diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bnw.scm | 146 |
1 files changed, 77 insertions, 69 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm index 5e00af4..842f327 100644 --- a/gn/packages/bnw.scm +++ b/gn/packages/bnw.scm @@ -13,11 +13,11 @@ #:use-module (gn packages web)) (define-public bnw - (let ((commit "2c16603cab7c917118d2d7b3c34813b29aa5af68") - (revision "1")) + (let ((commit "f39cd7ba681262de5658cfe7b9b0d46c6000b4fa") + (revision "2")) (package (name "bnw") - (version (git-version "genenet8_initial_1.3" revision commit)) ; Mar 2, 2021 + (version (git-version "genenet8_initial_1.3" revision commit)) ; Mar 4, 2021 (source (origin (method git-fetch) (uri (git-reference @@ -26,7 +26,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0pfcmx7swnxz48xn5bryx3a71if4j53iawkp05myhdl1c6mdvsw0")) + "1w5hf3pkp91lf697675hjmhir622nz49spx30d0vkvh4i791cpqh")) (modules '((guix build utils))) (snippet '(begin @@ -40,22 +40,23 @@ (lambda (file) (delete-file (string-append "sourcecodes/scripts/" file))) ;; accordion.js, create_table.js and table.css are original files. - '("FileSaver.min.js" - "canvas-toBlob.js" - "cytoscape-dagre.min.js" - "cytoscape-panzoom.js" - "cytoscape.js-panzoom.css" - "cytoscape.min.js" - "d3-selection-multi.v1.js" + '(;"FileSaver.min.js" ; sha256 mismatch + ;"canvas-toBlob.js" ; sha256 mismatch + ;"cytoscape-dagre.min.js" ; sha256 mismatch + ;"cytoscape-panzoom.js" ; sha256 mismatch + ;"cytoscape.js-panzoom.css" ; sha256 mismatch + ;"cytoscape.min.js" + ;"d3-selection-multi.v1.js" ;"d3.v4.min.js" ; some work needs to be done on our package - "dagre.js" - "font-awesome.css" - "fontawesome-webfont.eot" - "fontawesome-webfont.svg" - "fontawesome-webfont.ttf" - "fontawesome-webfont.woff" - "jquery.min.js" - "lodash.js")) + ;"dagre.js" ; sha256 mismatch + ;"font-awesome.css" ; sha256 mismatch + ;"fontawesome-webfont.eot" ; sha256 mismatch + ;"fontawesome-webfont.svg" ; sha256 mismatch + ;"fontawesome-webfont.ttf" ; sha256 mismatch + ;"fontawesome-webfont.woff" ; sha256 mismatch + ;"jquery.min.js" ; sha256 mismatch + ;"lodash.js" ; sha256 mismatch + )) #t)))) (build-system gnu-build-system) (arguments @@ -91,20 +92,6 @@ (substitute* "var_lib_genenet_bnw/build.sh" (("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so"))) - ;; Or we have to wrap everything with coreutils. - (substitute* (find-files "." "\\.sh$") - (("cat ") (string-append (which "cat") " ")) - (("cut ") (string-append (which "cut") " ")) - (("\\ cp") (string-append " " (which "cp"))) - (("date ") (string-append (which "date") " ")) - (("dirname \\$0") (string-append (which "dirname")" $0")) - (("dirname \"\\$0") (string-append (which "dirname")" \"$0")) - (("expr ") (string-append (which "expr") " ")) - (("head ") (string-append (which "head") " ")) - (("mkdir ") (string-append (which "mkdir") " ")) - (("^rm ") (string-append (which "rm") " ")) - (("rmdir ") (string-append (which "rmdir") " ")) - (("wc ") (string-append (which "wc") " "))) #t))) (add-after 'patch-source-shebangs 'replace-javascript (lambda* (#:key inputs #:allow-other-keys) @@ -178,42 +165,54 @@ (panzoom (assoc-ref inputs "panzoom")) (js-path "/share/genenetwork/javascript/") (js-path2 "/share/genenetwork2/javascript/")) - (symlink (string-append cyto js-path2 "cytoscape/cytoscape.min.js") - (string-append scripts "cytoscape.min.js")) - (symlink (string-append cs-dagre "/share/javascript/cytoscape-dagre.min.js") - (string-append scripts "cytoscape-dagre.min.js")) - (symlink (string-append dagre js-path2 "dagre/dagre.js") - (string-append scripts "dagre.js")) - (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape.js-panzoom.css") - (string-append scripts "cytoscape.js-panzoom.css")) - (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape-panzoom.js") - (string-append scripts "cytoscape-panzoom.js")) - (symlink (string-append awesome "/share/web/font-awesomecss/font-awesome.css") - (string-append scripts "font-awesome.css")) - ;; font-awesome.css depends on the other font-awesome files, - ;; by default in the ../fonts/ folder. Because we remove the - ;; bundled (and minimally modified) version we have to make - ;; some adjustments, namely moving the font files. - (mkdir-p fonts) - (for-each - (lambda (font) - (symlink (string-append awesome "/share/web/font-awesomefonts" - "/fontawesome-webfont." font) - (string-append