diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bnw.scm | 92 | ||||
| -rw-r--r-- | gn/services/bnw-container.scm | 12 | ||||
| -rw-r--r-- | gn/services/bnw.service | 2 |
3 files changed, 60 insertions, 46 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm index 5b7131b..5c97eab 100644 --- a/gn/packages/bnw.scm +++ b/gn/packages/bnw.scm @@ -14,7 +14,7 @@ (define-public bnw (let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04") - (revision "4")) + (revision "5")) (package (name "bnw") (version (git-version "1.22" revision commit)) ; June 28, 2019 @@ -38,7 +38,8 @@ (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")) + (("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") @@ -50,48 +51,58 @@ #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")) - (octave (assoc-ref inputs "octave")) - (python (assoc-ref inputs "python")) - (rmath (assoc-ref inputs "rmath")) - (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/genenetwork2/javascript/")) + (let ((bash (assoc-ref inputs "bash")) + (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 "." ".*")) - (substitute* '("sourcecodes/examplefilecopy.sh" - "sourcecodes/filecopy.sh") - (("^rm") (which "rm")) - (("\\ cp") (string-append " " (which "cp")))) (substitute* (find-files "sourcecodes" "(^run|py$)") - (("/home/jziebart/python/Python-2.7.15/python") (which "python2"))) + (("/home/jziebart/python/Python-2.7.15/python") + (which "python2"))) (substitute* (append (find-files "sourcecodes" ".php") (find-files "sourcecodes/run_scripts" ".*")) (("/usr/bin/dot") (string-append graphviz "/bin/dot"))) (substitute* '("sourcecodes/build.sh" "downloads/BNW/src/build.sh") - (("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so"))) - (substitute* "sourcecodes/run.sh" - (("rm ") (string-append (which "rm") " ")) - (("rmdir ") (string-append (which "rmdir") " ")) + (("./localscore/libRmath.so") + (string-append rmath "/lib/libRmath.so"))) + (substitute* (find-files "." "\\.sh$") + (("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")" \"$0")) + (("expr ") (string-append (which "expr") " ")) + (("head ") (string-append (which "head") " ")) (("mkdir ") (string-append (which "mkdir") " ")) - (("dirname ") (string-append (which "dirname")" "))) + (("^rm ") (string-append (which "rm") " ")) + (("rmdir ") (string-append (which "rmdir") " ")) + (("wc ") (string-append (which "wc") " "))) + #t))) + ;(add-after 'patch-source-shebangs 'replace-javascript + ; (lambda* (#:key inputs #:allow-other-keys) + ; (let ( + ; (jquery (assoc-ref inputs "jquery")) + ; (awesome (assoc-ref inputs "awesome")) + ; (cyto (assoc-ref inputs "cytoscape")) + ; (cyto2 (assoc-ref inputs "cytoscape-2")) + ; (cs-dagre (assoc-ref inputs "cyto-dagre")) + ; (d3js (assoc-ref inputs "d3js")) + ; (d3js-multi (assoc-ref inputs "d3js-multi")) + ; (dagre (assoc-ref inputs "dagre")) + ; (lodash (assoc-ref inputs "lodash")) + ; (canvas-toblob (assoc-ref inputs "canvas-toblob")) + ; (filesaver (assoc-ref inputs "filesaver")) + ; (panzoom (assoc-ref inputs "panzoom")) + ; (js-path "/share/genenetwork2/javascript/") + ; ) ;(substitute* "sourcecodes/layout_cyto.php" ; (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js") ; (string-append cyto js-path "cytoscape/cytoscape.min.js")) @@ -121,8 +132,8 @@ ; (string-append canvas-toblob js-path "canvas-toBlob/canvas-toBlob.js")) ; (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js") ; (string-append filesaver js-path "filesaver/filesaver.js"))) - ) - #t)) + ; ) + ; #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -136,7 +147,8 @@ (chmod file #o555)) (append (find-files out "\\.