gnu: perl-cworld-dekker: Drop labels from inputs.
* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use G-expression and avoid references to labeled inputs. [inputs]: Drop labels.
This commit is contained in:
Ricardo Wurmus
parent
0ce57ea4a1
commit
c36d4760c6
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@ -19246,77 +19246,77 @@ (define-public perl-cworld-dekker
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"1dvh23fx52m59y6304xi2j2pl2hiqadlqg8jyv2pm14j1hy71ych"))))
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(build-system perl-build-system)
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(arguments
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`(#:modules ((guix build perl-build-system)
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(list
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#:modules '((guix build perl-build-system)
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(guix build utils)
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(srfi srfi-26))
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'hardcode-references
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((bedtools (assoc-ref inputs "bedtools"))
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(r (assoc-ref inputs "r-minimal")))
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(substitute* '("scripts/python/getEigenVectors.py"
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"scripts/python/matrix2EigenVectors.py")
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(("bedtools intersect")
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(string-append bedtools "/bin/bedtools intersect")))
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(substitute* "lib/cworld/dekker.pm"
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(("bedtools --version")
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(string-append bedtools "/bin/bedtools --version")))
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(substitute* '("scripts/perl/correlateMatrices.pl"
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"scripts/perl/matrix2scaling.pl"
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"scripts/perl/matrix2distance.pl"
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"scripts/perl/coverageCorrect.pl"
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"scripts/perl/matrix2anchorPlot.pl"
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"scripts/python/matrix2EigenVectors.py"
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"scripts/python/matrix2insulation-lite.py"
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"scripts/perl/matrix2compartment.pl"
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"scripts/perl/anchorPurge.pl"
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"scripts/perl/applyCorrection.pl"
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"scripts/perl/compareInsulation.pl"
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"scripts/perl/fillMissingData.pl"
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"scripts/perl/matrix2loess.pl"
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"scripts/python/getEigenVectors.py"
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"scripts/perl/aggregateBED.pl"
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"scripts/perl/collapseMatrix.pl"
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"scripts/perl/matrix2direction.pl"
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"scripts/perl/singletonRemoval.pl"
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"lib/cworld/dekker.pm"
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"scripts/perl/matrix2insulation.pl")
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(("(`|\")Rscript" _ pre)
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(string-append pre r "/bin/Rscript"))))))
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(add-after 'install 'install-scripts
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(share (string-append out "/share/cworld-dekker")))
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(mkdir-p share)
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(copy-recursively "scripts" share)
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'hardcode-references
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((bedtools #$(this-package-input "bedtools"))
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(r #$(this-package-input "r-minimal")))
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(substitute* '("scripts/python/getEigenVectors.py"
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"scripts/python/matrix2EigenVectors.py")
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(("bedtools intersect")
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(string-append bedtools "/bin/bedtools intersect")))
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(substitute* "lib/cworld/dekker.pm"
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(("bedtools --version")
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(string-append bedtools "/bin/bedtools --version")))
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(substitute* '("scripts/perl/correlateMatrices.pl"
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"scripts/perl/matrix2scaling.pl"
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"scripts/perl/matrix2distance.pl"
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"scripts/perl/coverageCorrect.pl"
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"scripts/perl/matrix2anchorPlot.pl"
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"scripts/python/matrix2EigenVectors.py"
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"scripts/python/matrix2insulation-lite.py"
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"scripts/perl/matrix2compartment.pl"
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"scripts/perl/anchorPurge.pl"
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"scripts/perl/applyCorrection.pl"
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"scripts/perl/compareInsulation.pl"
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"scripts/perl/fillMissingData.pl"
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"scripts/perl/matrix2loess.pl"
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"scripts/python/getEigenVectors.py"
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"scripts/perl/aggregateBED.pl"
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"scripts/perl/collapseMatrix.pl"
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"scripts/perl/matrix2direction.pl"
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"scripts/perl/singletonRemoval.pl"
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"lib/cworld/dekker.pm"
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"scripts/perl/matrix2insulation.pl")
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(("(`|\")Rscript" _ pre)
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(string-append pre r "/bin/Rscript"))))))
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(add-after 'install 'install-scripts
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(lambda _
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(let ((share (string-append #$output "/share/cworld-dekker")))
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(mkdir-p share)
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(copy-recursively "scripts" share)
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;; Make all scripts executable and wrap them.
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(let ((r (find-files share "\\.R$"))
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(py (find-files share "\\.py$"))
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(pl (find-files share "\\.pl$"))
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(wrap (lambda* (script var #:optional (extra ""))
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(let ((path (string-append (getenv var)
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extra)))
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(wrap-program script
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`(,var ":" prefix (,path)))))))
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(for-each (cut chmod <> #o555) (append r py pl))
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(for-each (cut wrap <> "PERL5LIB"
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(string-append ":" out
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"/lib/perl5/site_perl"))
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pl)
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(for-each (cut wrap <> "GUIX_PYTHONPATH") py))))))))
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;; Make all scripts executable and wrap them.
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(let ((r (find-files share "\\.R$"))
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(py (find-files share "\\.py$"))
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(pl (find-files share "\\.pl$"))
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(wrap (lambda* (script var #:optional (extra ""))
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(let ((path (string-append (getenv var)
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extra)))
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(wrap-program script
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`(,var ":" prefix (,path)))))))
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(for-each (cut chmod <> #o555) (append r py pl))
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(for-each (cut wrap <> "PERL5LIB"
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(string-append ":" #$output
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"/lib/perl5/site_perl"))
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pl)
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(for-each (cut wrap <> "GUIX_PYTHONPATH") py))))))))
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(inputs
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`(("libgd" ,gd)
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("perl-gd" ,perl-gd)
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("bedtools" ,bedtools)
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("python" ,python-wrapper)
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("python-scipy" ,python-scipy)
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("python-numpy" ,python-numpy)
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("python-matplotlib" ,python-matplotlib)
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("python-h5py" ,python-h5py)
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("python-scikit-learn" ,python-scikit-learn)
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("r-minimal" ,r-minimal)))
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(list gd
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perl-gd
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bedtools
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python-wrapper
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python-scipy
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python-numpy
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python-matplotlib
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python-h5py
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python-scikit-learn
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r-minimal))
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(native-inputs
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(list perl-module-build))
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(home-page "https://github.com/dekkerlab/cworld-dekker")
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