diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 137 |
1 files changed, 69 insertions, 68 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 1b9babc..3208c61 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -251,7 +251,7 @@ Graphical Fragment Assembly} files and related formats.") (license license:expat))) (define-public genenetwork3 - (let ((commit "487e50e8f8304a65e7af3759c13256f921efb8be")) + (let ((commit "c9ee473ff7797f6bbd7507eb55c772a3a646acee")) (package (name "genenetwork3") (version (string-append "0.0.1-guix-" (string-take commit 7))) @@ -264,7 +264,7 @@ Graphical Fragment Assembly} files and related formats.") (file-name (git-file-name name version)) (sha256 (base32 - "1rm8pvl5x1350aivk7m2symdsf3iiacl4pnaz1q8fgxpr154qw93")))) + "1z25nr45kzy3vpk8gc1cq9r4j89dgpdmb83s1pgp75m9dcij5863")))) (propagated-inputs `(("coreutils" ,coreutils) ("gemma-wrapper" ,gemma-wrapper) ("csvdiff" ,go-github-com-aswinkarthik-csvdiff) @@ -292,7 +292,7 @@ Graphical Fragment Assembly} files and related formats.") (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "84cbf35adbb15c79638372d108308edb05f12683")) + (let ((commit "fe345c9f2e99be748511f6889420d6560a553a37")) (package (name "genenetwork2") (version (string-append "3.11-guix-" (string-take commit 7) )) @@ -304,7 +304,7 @@ Graphical Fragment Assembly} files and related formats.") (file-name (string-append name "-" version)) (sha256 (base32 - "1402g129ghfh0xwfxjj1i7gbib2yl9rahf55caj7b1psy24ys87x")))) + "1y6psmxpm3qn78dx6xfc11rdpf22vf807qb7grnp82gl19q6408w")))) (native-inputs `(("graphviz" ,graphviz) ;; And the graphs @@ -331,6 +331,7 @@ Graphical Fragment Assembly} files and related formats.") ("plink-ng-gn" ,plink-ng-gn) ; ("pylmm-gn2" ,pylmm-gn2) ("rust-qtlreaper" ,rust-qtlreaper) + ("glibc-utf8-locales" ,glibc-utf8-locales) ("nginx" ,nginx) ("python" ,python-wrapper) ("python-pillow" ,python-pillow) @@ -434,13 +435,13 @@ Graphical Fragment Assembly} files and related formats.") (("rm") (which "rm")) (("which") (which "which"))) #t)) - (add-after 'unpack 'patch-javascript - (lambda* (#:key inputs #:allow-other-keys) - (let ((colorbox (assoc-ref inputs "javascript-colorbox")) - (gn2 "/share/genenetwork2/javascript/")) - (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") - (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") - #t))) + ; (add-after 'unpack 'patch-javascript + ; (lambda* (#:key inputs #:allow-other-keys) + ; (let ((colorbox (assoc-ref inputs "javascript-colorbox")) + ; (gn2 "/share/genenetwork2/javascript/")) + ; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") + ; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") + ; #t))) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) (let* ( @@ -457,63 +458,63 @@ Graphical Fragment Assembly} files and related formats.") (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) ) ))) - (add-after 'install 'generate-graph - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file - (string-append - (assoc-ref outputs "out") - "/lib/python" - (python-version (assoc-ref inputs "python")) - "/site-packages" - "/wqflask/dependency-graph.html") - (lambda (port) - (format - port "~a" - ,(call-with-output-string - (lambda (p) - (with-output-to-port p - (lambda () - (run-with-store - (open-connection) - (export-graph - (list this-package) - p - #:node-type %package-node-type - #:backend %d3js-backend))))))))))) - (add-after 'install 'generate-dag-svg-file - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((output-dir - (string-append - (assoc-ref outputs "out") - "/lib/python" - (python-version (assoc-ref inputs "python")) - "/site-packages/wqflask/")) - (dot-file - (string-append - output-dir - "dependency-graph.dot")) - (svg-file - (string-append - output-dir - "dependency-graph.svg"))) - (begin - (call-with-output-file - dot-file - (lambda (port) - (format - port "~a" - ,(call-with-output-string - (lambda (p) - (with-output-to-port p - (lambda () - (run-with-store - (open-connection) - (export-graph - (list this-package) - p - #:node-type %package-node-type - #:backend %graphviz-backend))))))))) - (invoke "dot" "-Tsvg" "-o" svg-file dot-file))))) + ; (add-after 'install 'generate-graph + ; (lambda* (#:key inputs outputs #:allow-other-keys) + ; (call-with-output-file + ; (string-append + ; (assoc-ref outputs "out") + ; "/lib/python" + ; (python-version (assoc-ref inputs "python")) + ; "/site-packages" + ; "/wqflask/dependency-graph.html") + ; (lambda (port) + ; (format + ; port "~a" + ; ,(call-with-output-string + ; (lambda (p) + ; (with-output-to-port p + ; (lambda () + ; (run-with-store + ; (open-connection) + ; (export-graph + ; (list this-package) + ; p + ; #:node-type %package-node-type + ; #:backend %d3js-backend))))))))))) + ;(add-after 'install 'generate-dag-svg-file + ; (lambda* (#:key inputs outputs #:allow-other-keys) + ; (let* ((output-dir + ; (string-append + ; (assoc-ref outputs "out") + ; "/lib/python" + ; (python-version (assoc-ref inputs "python")) + ; "/site-packages/wqflask/")) + ; (dot-file + ; (string-append + ; output-dir + ; "dependency-graph.dot")) + ; (svg-file + ; (string-append + ; output-dir + ; "dependency-graph.svg"))) + ; (begin + ; (call-with-output-file + ; dot-file + ; (lambda (port) + ; (format + ; port "~a" + ; ,(call-with-output-string + ; (lambda (p) + ; (with-output-to-port p + ; (lambda () + ; (run-with-store + ; (open-connection) + ; (export-graph + ; (list this-package) + ; p + ; #:node-type %package-node-type + ; #:backend %graphviz-backend))))))))) + ; (invoke "dot" "-Tsvg" "-o" svg-file dot-file))))) ;; TODO: Use this to replace the two previous phases. ;(add-after 'install 'install-generated-files |