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authorEfraim Flashner2021-03-04 15:17:27 +0200
committerEfraim Flashner2021-03-04 15:22:29 +0200
commit697a66bf0e897a101e8e3cefbaf250491039fe93 (patch)
treed40eb3aabad0b8c68e0dff6df1ea52d25aa8565d /gn
parentb08410a9944e677ef71267410b235ba869f3935f (diff)
downloadguix-bioinformatics-697a66bf0e897a101e8e3cefbaf250491039fe93.tar.gz
gn: Update bnw to latest version.
Update bnw and the service
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bnw.scm246
-rw-r--r--gn/services/bnw-container.scm17
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