diff options
Diffstat (limited to 'gn/packages/bnw.scm')
| -rw-r--r-- | gn/packages/bnw.scm | 297 |
1 files changed, 169 insertions, 128 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm index bdcaeb0..9b36c51 100644 --- a/gn/packages/bnw.scm +++ b/gn/packages/bnw.scm @@ -4,29 +4,60 @@ #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (gnu packages gcc) + #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) + #:use-module (gnu packages maths) #:use-module (gnu packages python) #:use-module (gnu packages statistics) - #:use-module (past packages graphviz) #:use-module (gn packages javascript) - #:use-module (gn packages maths) - #:use-module (gn packages python) #:use-module (gn packages web)) (define-public bnw - (let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04") - (revision "6")) + (let ((commit "9ba1e1cf346771581d02133b73f359be28b323e7") + (revision "4")) (package (name "bnw") - (version (git-version "1.22" revision commit)) ; June 28, 2019 + (version (git-version "genenet8_initial_1.3" revision commit)) ; Mar 16, 2021 (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/ziejd2/BNW.git") + (url "https://github.com/ziejd2/BNW") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "10qwykp2zcyxih6a52icvy30ps69qk4v3jgirmdpw1l15zi4p2wq")))) + "0ibrmaq1b7x8l2f8q988njbgzgy6d7x4f3za4ry5j1swv4p9skdp")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file "var_lib_genenet_bnw/localscore/libRmath.so") + (delete-file-recursively "bnw-env") + (delete-file "var_lib_genenet_bnw/k-best/src/get_kbest_nets") + (delete-file "var_lib_genenet_bnw/k-best/src/get_kbest_parents") + (for-each delete-file (find-files "." "\\.dll$")) + (for-each delete-file (find-files "." "\\.o$")) + (for-each + (lambda (file) + (delete-file (string-append "sourcecodes/scripts/" file))) + ;; accordion.js, create_table.js and table.css are original files. + '(;"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" ; 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 `(#:tests? #f ; no test suite @@ -35,65 +66,40 @@ (delete 'configure) (add-after 'unpack 'patch-source (lambda _ - (substitute* "index.html" - (("url=home.php") "url=sourcecodes/home.php")) - (substitute* "home.php" - (("http://bnw.genenetwork.org/BNW_1.22") - "http://bnw-test.genenetwork.org")) - (substitute* "sourcecodes/header_batchsearch.inc" - (("my_style.css") "my_new_style.css")) - (substitute* (find-files "." "\\.php") - (("HTTP_POST_VARS") "_POST") - (("HTTP_POST_FILES") "_FILES")) - ;; change $dir to a writable directory - ;(substitute* (find-files "sourcecodes" "\\.php$") - ; (("\\$dir=\"./data") "$dir=\"./data/tmp")) + ;; sourcecodes/matrix.php hardcodes $dir=/tmp/bnw + (substitute* "sourcecodes/matrix.php" + (("/tmp/bnw") "/var/lib/genenet/bnw/")) #t)) (add-after 'patch-source-shebangs 'patch-more-shebangs (lambda* (#:key inputs #:allow-other-keys) - (let ((bash (assoc-ref inputs "bash")) - (graphviz (assoc-ref inputs "graphviz")) + (let ((graphviz (assoc-ref inputs "graphviz")) (octave (assoc-ref inputs "octave")) (python (assoc-ref inputs "python")) (rmath (assoc-ref inputs "rmath"))) (for-each (lambda (file) (patch-shebang file - (list (string-append bash "/bin") - (string-append octave "/bin") - (string-append python "/bin")))) - (find-files "." ".*")) + (list (string-append octave "/bin")))) + (find-files "sourcecodes/run_scripts" "^run")) (substitute* (find-files "sourcecodes" "(^run|py$)") - (("/home/jziebart/python/Python-2.7.15/python") - (which "python2"))) + (("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python3") + (which "python3")) + (("/var/www/html/compbio/BNW_1.3/bnw-env/bin/python") + (which "python3"))) (substitute* (append (find-files "sourcecodes" ".php") - (find-files "sourcecodes/run_scripts" ".