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authorEfraim Flashner2020-02-05 06:30:11 -0600
committerEfraim Flashner2020-02-05 06:30:11 -0600
commit5eb0b0bdba3374cee96006cd1006603bbe13e36b (patch)
treec58dff4a2343de0a376de41cd38a9c31562ea8ed /gn/packages/ratspub.scm
parentf57261e371cfec6dd067b7760abb6458704e7690 (diff)
downloadguix-bioinformatics-5eb0b0bdba3374cee96006cd1006603bbe13e36b.tar.gz
gn: ratspub: Update to 0.1.
Diffstat (limited to 'gn/packages/ratspub.scm')
-rw-r--r--gn/packages/ratspub.scm126
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)))