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+(define-module (gn packages genecup)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix git)
+ #:use-module (guix utils)
+ #:use-module (gnu packages)
+ #:use-module (guix packages)
+ #:use-module (guix git-download)
+ #:use-module (guix build-system python)
+ #:use-module (gnu packages admin)
+ #:use-module (gnu packages bioinformatics)
+ #:use-module (gnu packages javascript)
+ #:use-module (gnu packages machine-learning)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages python-crypto)
+ #:use-module (gnu packages python-science)
+ #:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
+ #:use-module (gn packages javascript)
+ #:use-module (gn packages machine-learning)
+ #:use-module (gn packages python)
+ #:use-module (gn packages web))
+
+(define use-corrected-inputs
+ (package-input-rewriting/spec
+ ;; Tensorflow-native provides much improved speeds. python-h5py@2 provides
+ ;; compatibility with our version of tensorflow.
+ `(("tensorflow" . ,(const tensorflow-native))
+ ("python-h5py" . ,(const python-h5py-2)))))
+
+(define-public python-keras-no-tests
+ (hidden-package
+ (package
+ (inherit python-keras)
+ (source
+ (origin
+ (inherit (package-source python-keras))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments python-keras)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (delete 'check))))))))
+
+
+(define-public hrdp-project
+ (package
+ (name "hrdp-project")
+ (version "0.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/noderboarder/hrdp-project")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ag7jm43p35yh0cqcn53wg4iw7sgfypw10mxq5klxvhgj3r6cf7i"))))
+ (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 _
+ (substitute* "./app/templates/layout.html"
+ (("https://.*.bootstrapcdn.com/bootstrap/4.*/css/bootstrap.min.css.*")
+ "/static/bootstrap.min.css\">\n")
+ (("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
+ "/static/bootstrap.min.js\"></script>\n")
+ (("https://code.jquery.com/jquery-3.*.slim.min.js.*")
+ "/static/jquery.slim.min.js\"></script>\n")
+ ;(("https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js.*")
+ ; "/static/popper.min.js\"></script>\n")
+ )))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (python (assoc-ref inputs "python")))
+ (delete-file "main.py")
+ (with-output-to-file "main.py"
+ (lambda ()
+ (format #t "#!~a/bin/python
+from app import create_app
+
+app = create_app()
+
+if __name__ == '__main__':
+ app.run(debug=True, port=4222)~%"
+ python)))
+ (chmod "main.py" #o555)
+ (copy-recursively "." out))))
+ (add-after 'install 'install-javascript
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (bootstrap (assoc-ref inputs "bootstrap"))
+ (jquery (assoc-ref inputs "jquery"))
+ ;(js-popper (assoc-ref inputs "js-popper"))
+ )
+ (symlink (string-append bootstrap
+ "/share/web/bootstrap/css/bootstrap.min.css")
+ (string-append out "/app/static/bootstrap.min.css"))
+ (symlink (string-append bootstrap
+ "/share/web/bootstrap/js/bootstrap.min.js")
+ (string-append out "/app/static/bootstrap.min.js"))
+ (symlink (string-append jquery
+ "/share/web/jquery/jquery.slim.min.js")
+ (string-append out "/app/static/jquery.slim.min.js"))
+ ;(symlink (string-append js-popper
+ ; "/share/web/popper/popper.min.js")
+ ; (string-append out "/static/popper.min.js"))
+ )))
+ (add-after 'install 'wrap-executable
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (path (getenv "GUIX_PYTHONPATH")))
+ (wrap-program (string-append out "/main.py")
+ `("GUIX_PYTHONPATH" ":" prefix (,path)))))))))
+ (inputs
+ `(("python" ,python)
+ ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)))
+ (native-inputs
+ `(("bootstrap" ,web-bootstrap)
+ ("jquery" ,web-jquery)
+ ;("js-popper" ,js-popper) ; empty output
+ ))
+ (home-page "https://github.com/noderboarder/hrdp-project")
+ (synopsis "")
+ (description "")
+ (license license:expat)))
+
+(define-public genecup
+ (package
+ (name "genecup")
+ (version "1.8")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/hakangunturkun/GeneCup")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0clnlnj6cl816yj3nalh1h6hsvnh3sjq2g84x1kmj1zkqkw184ri"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ; no test suite
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ ;; Change the port for running the service.
+ (add-after 'unpack 'use-different-port
+ (lambda _
+ (substitute* "server.py"
+ (("4200") "4204"))))
+ (add-after 'unpack 'make-files-writable
+ (lambda _
+ (for-each make-file-writable (find-files "."))))
