diff options
| -rw-r--r-- | gn/packages/bnw.scm | 246 | ||||
| -rw-r--r-- | gn/services/bnw-container.scm | 17 |
2 files changed, 149 insertions, 114 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm index bdcaeb0..5e00af4 100644 --- a/gn/packages/bnw.scm +++ b/gn/packages/bnw.scm @@ -4,29 +4,59 @@ #: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 "2c16603cab7c917118d2d7b3c34813b29aa5af68") + (revision "1")) (package (name "bnw") - (version (git-version "1.22" revision commit)) ; June 28, 2019 + (version (git-version "genenet8_initial_1.3" revision commit)) ; Mar 2, 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")))) + "0pfcmx7swnxz48xn5bryx3a71if4j53iawkp05myhdl1c6mdvsw0")) + (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" + "canvas-toBlob.js" + "cytoscape-dagre.min.js" + "cytoscape-panzoom.js" + "cytoscape.js-panzoom.css" + "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")) + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no test suite @@ -35,46 +65,36 @@ (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"))) + ;; 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")) @@ -91,9 +111,8 @@ (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 +122,38 @@ (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 +162,58 @@ #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")) + (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/")) + (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 out "/javascript/dagre.js")) + (string-append scripts "dagre.js")) (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape.js-panzoom.css") - (string-append out "/javascript/cytoscape.js-panzoom.css")) + (string-append scripts "cytoscape.js-panzoom.css")) (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape-panzoom.js") - (string-append out "/javascript/cytoscape-panzoom.js")) + (string-append scripts "cytoscape-panzoom.js")) (symlink (string-append awesome "/share/web/font-awesomecss/font-awesome.css") - (string-append out "/javascript/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 out "/javascript/jquery.min.js")) + (string-append scripts "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")) + (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 out "/javascript/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 out "/javascript/canvas-toBlob.js")) + (string-append scripts "canvas-toBlob.js")) (symlink (string-append filesaver js-path2 "filesaver/FileSaver.js") - (string-append out "/javascript/filesaver.js")) + (string-append scripts "FileSaver.min.js")) #t))) (add-after 'install 'make-files-executable (lambda* (#:key outputs #:allow-other-keys) @@ -188,37 +222,34 @@ (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-in-pythonpath + (lambda* (#:key outputs #:allow-other-keys) + (for-each + (lambda (script) + (wrap-program script + `("PYTHONPATH" prefix (,(getenv "PYTHONPATH"))))) + (find-files (string-append (assoc-ref outputs "out") + "/sourcecodes/run_scripts") "^run")) + #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) + ("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 +257,8 @@ ("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 diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm index 39da38d..4046a4f 100644 --- a/gn/services/bnw-container.scm +++ b/gn/services/bnw-container.scm @@ -5,6 +5,7 @@ (guix records) (ice-9 match)) (use-service-modules networking web) +(use-package-modules base) (define-record-type* <bnw-configuration> bnw-configuration @@ -21,10 +22,12 @@ (match-lambda (($ <bnw-configuration> package deploy-directory port) #~(begin - (mkdir-p #$deploy-directory) - (copy-recursively #$package #$deploy-directory) - (invoke #$(file-append coreutils "/bin/chmod") "a+w" - (string-append #$deploy-directory "/sourcecodes/data")))))) + (let ((genenet "/var/lib/genenet/bnw")) + ;(mkdir-p #$deploy-directory) + ;(copy-recursively #$package #$deploy-directory) + (mkdir-p genenet) + (copy-recursively #$(file-append package "/var_lib_genenet_bnw") genenet) + (invoke #$(file-append coreutils "/bin/chmod") "a+w" genenet)))))) (define bnw-nginx-config (match-lambda @@ -33,8 +36,8 @@ (nginx-server-configuration (server-name '("Bayesian Network")) (listen port) - ;(root package) - (root deploy-directory) + (root package) + ;(root deploy-directory) (locations (list (nginx-php-location) @@ -74,7 +77,7 @@ ;; No firmware for VMs. (firmware '()) ;; We don't need any packages inside the container. - (packages '()) + (packages (list coreutils)) (services (list (service dhcp-client-service-type) (service bnw-service-type |