diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/ratspub.scm | 50 |
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) |