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authorEfraim Flashner2019-12-03 04:16:15 -0600
committerEfraim Flashner2019-12-03 04:16:15 -0600
commit21c3ce9c0a80695dcb15a792a0871f59cf3aa441 (patch)
tree82e45b01406266c22e03177ee7312a1690de13a5 /gn/packages/ratspub.scm
parent900ec50459658207406b0d4dd3faaf3923d7d137 (diff)
downloadguix-bioinformatics-21c3ce9c0a80695dcb15a792a0871f59cf3aa441.tar.gz
gn: ratspub: Update package and definition.
Diffstat (limited to 'gn/packages/ratspub.scm')
-rw-r--r--gn/packages/ratspub.scm50
1 files changed, 29 insertions, 21 deletions
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 7164229..da6df5f 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -3,17 +3,19 @@
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system python)
+ #:use-module (gnu packages admin)
+ #:use-module (gn packages bioinformatics)
#:use-module (gn packages javascript)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gn packages web))
(define-public ratspub
- (let ((commit "19bc3078c06bef3c10c55dc6e69018e595d07d17")
- (revision "1"))
+ (let ((commit "88ab6a3a21fcc2715c9a7528d8b4d15bb7ea85ed")
+ (revision "2"))
(package
(name "ratspub")
- (version (git-version "0.0.0" revision commit)) ; June 1, 2019
+ (version (git-version "0.0.0" revision commit)) ; Aug 30, 2019
(source (origin
(method git-fetch)
(uri (git-reference
@@ -22,7 +24,7 @@
(file-name (git-file-name name version))
(sha256
(base32
- "1v05rrjmiwrjmjspn487hd39403vb452hmk2l1l55rkm26781hwk"))))
+ "0gg2wikajbz248qgg7vyclrmjhdw01wb721zvzgil9qd2gm0g4c6"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test suite
@@ -30,34 +32,40 @@
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
- (add-after 'unpack 'patch-javascript-references
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((cytoscape (assoc-ref inputs "cytoscape"))
- (bootstrap (assoc-ref inputs "bootstrap")))
- (substitute* "templates/cytoscape.html"
- (("script src=.*")
- (string-append "script src=\"" cytoscape
- "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js\"></script>\n")))
- (substitute* "templates/layout.html"
- (("https://stackpath.bootstrapcdn.com/bootstrap/.*")
- (string-append bootstrap "/share/web/bootstrap/css/bootstrap.min.css\">\n"))))
+ (add-after 'unpack 'patch-sources
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (cytoscape (assoc-ref inputs "cytoscape"))
+ (bootstrap (assoc-ref inputs "bootstrap"))
+ (inetutils (assoc-ref inputs "inetutils")))
+ ;; Source cannot find the substituted css currently.
+ ;(substitute* "templates/cytoscape.html"
+ ; (("script src=.*")
+ ; (string-append "script src=\"" cytoscape
+ ; "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js\"></script>\n")))
+ ;(substitute* "templates/layout.html"
+ ; (("https://stackpath.bootstrapcdn.com/bootstrap/.*")
+ ; (string-append bootstrap "/share/web/bootstrap/css/bootstrap.min.css\">\n")))
+ (substitute* "ratspub.py"
+ (("hostname") (string-append inetutils "/bin/hostname"))))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (copy-recursively "static" (string-append out "/static"))
- (copy-recursively "templates" (string-append out "/templates"))
- (install-file "server.py" out))
+ (copy-recursively "." out))
#t))
(add-after 'install 'wrap-executable
- (lambda* (#:key outputs #:allow-other-keys)
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/server.py")
- `("PYTHONPATH" ":" prefix (,path))))
+ `("PATH" ":" prefix (,(dirname (which "edirect.pl"))))
+ `("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
- `(("python-flask" ,python-flask)
+ `(("edirect" ,edirect-gn)
+ ("inetutils" ,inetutils)
+ ("python-flask" ,python-flask)
("python-nltk" ,python-nltk)))
(native-inputs
`(("cytoscape" ,javascript-cytoscape)