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authorEfraim Flashner2019-08-04 03:37:14 -0500
committerEfraim Flashner2019-08-04 03:39:50 -0500
commit0a1c7baafb5107b452c33e9c53526befe458ed16 (patch)
treecde837a24d9d5711722f5a619c1d3751d4adcc47
parent25db4463972bc8729436d84d8be003ea7eacad71 (diff)
downloadguix-bioinformatics-0a1c7baafb5107b452c33e9c53526befe458ed16.tar.gz
bnw: Build binaries.
* gn/packages/bnw.scm (bnw)[build-system]: Use gnu-build-system. [arguments]: Adjust accordingly. [native-inputs]: Remove source. [inputs]: Remove bash-minimal, add rmath-standalone.
-rw-r--r--gn/packages/bnw.scm90
1 files changed, 52 insertions, 38 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index 2c34256..7b6662c 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -2,12 +2,12 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix git-download)
- #:use-module (guix build-system trivial)
- #:use-module (gnu packages bash)
+ #:use-module (guix build-system gnu)
#:use-module (gn packages graphviz)
#:use-module (gn packages javascript)
#:use-module (gn packages maths)
#:use-module (gnu packages python)
+ #:use-module (gnu packages statistics)
#:use-module (gn packages web))
(define-public bnw
@@ -25,44 +25,45 @@
(sha256
(base32
"10qwykp2zcyxih6a52icvy30ps69qk4v3jgirmdpw1l15zi4p2wq"))))
- (build-system trivial-build-system)
+ (build-system gnu-build-system)
(arguments
- `(#:modules ((guix build utils))
- #:builder
- (begin
- (use-modules (guix build utils))
- (let* ((out (assoc-ref %outputs "out"))
- (source (assoc-ref %build-inputs "source"))
- (bash (assoc-ref %build-inputs "bash"))
- (graphviz (assoc-ref %build-inputs "graphviz"))
- (octave (assoc-ref %build-inputs "octave"))
- (python (assoc-ref %build-inputs "python"))
- (jquery (assoc-ref %build-inputs "jquery"))
- (awesome (assoc-ref %build-inputs "awesome"))
- (cyto (assoc-ref %build-inputs "cytoscape"))
- (cyto2 (assoc-ref %build-inputs "cytoscape-2"))
- (cs-dagre (assoc-ref %build-inputs "cyto-dagre"))
- (d3js (assoc-ref %build-inputs "d3js"))
- (d3js-multi (assoc-ref %build-inputs "d3js-multi"))
- (dagre (assoc-ref %build-inputs "dagre"))
- (lodash (assoc-ref %build-inputs "lodash"))
- (canvas-toblob (assoc-ref %build-inputs "canvas-toblob"))
- (filesaver (assoc-ref %build-inputs "filesaver"))
- (panzoom (assoc-ref %build-inputs "panzoom"))
- (js-path "/share/genenetwork2/javascript/"))
- (copy-recursively source out)
- (for-each (lambda (file)
- (patch-shebang file
- (list (string-append bash "/bin")
- (string-append octave "/bin")
- (string-append python "/bin"))))
- (find-files out ".*"))
- (with-directory-excursion out
+ `(#:tests? #f ; no test suite
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (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/"))
+ (for-each (lambda (file)
+ (patch-shebang file
+ (list (string-append bash "/bin")
+ (string-append octave "/bin")
+ (string-append python "/bin"))))
+ (find-files "." ".*"))
(substitute*
(append '("home.php")
(find-files "sourcecodes" ".php")
(find-files "sourcecodes/run_scripts" ".*"))
(("/usr/bin/dot") (string-append graphviz "/bin/dot")))
+ (substitute* "sourcecodes/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"))
@@ -91,13 +92,26 @@
(("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"))))))))
- (native-inputs `(("source" ,source)))
+ (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))
+ (replace 'build
+ (lambda _
+ (with-directory-excursion "sourcecodes"
+ (substitute* "build.sh"
+ (("./localscore") "localscore"))
+ (chmod "k-best/src/buildk_poster.sh" #o755)
+ (invoke "sh" "build.sh")))))))
(inputs
- `(("bash" ,bash-minimal)
- ("graphviz" ,graphviz-2.26)
+ `(("graphviz" ,graphviz-2.26)
("octave" ,octave-3.4.3)
("python" ,python-2)
+ ("rmath" ,rmath-standalone) ; Should this be r-minimal? Which version?
("jquery" ,web-jquery)
("awesome" ,web-font-awesome)
("cytoscape" ,javascript-cytoscape)