*")) + (find-files "sourcecodes/run_scripts")) (("/usr/bin/dot") (string-append graphviz "/bin/dot"))) - (substitute* '("sourcecodes/build.sh" - "downloads/BNW/src/build.sh") + (substitute* "var_lib_genenet_bnw/build.sh" (("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so"))) - (substitute* (find-files "." "\\.sh$") - (("cat ") (string-append (which "cat") " ")) - (("\\ 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) (let ((jquery (assoc-ref inputs "jquery")) (awesome (assoc-ref inputs "awesome")) (cyto (assoc-ref inputs "cytoscape")) - (cyto2 (assoc-ref inputs "cytoscape-2")) (cs-dagre (assoc-ref inputs "cyto-dagre")) - (d3js (assoc-ref inputs "d3js")) + (d3js-4 (assoc-ref inputs "d3js-4")) (d3js-multi (assoc-ref inputs "d3js-multi")) (dagre (assoc-ref inputs "dagre")) (lodash (assoc-ref inputs "lodash")) @@ -103,33 +109,38 @@ (js-path "/share/genenetwork2/javascript/")) (substitute* "sourcecodes/layout_cyto.php" (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js") - "/javascript/cytoscape.min.js") - (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/2.7.29/cytoscape.min.js") - "/javascript/cytoscape2.min.js") - (("http://spades.bioinf.spbau.ru/~alla/graph_viewer/js/cytoscape-dagre.js") - "/javascript/cytoscape-dagre.js") + "./scripts/cytoscape.min.js") + (("https://cdn.jsdelivr.net/npm/cytoscape-dagre@2.2.2/cytoscape-dagre.min.js") + "./scripts/cytoscape-dagre.min.js") (("https://unpkg.com/dagre@0.7.4/dist/dagre.js") - "/javascript/dagre.js") + "./scripts/dagre.js") (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css") - "/javascript/cytoscape.js-panzoom.css") + "./scripts/cytoscape.js-panzoom.css") (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js") - "/javascript/cytoscape-panzoom.js") + "./scripts/cytoscape-panzoom.js") (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css") - "/javascript/font-awesome.css") + "./scripts/font-awesome.css") (("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js") - "/javascript/jquery.min.js") + "./scripts/jquery.min.js") (("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js") - "/javascript/lodash.js")) - (substitute* '("sourcecodes/layout_svg_wt.php" - "sourcecodes/layout_svg_no.php") + "./scripts/lodash.js")) + (substitute* "sourcecodes/layout_svg_no.php" (("http://d3js.org/d3.v4.min.js") - "/javascript/d3.min.js") + "./scripts/d3.v4.min.js") (("http://d3js.org/d3-selection-multi.v1.js") - "/javascript/d3-selection-multi.js") + "./scripts/d3-selection-multi.v1.js") (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js") - "/javascript/canvas-toBlob.js") + "./scripts/canvas-toBlob.js") (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js") - "/javascript/filesaver.js"))) + "./scripts/FileSaver.min.js")) + ;; Against Google's ToS to make available offline: + ;; https://developers.google.com/chart/interactive/faq?csw=1#offline + ;(substitute* '("sourcecodes/network_layout_evd.php" + ; "sourcecodes/network_layout_evd_2.php" + ; "sourcecodes/network_layout_inv.php" + ; "sourcecodes/network_layout_inv_2.php") + ; (("https://www.google.com/jsapi") "https://www.gstatic.com/charts/loader.js")) + ) #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) @@ -138,48 +149,70 @@ #t)) (add-after 'install 'install-javascript-libraries (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (jquery (assoc-ref inputs "jquery")) - (awesome (assoc-ref inputs "awesome")) - (cyto (assoc-ref inputs "cytoscape")) - (cyto2 (assoc-ref inputs "cytoscape-2")) - (cs-dagre (assoc-ref inputs "cyto-dagre")) - (d3js (assoc-ref inputs "d3js")) - (d3js-multi (assoc-ref inputs "d3js-multi")) - (dagre (assoc-ref inputs "dagre")) - (lodash (assoc-ref inputs "lodash")) - (canvas-toblob (assoc-ref inputs "canvas-toblob")) - (filesaver (assoc-ref inputs "filesaver")) - (panzoom (assoc-ref inputs "panzoom")) - (js-path "/share/genenetwork/javascript/") - (js-path2 "/share/genenetwork2/javascript/")) - (mkdir-p (string-append out "/javascript")) - (symlink (string-append (string-append cyto2 js-path2 "cytoscape/cytoscape.min.js")) - (string-append out "/javascript/cytoscape.min.js")) - (symlink (string-append (string-append cyto js-path2 "cytoscape/cytoscape.min.js")) - (string-append out "/javascript/cytoscape2.min.js")) - (symlink (string-append cs-dagre js-path2 "cytoscape-dagre/cytoscape-dagre.js") - (string-append out "/javascript/cytoscape-dagre.js")) - (symlink (string-append dagre js-path2 "dagre/dagre.js") - (string-append out "/javascript/dagre.js")) - (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape.js-panzoom.css") - (string-append out "/javascript/cytoscape.js-panzoom.css")) - (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape-panzoom.js") - (string-append out "/javascript/cytoscape-panzoom.js")) - (symlink (string-append awesome "/share/web/font-awesomecss/font-awesome.css") - (string-append out "/javascript/font-awesome.css")) - (symlink (string-append jquery "/share/web/jquery/jquery.min.js") - (string-append out "/javascript/jquery.min.js")) - (symlink (string-append lodash js-path2 "lodash/lodash.js") - (string-append out "/javascript/lodash.js")) - (symlink (string-append d3js js-path "d3js/d3.min.js") - (string-append out "/javascript/d3.min.js")) - (symlink (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js") - (string-append out "/javascript/d3-selection-multi.js")) - (symlink (string-append canvas-toblob js-path "canvas-toblob/canvas-toBlob.js") - (string-append out "/javascript/canvas-toBlob.js")) - (symlink (string-append filesaver js-path2 "filesaver/FileSaver.js") - (string-append out "/javascript/filesaver.js")) + (let* ((out (assoc-ref outputs "out")) + (scripts (string-append out "/sourcecodes/scripts/")) + (fonts (string-append out "/sourcecodes/fonts/")) + (jquery (assoc-ref inputs "jquery")) + (awesome (assoc-ref inputs "awesome")) + (cyto (assoc-ref inputs "cytoscape")) + (cs-dagre (assoc-ref inputs "cyto-dagre")) + (d3js-4 (assoc-ref inputs "d3js-4")) + (d3js-multi (assoc-ref inputs "d3js-multi")) + (dagre (assoc-ref inputs "dagre")) + (lodash (assoc-ref inputs "lodash")) + (canvas-toblob (assoc-ref inputs "canvas-toblob")) + (filesaver (assoc-ref inputs "filesaver")) + (panzoom (assoc-ref inputs "panzoom")) + (js-path "/share/genenetwork/javascript/") + (js-path2 "/share/genenetwork2/javascript/")) + (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"))) + + (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) @@ -188,37 +221,44 @@ (lambda (file) (chmod file #o555)) (append (find-files out "\\.(sh|py)$") - (find-files (string-append out "/sourcecodes/run_scripts/" ".")))) - ;; This folder needs to be writable. - (chmod (string-append out "/sourcecodes/data") #o777) + (find-files + (string-append out "/sourcecodes/run_scripts/") "^run"))) #t))) + (add-after 'make-files-executable 'wrap-executables + (lambda* (#:key outputs #:allow-other-keys) + (for-each + (lambda (script) + (wrap-program script + `("PATH" prefix (,(dirname (which "cp")))) + `("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 _ - (with-directory-excursion "sourcecodes" - (substitute* "build.sh" - (("./localscore") "localscore")) - (chmod "k-best/src/buildk_poster.sh" #o555) - (invoke "sh" "build.sh") - ;; from info_files/plotly_notes.txt - ;(with-directory-excursion "data" - ; (setenv "HOME" "/tmp") - ; (invoke "python" "../cv_plotly.py" "LvQ") - ; (invoke "sh" "../plotly_loo.sh")) - ;(invoke "./run_scripts/run_loo" "LvQ Weight") - )))))) + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "var_lib_genenet_bnw" + (invoke "sh" "build.sh"))))))) (inputs - `(("graphviz" ,graphviz-2.26) - ("octave" ,octave-3.4.3) - ("plotly" ,python2-plotly-3.2.1) - ("python" ,python-2) + `(("graphviz" ,graphviz) + ("octave" ,octave-cli) + ("python" ,python) + ("python-plotly" ,python-plotly) ("rmath" ,rmath-standalone) ;; the javascript libraries: ("awesome" ,web-font-awesome) ("canvas-toblob" ,javascript-canvas-toblob) ("cyto-dagre" ,javascript-cytoscape-dagre) ("cytoscape" ,javascript-cytoscape) - ("cytoscape-2" ,javascript-cytoscape-2) - ("d3js" ,javascript-d3js-4) + ("d3js-4" ,javascript-d3js-4) ("d3js-multi" ,javascript-d3js-multi) ("dagre" ,javascript-dagre) ("filesaver" ,javascript-filesaver) @@ -226,7 +266,8 @@ ("lodash" ,javascript-lodash) ("panzoom" ,javascript-cytoscape-panzoom))) (native-inputs - `(("gcc" ,gcc-5))) + ;; get_best_knets isn't buildable with anything newer than gcc-5. + `(("gcc" ,(@ (gnu packages commencement) gcc-toolchain-5)))) (home-page "http://compbio.uthsc.edu/BNW/") (synopsis "Bayesian Network Webserver") (description |