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(define-module (gn packages ratspub)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system python)
#: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"))
(package
(name "ratspub")
(version (git-version "0.0.0" revision commit)) ; June 1, 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
"1v05rrjmiwrjmjspn487hd39403vb452hmk2l1l55rkm26781hwk"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(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"))))
#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))
#t))
(add-after 'install 'wrap-executable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/server.py")
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("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))))
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