fonts "fontawesome-webfont." font))) - '("eot" "woff" "woff2" "ttf" "svg")) + (unless (file-exists? (string-append scripts "cytoscape.min.js")) + (symlink (string-append cyto js-path2 "cytoscape/cytoscape.min.js") + (string-append scripts "cytoscape.min.js"))) + (unless (file-exists? (string-append scripts "cytoscape-dagre.min.js")) + (symlink (string-append cs-dagre "/share/javascript/cytoscape-dagre.min.js") + (string-append scripts "cytoscape-dagre.min.js"))) + (unless (file-exists? (string-append scripts "dagre.js")) + (symlink (string-append dagre js-path2 "dagre/dagre.js") + (string-append scripts "dagre.js"))) + (unless (file-exists? (string-append scripts "cytoscape.js-panzoom.css")) + (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape.js-panzoom.css") + (string-append scripts "cytoscape.js-panzoom.css"))) + (unless (file-exists? (string-append scripts "cytoscape-panzoom.js")) + (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape-panzoom.js") + (string-append scripts "cytoscape-panzoom.js"))) + (unless (file-exists? (string-append scripts "font-awesome.css")) + (symlink (string-append awesome "/share/web/font-awesomecss/font-awesome.css") + (string-append scripts "font-awesome.css")) + ;; font-awesome.css depends on the other font-awesome files, + ;; by default in the ../fonts/ folder. Because we remove the + ;; bundled (and minimally modified) version we have to make + ;; some adjustments, namely moving the font files. + (mkdir-p fonts) + (for-each + (lambda (font) + (symlink (string-append awesome "/share/web/font-awesomefonts" + "/fontawesome-webfont." font) + (string-append fonts "fontawesome-webfont." font))) + '("eot" "woff" "woff2" "ttf" "svg"))) - (symlink (string-append jquery "/share/web/jquery/jquery.min.js") - (string-append scripts "jquery.min.js")) - (symlink (string-append lodash js-path2 "lodash/lodash.js") - (string-append scripts "lodash.js")) - ;(symlink (string-append d3js-4 js-path "d3js/d3.min.js") - ; (string-append scripts "d3.v4.min.js")) - (symlink (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js") - (string-append scripts "d3-selection-multi.v1.js")) - (symlink (string-append canvas-toblob js-path "canvas-toblob/canvas-toBlob.js") - (string-append scripts "canvas-toBlob.js")) - (symlink (string-append filesaver js-path2 "filesaver/FileSaver.js") - (string-append scripts "FileSaver.min.js")) + (unless (file-exists? (string-append scripts "jquery.min.js")) + (symlink (string-append jquery "/share/web/jquery/jquery.min.js") + (string-append scripts "jquery.min.js"))) + (unless (file-exists? (string-append scripts "lodash.js")) + (symlink (string-append lodash js-path2 "lodash/lodash.js") + (string-append scripts "lodash.js"))) + (unless (file-exists? (string-append scripts "d3.v4.min.js")) + (symlink (string-append d3js-4 js-path "d3js/d3.min.js") + (string-append scripts "d3.v4.min.js"))) + (unless (file-exists? (string-append scripts "d3-selection-multi.v1.js")) + (symlink (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js") + (string-append scripts "d3-selection-multi.v1.js"))) + (unless (file-exists? (string-append scripts "canvas-toBlob.js")) + (symlink (string-append canvas-toblob js-path "canvas-toblob/canvas-toBlob.js") + (string-append scripts "canvas-toBlob.js"))) + (unless (file-exists? (string-append scripts "FileSaver.min.js")) + (symlink (string-append filesaver js-path2 "filesaver/FileSaver.min.js") + (string-append scripts "FileSaver.min.js"))) #t))) (add-after 'install 'make-files-executable (lambda* (#:key outputs #:allow-other-keys) @@ -225,7 +224,7 @@ (find-files (string-append out "/sourcecodes/run_scripts/") "^run"))) #t))) - (add-after 'make-files-executable 'wrap-executables-in-pythonpath + (add-after 'make-files-executable 'wrap-executables (lambda* (#:key outputs #:allow-other-keys) (for-each (lambda (script) @@ -233,6 +232,15 @@ `("PYTHONPATH" prefix (,(getenv "PYTHONPATH"))))) (find-files (string-append (assoc-ref outputs "out") "/sourcecodes/run_scripts") "^run")) + (for-each + (lambda (script) + (wrap-program script + `("PATH" prefix (,(dirname (which "cut")))))) + (append + (find-files (string-append (assoc-ref outputs "out") + "/sourcecodes") "\\.sh$") + (find-files (string-append (assoc-ref outputs "out") + "/var_lib_genenet_bnw") "\\.sh$"))) #t)) (replace 'build (lambda* (#:key inputs #:allow-other-keys) |