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
parent
b17ee44212
commit
ebb8e44a4a
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@ -1147,62 +1147,63 @@ alignments and perform the following operations:
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(license license:expat)))
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(define-public bioperl-minimal
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(let* ((inputs `(("perl-module-build" ,perl-module-build)
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("perl-data-stag" ,perl-data-stag)
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("perl-libwww" ,perl-libwww)
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("perl-uri" ,perl-uri)))
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(transitive-inputs
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(map (compose package-name cadr)
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(delete-duplicates
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(concatenate
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(map (compose package-transitive-target-inputs cadr) inputs))))))
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(package
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(name "bioperl-minimal")
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(version "1.7.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/bioperl/bioperl-live")
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(commit (string-append "release-"
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(string-map (lambda (c)
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(if (char=? c #\.)
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#\- c)) version)))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
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(build-system perl-build-system)
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(arguments
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(package
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(name "bioperl-minimal")
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(version "1.7.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/bioperl/bioperl-live")
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(commit (string-append "release-"
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(string-map (lambda (c)
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(if (char=? c #\.)
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#\- c)) version)))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
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(build-system perl-build-system)
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(arguments
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(let ((transitive-inputs
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(map (compose package-name cadr)
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(delete-duplicates
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(concatenate
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(map (compose package-transitive-target-inputs cadr)
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(package-inputs this-package)))))))
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`(#:phases
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(modify-phases %standard-phases
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(add-after
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'install 'wrap-programs
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(lambda* (#:key outputs #:allow-other-keys)
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;; Make sure all executables in "bin" find the required Perl
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;; modules at runtime. As the PERL5LIB variable contains also
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;; the paths of native inputs, we pick the transitive target
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;; inputs from %build-inputs.
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin/"))
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(path (string-join
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(cons (string-append out "/lib/perl5/site_perl")
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(map (lambda (name)
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(assoc-ref %build-inputs name))
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',transitive-inputs))
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":")))
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(for-each (lambda (file)
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(wrap-program file
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`("PERL5LIB" ":" prefix (,path))))
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(find-files bin "\\.pl$"))
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#t))))))
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(inputs inputs)
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(native-inputs
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`(("perl-test-most" ,perl-test-most)))
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(home-page "https://metacpan.org/release/BioPerl")
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(synopsis "Bioinformatics toolkit")
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(description
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"BioPerl is the product of a community effort to produce Perl code which
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'install 'wrap-programs
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(lambda* (#:key outputs #:allow-other-keys)
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;; Make sure all executables in "bin" find the required Perl
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;; modules at runtime. As the PERL5LIB variable contains also
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;; the paths of native inputs, we pick the transitive target
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;; inputs from %build-inputs.
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin/"))
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(path (string-join
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(cons (string-append out "/lib/perl5/site_perl")
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(map (lambda (name)
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(assoc-ref %build-inputs name))
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',transitive-inputs))
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":")))
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(for-each (lambda (file)
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(wrap-program file
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`("PERL5LIB" ":" prefix (,path))))
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(find-files bin "\\.pl$"))
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#t)))))))
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(inputs
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`(("perl-module-build" ,perl-module-build)
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("perl-data-stag" ,perl-data-stag)
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("perl-libwww" ,perl-libwww)
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("perl-uri" ,perl-uri)))
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(native-inputs
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`(("perl-test-most" ,perl-test-most)))
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(home-page "https://metacpan.org/release/BioPerl")
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(synopsis "Bioinformatics toolkit")
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(description
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"BioPerl is the product of a community effort to produce Perl code which
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is useful in biology. Examples include Sequence objects, Alignment objects
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and database searching objects. These objects not only do what they are
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advertised to do in the documentation, but they also interact - Alignment
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@ -1210,7 +1211,7 @@ objects are made from the Sequence objects, Sequence objects have access to
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Annotation and SeqFeature objects and databases, Blast objects can be
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converted to Alignment objects, and so on. This means that the objects
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provide a coordinated and extensible framework to do computational biology.")
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(license license:perl-license))))
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(license license:perl-license)))
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(define-public perl-bio-db-hts
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(package
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