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-rw-r--r--gn/packages/bnw.scm84
-rw-r--r--gn/services/bnw-container.scm18
2 files changed, 58 insertions, 44 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index bdb6ac5..f7e95e3 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -14,7 +14,7 @@
(define-public bnw
(let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04")
- (revision "3"))
+ (revision "4"))
(package
(name "bnw")
(version (git-version "1.22" revision commit)) ; June 28, 2019
@@ -41,6 +41,9 @@
(("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"))
#t))
(add-after 'patch-source-shebangs 'patch-more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
@@ -70,48 +73,51 @@
(find-files "." ".*"))
(substitute* '("sourcecodes/examplefilecopy.sh"
"sourcecodes/filecopy.sh")
- (("rm") (which "rm"))
- (("cp") (which "cp")))
+ (("^rm") (which "rm"))
+ (("\\ cp") (string-append " " (which "cp"))))
+ (substitute* (find-files "sourcecodes" "(^run|py$)")
+ (("/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"
+ (substitute* '("sourcecodes/build.sh"
+ "downloads/BNW/src/build.sh")
(("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so")))
- (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"))
- (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/2.7.29/cytoscape.min.js")
- (string-append cyto2 js-path "cytoscape/cytoscape.min.js"))
- (("http://spades.bioinf.spbau.ru/~alla/graph_viewer/js/cytoscape-dagre.js")
- (string-append cs-dagre js-path "cytoscape-dagre/cytoscape-dagre.js"))
- (("https://unpkg.com/dagre@0.7.4/dist/dagre.js")
- (string-append dagre js-path "dagre/dagre.js"))
- (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css")
- (string-append panzoom js-path "cytoscape-panzoom/cytoscape.js-panzoom.css"))
- (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js")
- (string-append panzoom js-path "cytoscape-panzoom/cytoscape-panzoom.js"))
- (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css")
- (string-append awesome "/share/web/font-awesome/css/font-awesome.css"))
- (("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js")
- (string-append jquery "/share/web/jquery/jquery.min.js"))
- (("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js")
- (string-append lodash js-path "lodash/lodash.js")))
- (substitute* '("sourcecodes/layout_svg_wt.php"
- "sourcecodes/layout_svg_no.php")
- (("http://d3js.org/d3.v4.min.js")
- (string-append d3js js-path "d3js/d3.min.js"))
- (("http://d3js.org/d3-selection-multi.v1.js")
- (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js"))
- (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js")
- (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"))))
+ ;(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"))
+ ; (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/2.7.29/cytoscape.min.js")
+ ; (string-append cyto2 js-path "cytoscape/cytoscape.min.js"))
+ ; (("http://spades.bioinf.spbau.ru/~alla/graph_viewer/js/cytoscape-dagre.js")
+ ; (string-append cs-dagre js-path "cytoscape-dagre/cytoscape-dagre.js"))
+ ; (("https://unpkg.com/dagre@0.7.4/dist/dagre.js")
+ ; (string-append dagre js-path "dagre/dagre.js"))
+ ; (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css")
+ ; (string-append panzoom js-path "cytoscape-panzoom/cytoscape.js-panzoom.css"))
+ ; (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js")
+ ; (string-append panzoom js-path "cytoscape-panzoom/cytoscape-panzoom.js"))
+ ; (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css")
+ ; (string-append awesome "/share/web/font-awesome/css/font-awesome.css"))
+ ; (("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js")
+ ; (string-append jquery "/share/web/jquery/jquery.min.js"))
+ ; (("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js")
+ ; (string-append lodash js-path "lodash/lodash.js")))
+ ;(substitute* '("sourcecodes/layout_svg_wt.php"
+ ; "sourcecodes/layout_svg_no.php")
+ ; (("http://d3js.org/d3.v4.min.js")
+ ; (string-append d3js js-path "d3js/d3.min.js"))
+ ; (("http://d3js.org/d3-selection-multi.v1.js")
+ ; (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js"))
+ ; (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js")
+ ; (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))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (delete-file "sourcecodes/localscore/libRmath.so")
(copy-recursively "." out))
#t))
(add-after 'install 'make-files-executable
@@ -120,28 +126,30 @@
(for-each
(lambda (file)
(chmod file #o555))
- (find-files out "\\.sh$"))
+ (append (find-files out "\\.(sh|py)$")
+ (find-files (string-append out "/sourcecodes/run_scripts" ".*"))
+ ))
#t)))
(replace 'build
(lambda _
(with-directory-excursion "sourcecodes"
(substitute* "build.sh"
(("./localscore") "localscore"))
- (chmod "k-best/src/buildk_poster.sh" #o755)
+ (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_loo" "LvQ Weight")
+ ;(invoke "./run_scripts/run_loo" "LvQ Weight")
))))))
(inputs
`(("graphviz" ,graphviz-2.26)
("octave" ,octave-3.4.3)
("python" ,python-2)
("plotly" ,python2-plotly-3.2.1)
- ("rmath" ,rmath-standalone) ; Should this be r-minimal? Which version?
+ ("rmath" ,rmath-standalone)
("jquery" ,web-jquery)
("awesome" ,web-font-awesome)
("cytoscape" ,javascript-cytoscape)
diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm
index cd8562f..13a9317 100644
--- a/gn/services/bnw-container.scm
+++ b/gn/services/bnw-container.scm
@@ -1,6 +1,7 @@
(define-module (gn services bnw-container))
-(use-modules (gnu))
+(use-modules (gnu)
+ (gn packages bnw))
(use-service-modules base networking web)
(operating-system
@@ -22,9 +23,14 @@
(server-blocks
(list
(nginx-server-configuration
- (root "/srv/http/bnw")
+ (server-name '("Bayesian Network"))
+ (listen '("8888"))
+ (root bnw)
(locations
- (list (nginx-php-location)))
- (listen '("8880"))
- (ssl-certificate #f)
- (ssl-certificate-key #f)))))))))
+ (list
+ (nginx-php-location)
+ (nginx-location-configuration
+ (uri "/sourcecodes/data/")
+ (body (list "alias /tmp/bnw/;")))
+ ))
+ ))))))))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-04 21:28:23 +0000