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

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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'.
This commit is contained in:
Ludovic Courtès 2021-07-01 17:11:16 +02:00
parent b17ee44212
commit ebb8e44a4a
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1 changed files with 55 additions and 54 deletions
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109
gnu/packages/bioinformatics.scm
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@ -1147,62 +1147,63 @@ alignments and perform the following operations:
(license license:expat)))
(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 "1.7.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bioperl/bioperl-live")
(commit (string-append "release-"
(string-map (lambda (c)
(if (char=? c #\.)
#\- c)) version)))))
(file-name (git-file-name name version))
(sha256
(base32
"0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
(build-system perl-build-system)
(arguments
(package
(name "bioperl-minimal")
(version "1.7.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bioperl/bioperl-live")
(commit (string-append "release-"
(string-map (lambda (c)
(if (char=? c #\.)
#\- c)) version)))))
(file-name (git-file-name name version))
(sha256
(base32
"0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
(build-system perl-build-system)
(arguments
(let ((transitive-inputs
(map (compose package-name cadr)
(delete-duplicates
(concatenate
(map (compose package-transitive-target-inputs cadr)
(package-inputs this-package)))))))
`(#: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$"))
#t))))))
(inputs inputs)
(native-inputs
`(("perl-test-most" ,perl-test-most)))
(home-page "https://metacpan.org/release/BioPerl")
(synopsis "Bioinformatics toolkit")
(description
"BioPerl is the product of a community effort to produce Perl code which
'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure all executables in "bin" find the required Perl
;; modules at runtime. As the PERL5LIB variable contains also
;; the paths of native inputs, we pick the transitive target
;; inputs from %build-inputs.
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin/"))
(path (string-join
(cons (string-append out "/lib/perl5/site_perl")
(map (lambda (name)
(assoc-ref %build-inputs name))
',transitive-inputs))
":")))
(for-each (lambda (file)
(wrap-program file
`("PERL5LIB" ":" prefix (,path))))
(find-files bin "\\.pl$"))
#t)))))))
(inputs
`(("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 "https://metacpan.org/release/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
@ -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
converted to Alignment objects, and so on. This means that the objects
provide a coordinated and extensible framework to do computational biology.")
(license license:perl-license))))
(license license:perl-license)))
(define-public perl-bio-db-hts
(package