wrap-program file
`("PERL5LIB" ":" prefix (,path)))) `("PERL5LIB" ":" prefix (,path))))
(find-files bin "\\.pl$")) (find-files bin "\\.pl$"))
#t)))))) #t)))))))
(inputs inputs) (inputs
`(("perl-module-build" ,perl-module-build)
("perl-data-stag" ,perl-data-stag)
("perl-libwww" ,perl-libwww)
("perl-uri" ,perl-uri)))
(native-inputs (native-inputs
`(("perl-test-most" ,perl-test-most))) `(("perl-test-most" ,perl-test-most)))
(home-page "https://metacpan.org/release/BioPerl") (home-page "https://metacpan.org/release/BioPerl")
@ -1210,7 +1211,7 @@ objects are made from the Sequence objects, Sequence objects have access to
Annotation and SeqFeature objects and databases, Blast objects can be Annotation and SeqFeature objects and databases, Blast objects can be
converted to Alignment objects, and so on. This means that the objects converted to Alignment objects, and so on. This means that the objects
provide a coordinated and extensible framework to do computational biology.") provide a coordinated and extensible framework to do computational biology.")
(license license:perl-license)))) (license license:perl-license)))
(define-public perl-bio-db-hts (define-public perl-bio-db-hts
(package (package