From c36d4760c6a32864c10809b996e1c093928a3653 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Sep 2023 11:16:29 +0200 Subject: 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. --- gnu/packages/bioinformatics.scm | 136 ++++++++++++++++++++-------------------- 1 file changed, 68 insertions(+), 68 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa88692204..c78f017a24 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19246,77 +19246,77 @@ large-scale data-analysis.") "1dvh23fx52m59y6304xi2j2pl2hiqadlqg8jyv2pm14j1hy71ych")))) (build-system perl-build-system) (arguments - `(#:modules ((guix build perl-build-system) + (list + #:modules '((guix build perl-build-system) (guix build utils) (srfi srfi-26)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'hardcode-references - (lambda* (#:key inputs #:allow-other-keys) - (let ((bedtools (assoc-ref inputs "bedtools")) - (r (assoc-ref inputs "r-minimal"))) - (substitute* '("scripts/python/getEigenVectors.py" - "scripts/python/matrix2EigenVectors.py") - (("bedtools intersect") - (string-append bedtools "/bin/bedtools intersect"))) - (substitute* "lib/cworld/dekker.pm" - (("bedtools --version") - (string-append bedtools "/bin/bedtools --version"))) - (substitute* '("scripts/perl/correlateMatrices.pl" - "scripts/perl/matrix2scaling.pl" - "scripts/perl/matrix2distance.pl" - "scripts/perl/coverageCorrect.pl" - "scripts/perl/matrix2anchorPlot.pl" - "scripts/python/matrix2EigenVectors.py" - "scripts/python/matrix2insulation-lite.py" - "scripts/perl/matrix2compartment.pl" - "scripts/perl/anchorPurge.pl" - "scripts/perl/applyCorrection.pl" - "scripts/perl/compareInsulation.pl" - "scripts/perl/fillMissingData.pl" - "scripts/perl/matrix2loess.pl" - "scripts/python/getEigenVectors.py" - "scripts/perl/aggregateBED.pl" - "scripts/perl/collapseMatrix.pl" - "scripts/perl/matrix2direction.pl" - "scripts/perl/singletonRemoval.pl" - "lib/cworld/dekker.pm" - "scripts/perl/matrix2insulation.pl") - (("(`|\")Rscript" _ pre) - (string-append pre r "/bin/Rscript")))))) - (add-after 'install 'install-scripts - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share/cworld-dekker"))) - (mkdir-p share) - (copy-recursively "scripts" share) - - ;; Make all scripts executable and wrap them. - (let ((r (find-files share "\\.R$")) - (py (find-files share "\\.py$")) - (pl (find-files share "\\.pl$")) - (wrap (lambda* (script var #:optional (extra "")) - (let ((path (string-append (getenv var) - extra))) - (wrap-program script - `(,var ":" prefix (,path))))))) - (for-each (cut chmod <> #o555) (append r py pl)) - (for-each (cut wrap <> "PERL5LIB" - (string-append ":" out - "/lib/perl5/site_perl")) - pl) - (for-each (cut wrap <> "GUIX_PYTHONPATH") py)))))))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'hardcode-references + (lambda* (#:key inputs #:allow-other-keys) + (let ((bedtools #$(this-package-input "bedtools")) + (r #$(this-package-input "r-minimal"))) + (substitute* '("scripts/python/getEigenVectors.py" + "scripts/python/matrix2EigenVectors.py") + (("bedtools intersect") + (string-append bedtools "/bin/bedtools intersect"))) + (substitute* "lib/cworld/dekker.pm" + (("bedtools --version") + (string-append bedtools "/bin/bedtools --version"))) + (substitute* '("scripts/perl/correlateMatrices.pl" + "scripts/perl/matrix2scaling.pl" + "scripts/perl/matrix2distance.pl" + "scripts/perl/coverageCorrect.pl" + "scripts/perl/matrix2anchorPlot.pl" + "scripts/python/matrix2EigenVectors.py" + "scripts/python/matrix2insulation-lite.py" + "scripts/perl/matrix2compartment.pl" + "scripts/perl/anchorPurge.pl" + "scripts/perl/applyCorrection.pl" + "scripts/perl/compareInsulation.pl" + "scripts/perl/fillMissingData.pl" + "scripts/perl/matrix2loess.pl" + "scripts/python/getEigenVectors.py" + "scripts/perl/aggregateBED.pl" + "scripts/perl/collapseMatrix.pl" + "scripts/perl/matrix2direction.pl" + "scripts/perl/singletonRemoval.pl" + "lib/cworld/dekker.pm" + "scripts/perl/matrix2insulation.pl") + (("(`|\")Rscript" _ pre) + (string-append pre r "/bin/Rscript")))))) + (add-after 'install 'install-scripts + (lambda _ + (let ((share (string-append #$output "/share/cworld-dekker"))) + (mkdir-p share) + (copy-recursively "scripts" share) + + ;; Make all scripts executable and wrap them. + (let ((r (find-files share "\\.R$")) + (py (find-files share "\\.py$")) + (pl (find-files share "\\.pl$")) + (wrap (lambda* (script var #:optional (extra "")) + (let ((path (string-append (getenv var) + extra))) + (wrap-program script + `(,var ":" prefix (,path))))))) + (for-each (cut chmod <> #o555) (append r py pl)) + (for-each (cut wrap <> "PERL5LIB" + (string-append ":" #$output + "/lib/perl5/site_perl")) + pl) + (for-each (cut wrap <> "GUIX_PYTHONPATH") py)))))))) (inputs - `(("libgd" ,gd) - ("perl-gd" ,perl-gd) - ("bedtools" ,bedtools) - ("python" ,python-wrapper) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-matplotlib" ,python-matplotlib) - ("python-h5py" ,python-h5py) - ("python-scikit-learn" ,python-scikit-learn) - ("r-minimal" ,r-minimal))) + (list gd + perl-gd + bedtools + python-wrapper + python-scipy + python-numpy + python-matplotlib + python-h5py + python-scikit-learn + r-minimal)) (native-inputs (list perl-module-build)) (home-page "https://github.com/dekkerlab/cworld-dekker") -- cgit v1.2.3