diff options
Diffstat (limited to 'gn/packages/genecup.scm')
| -rw-r--r-- | gn/packages/genecup.scm | 279 |
1 files changed, 279 insertions, 0 deletions
diff --git a/gn/packages/genecup.scm b/gn/packages/genecup.scm new file mode 100644 index 0000000..0cd776f --- /dev/null +++ b/gn/packages/genecup.scm @@ -0,0 +1,279 @@ +(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"))) |