rename ratspub.scm to genecup.scm

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")))