rename ratspub.scm to genecup.scm

1 files changed, 0 insertions, 279 deletions

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
deleted file mode 100644
index c530979..0000000
--- a/gn/packages/ratspub.scm
+++ /dev/null
@@ -1,279 +0,0 @@
-(define-module (gn packages ratspub)
-  #: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")))