+ (add-after 'unpack 'patch-datadir
+ (lambda _
+ (substitute* "server.py"
+ (("^datadir.*") "datadir = \"/export/ratspub/\"\n"))))
+ (add-after 'unpack 'patch-sources
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (inetutils (assoc-ref inputs "inetutils")))
+ (substitute* '("templates/cytoscape.html"
+ "templates/tableview.html"
+ "templates/tableview0.html"
+ "templates/userarchive.html")
+ (("https.*FileSaver.js.*\\\">") "/static/FileSaver.js\">")
+ (("https.*cytoscape-svg.js.*\\\">") "/static/cytoscape-svg.js\">")
+ (("https.*cytoscape.min.js.*\\\">") "/static/cytoscape.min.js\">"))
+ (substitute* "templates/layout.html"
+ (("https.*bootstrap.min.css.*\\\">") "/static/bootstrap.min.css\">")
+ (("https.*4.*bootstrap.min.js.*\\\">") "/static/bootstrap.min.js\">")
+ (("https.*4.7.0/css/font-awesome.min.css") "/static/font-awesome.min.css")
+ (("https.*jquery-3.2.1.slim.min.js.*\\\">") "/static/jquery.slim.min.js\">")
+ (("https.*1.12.9/umd/popper.min.js.*\\\">") "/static/popper.min.js\">"))
+ (substitute* "ratspub.py"
+ (("hostname") (string-append inetutils "/bin/hostname"))))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (copy-recursively "." out))))
+ (add-after 'install 'install-javascript
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (awesome (assoc-ref inputs "font-awesome"))
+ (bootstrap (assoc-ref inputs "bootstrap"))
+ (cytoscape (assoc-ref inputs "cytoscape"))
+ (cytoscape-svg (assoc-ref inputs "cytoscape-svg"))
+ (jquery (assoc-ref inputs "jquery"))
+ (js-filesaver (assoc-ref inputs "js-filesaver"))
+ (js-popper (assoc-ref inputs "js-popper")))
+ (symlink (string-append awesome
+ "/share/web/font-awesomecss/font-awesome.min.css")
+ (string-append out "/static/font-awesome.min.css"))
+ (symlink (string-append bootstrap
+ "/share/web/bootstrap/css/bootstrap.min.css")
+ (string-append out "/static/bootstrap.min.css"))
+ (symlink (string-append bootstrap
+ "/share/web/bootstrap/js/bootstrap.min.js")
+ (string-append out "/static/bootstrap.min.js"))
+ (symlink (string-append cytoscape
+ "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js")
+ (string-append out "/static/cytoscape.min.js"))
+ (symlink (string-append cytoscape-svg
+ "/share/javascript/cytoscape-svg.js")
+ (string-append out "/static/cytoscape-svg.js"))
+ (symlink (string-append jquery
+ "/share/web/jquery/jquery.slim.min.js")
+ (string-append out "/static/jquery.slim.min.js"))
+ (symlink (string-append js-filesaver
+ "/share/javascript/FileSaver.js")
+ (string-append out "/static/FileSaver.js"))
+ (symlink (string-append js-popper
+ "/share/javascript/popper.min.js")
+ (string-append out "/static/popper.min.js")))))
+ (add-after 'install 'wrap-executable
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (path (getenv "GUIX_PYTHONPATH")))
+ (wrap-program (string-append out "/server.py")
+ `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
+ ,(dirname (which "dirname"))
+ ,(dirname (which "grep"))
+ ,(dirname (which "sed"))))
+ `("GUIX_PYTHONPATH" ":" prefix (,path)))))))))
+ (inputs
+ `(("edirect" ,edirect)
+ ("inetutils" ,inetutils)
+ ("python-bcrypt" ,python-bcrypt)
+ ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+ ("python-keras" ,python-keras-no-tests)
+ ("python-nltk" ,python-nltk)
+ ("python-pandas" ,python-pandas)
+ ("python-regex" ,python-regex)
+ ("tensorflow" ,tensorflow)))
+ (native-inputs
+ `(("bootstrap" ,web-bootstrap)
+ ("cytoscape" ,javascript-cytoscape-3.17)
+ ;("cytoscape-svg" ,js-cytoscape-svg-0.3.1) ; TODO
+ ("cytoscape-svg" ,js-cytoscape-svg-vendor-0.3.1)
+ ("font-awesome" ,web-font-awesome)
+ ("jquery" ,web-jquery)
+ ("js-filesaver" ,js-filesaver-1.3.2)
+ ("js-popper" ,js-popper-1.12.9)))
+ (home-page "http://genecup.org")
+ (synopsis "Using PubMed to find out how a gene contributes to addiction")
+ (description "GeneCup automatically extracts information from PubMed and
+@url{https://www.ebi.ac.uk/gwas/, @acronym{NHGRI-EBI GWAS, European
+Bioinformatics Institute Genome-Wide Association Studies}} catalog on the
+relationship of any gene with a custom list of keywords hierarchically organized
+into an ontology. The users create an ontology by identifying categories of
+concepts and a list of keywords for each concept.")
+ (license license:expat)))
+
+(define genecup-master
+ (package
+ (inherit genecup)
+ (name "genecup-master")
+ (version "HEAD-of-master-branch")
+ (source
+ (git-checkout
+ (url "https://github.com/hakangunturkun/GeneCup")
+ (branch "master")))))
+
+(define-public genecup-with-tensorflow-native
+ (package
+ (inherit
+ (use-corrected-inputs genecup))
+ (name "genecup-with-tensorflow-native")))
+
+(define-public genecup-latest-with-tensorflow-native
+ (package
+ (inherit
+ (use-corrected-inputs genecup-master))
+ (name "genecup-latest-with-tensorflow-native")))