diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/ratspub.scm | 126 |
1 files changed, 62 insertions, 64 deletions
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm index da6df5f..81959a0 100644 --- a/gn/packages/ratspub.scm +++ b/gn/packages/ratspub.scm @@ -11,73 +11,71 @@ #:use-module (gn packages web)) (define-public ratspub - (let ((commit "88ab6a3a21fcc2715c9a7528d8b4d15bb7ea85ed") - (revision "2")) - (package - (name "ratspub") - (version (git-version "0.0.0" revision commit)) ; Aug 30, 2019 - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/chen42/ratspub.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0gg2wikajbz248qgg7vyclrmjhdw01wb721zvzgil9qd2gm0g4c6")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; no test suite - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (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 "." out)) - #t)) - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (path (getenv "PYTHONPATH"))) - (wrap-program (string-append out "/server.py") - `("PATH" ":" prefix (,(dirname (which "edirect.pl")))) - `("PYTHONPATH" ":" prefix (,path)))) - #t))))) - (inputs - `(("edirect" ,edirect-gn) - ("inetutils" ,inetutils) - ("python-flask" ,python-flask) - ("python-nltk" ,python-nltk))) - (native-inputs - `(("cytoscape" ,javascript-cytoscape) - ("bootstrap" ,web-bootstrap))) - (home-page "http://rats.pub/") - (synopsis "Relationship with Addiction Through Searches of PubMed") - (description - "RatsPub searches PubMed to find sentences that contain the query terms + (package + (name "ratspub") + (version "0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chen42/ratspub.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0cm9g38fxpa52458mdmhzhghj5c7b8l3k1b764zs9hdrki5s7wi7")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; no test suite + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (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 "." out)) + #t)) + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out "/server.py") + `("PATH" ":" prefix (,(dirname (which "edirect.pl")))) + `("PYTHONPATH" ":" prefix (,path)))) + #t))))) + (inputs + `(("edirect" ,edirect-gn) + ("inetutils" ,inetutils) + ("python-flask" ,python-flask) + ("python-nltk" ,python-nltk))) + (native-inputs + `(("cytoscape" ,javascript-cytoscape) + ("bootstrap" ,web-bootstrap))) + (home-page "http://rats.pub/") + (synopsis "Relationship with Addiction Through Searches of PubMed") + (description + "RatsPub searches PubMed to find sentences that contain the query terms (i.e., gene symbols) and drug addiction-related keywords. These gene-keyword relationships are presented as an interactive graph that can efficiently answer the question \"What do we know about these genes and addiction?\". Data from @acronym{EBI GWAS, European Bioinformatics Institute Genome-Wide Association Studies} catalog are also included in the search to better answer this question.") - (license #f)))) + (license #f))) |