(sh|py)$") (find-files (string-append out "/sourcecodes/run_scripts/" ".")))) - (chmod (string-append out "/sourcecodes/data") #o777) ; needs to be writable + ;; This folder needs to be writable. + (chmod (string-append out "/sourcecodes/data") #o777) #t))) (replace 'build (lambda _ @@ -155,26 +167,28 @@ (inputs `(("graphviz" ,graphviz-2.26) ("octave" ,octave-3.4.3) - ("python" ,python-2) ("plotly" ,python2-plotly-3.2.1) + ("python" ,python-2) ("rmath" ,rmath-standalone) - ("jquery" ,web-jquery) + ;; 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-multi" ,javascript-d3js-multi) ("dagre" ,javascript-dagre) - ("lodash" ,javascript-lodash) - ("canvas-toblob" ,javascript-canvas-toblob) ("filesaver" ,javascript-filesaver) - ("cyto-dagre" ,javascript-cytoscape-dagre) + ("jquery" ,web-jquery) + ("lodash" ,javascript-lodash) ("panzoom" ,javascript-cytoscape-panzoom))) (native-inputs `(("gcc" ,gcc-5))) (home-page "http://compbio.uthsc.edu/BNW/") (synopsis "Bayesian Network Webserver") - (description "This contains the code for the @dfn{Bayesian Network Webserver} (BNW).") + (description + "This contains the code for the @dfn{Bayesian Network Webserver} (BNW).") (license (list license:gpl2 license:gpl2+ license:lgpl2.1+))))) diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm index 2e5e521..c896020 100644 --- a/gn/services/bnw-container.scm +++ b/gn/services/bnw-container.scm @@ -13,7 +13,7 @@ (package bnw-configuration-package ; package (default bnw)) (deploy-directory bnw-deploy-directory ; string - (default "/home/bnw/server")) + (default "/srv/http")) (port bnw-configuration-port ; list of strings (default '("8880")))) @@ -23,11 +23,12 @@ #~(begin (use-modules (guix build utils)) (when (directory-exists? #$deploy-directory) - (delete-file-recusively #$deploy-directory)) + ;; Not 'delete-file-recursively' because the directory might be empty. + (system* "rm" "-r" #$(string-append deploy-directory "/*"))) (mkdir-p #$deploy-directory) (copy-recursively #$package #$deploy-directory) - (system* #$(file-append coreutils "/bin/chmod") "a+w" - (string-append #$deploy-directory "/sourcecodes/data")))))) + (invoke #$(file-append coreutils "/bin/chmod") "a+w" + (string-append #$deploy-directory "/sourcecodes/data")))))) (define bnw-nginx-config (match-lambda @@ -37,7 +38,7 @@ (server-name '("Bayesian Network")) (listen port) ;(root package) - (root "/srv/http") + (root deploy-directory) (locations (list (nginx-php-location) @@ -81,6 +82,5 @@ (service bnw-service-type ;; The following is for testing: ;(bnw-configuration - ; (deploy-directory "/home/efraimf/bnw") ; (port '("8888"))) )))) diff --git a/gn/services/bnw.service b/gn/services/bnw.service index ec7b3f8..5ba8f3f 100644 --- a/gn/services/bnw.service +++ b/gn/services/bnw.service @@ -3,7 +3,7 @@ Description=BNW web server Wants=guix-daemon.service [Service] -Environment="BNW_COMMAND=$(/bin/su -l bnw -c '/var/guix/profiles/per-user/bnw/current-guix/bin/guix system container /home/bnw/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/bnw/server=/srv/http --network')" +Environment="BNW_COMMAND=$(/bin/su -l bnw -c '/var/guix/profiles/per-user/bnw/current-guix/bin/guix system container /home/bnw/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/bnw/server=/srv/http --share=/home/bnw/server/var-log=/var/log --network')" ExecStart=/bin/bash -c '${BNW_COMMAND}' [Install] |