From c54d99b582e00e083da128fbe94d8237f8ddfabc Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 5 Aug 2019 04:14:56 -0500
Subject: gn: Add ratspub.

* gn/packages/ratspub.scm (ratspub): New variable.
---
 gn/packages/ratspub.scm | 75 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 gn/packages/ratspub.scm

(limited to 'gn/packages/ratspub.scm')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
new file mode 100644
index 0000000..7164229
--- /dev/null
+++ b/gn/packages/ratspub.scm
@@ -0,0 +1,75 @@
+(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))))
-- 
cgit v1.2.3