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authorEfraim Flashner2021-05-27 02:27:29 -0500
committerEfraim Flashner2021-05-27 02:27:38 -0500
commit2df25a354555437cfe149f4293adb0ad8cbc5160 (patch)
treec19940f46e9dd451a0dd707a440873ee0f41b1b7 /gn/packages
parent76a0deb6f1a6898814cb257afc0b6b61c38e63a2 (diff)
downloadguix-bioinformatics-2df25a354555437cfe149f4293adb0ad8cbc5160.tar.gz
gn: genecup testing
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/ratspub.scm142
1 files changed, 141 insertions, 1 deletions
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 85c73c7..1c00139 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -11,6 +11,7 @@
#: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)
@@ -139,7 +140,7 @@
("jquery" ,web-jquery)
("js-filesaver" ,js-filesaver-1.3.2)
("js-popper" ,js-popper-1.12.9)))
- (home-page "http://rats.pub/")
+ (home-page "https://rats.pub/")
(synopsis "Relationship with Addiction Through Searches of PubMed")
(description
"RatsPub is a tool to efficiently and comprehensively answer the question
@@ -266,3 +267,142 @@ if __name__ == '__main__':
(synopsis "")
(description "")
(license license:expat)))
+
+(define-public genecup
+ (package
+ (name "genecup")
+ (version "1.0")
+ (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))
+ ;; Change the port for running the service.
+ (modules '((guix build utils)))
+ (snippet
+ '(begin (substitute* "server.py"
+ (("4200") "4204"))
+ #t))
+ (sha256
+ (base32 "0ddgqjiacr0f33x0f9s10v3rqr3mmr92jwniprk22a167ncvfgx3"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ; no test suite
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (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"))
+ #t))
+ (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"))))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (copy-recursively "." out))
+ #t))
+ (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")))
+ #t))
+ (add-after 'install 'wrap-executable
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (path (getenv "PYTHONPATH")))
+ (wrap-program (string-append out "/server.py")
+ `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
+ ,(dirname (which "dirname"))
+ ,(dirname (which "grep"))
+ ,(dirname (which "sed"))))
+ `("PYTHONPATH" ":" prefix (,path))))
+ #t)))))
+ (inputs
+ `(("edirect" ,edirect)
+ ("inetutils" ,inetutils)
+ ("python-bcrypt" ,python-bcrypt)
+ ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+ ("python-keras" ,python-keras-for-ratspub)
+ ("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://genecut.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-public genecup-with-tensorflow-native
+ (package
+ (inherit
+ (tensowflow-native-instead-of-tensorflow genecup))
+ (name "genecup-with-tensorflow-native")))