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authorShepherd on Tux022024-06-21 04:51:09 -0500
committerShepherd on Tux022024-06-21 04:51:17 -0500
commitd5aa746d3f7ecf46fcab2c527fb2d033a77c5143 (patch)
tree3b122d45d1ca6c5ba62ea8a05c2270c6e27996f2 /gn/packages/ratspub.scm
parentfe579ad20464adae86939345c214cc41028825f3 (diff)
downloadguix-bioinformatics-d5aa746d3f7ecf46fcab2c527fb2d033a77c5143.tar.gz
ratspub: remove definitions as they are replaced by genecup
Diffstat (limited to 'gn/packages/ratspub.scm')
-rw-r--r--gn/packages/ratspub.scm152
1 files changed, 0 insertions, 152 deletions
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index d797e8a..c530979 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -20,135 +20,6 @@
#:use-module (gn packages python)
#:use-module (gn packages web))
-(define-public ratspub
- (package
- (name "ratspub")
- (version "0.4.5")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/chen42/ratspub")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- ;; Keep the service running on port 4200.
- (modules '((guix build utils)))
- (snippet
- '(begin (substitute* "server.py"
- (("4201") "4200"))))
- (sha256
- (base32
- "1y89rkqdxcnl2jjsy1wfp9p8qkgh6nzqs1r37wyhc8y7r3dva7kf"))))
- (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"))))
- (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-for-ratspub)
- ("python-nltk" ,python-nltk)
- ("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 "https://rats.pub/")
- (synopsis "Relationship with Addiction Through Searches of PubMed")
- (description
- "RatsPub is a tool to efficiently and comprehensively answer the question
-\"What do we know about these genes and addiction?\". RatsPub answers this
-question by searching PubMed to find sentences containing the query terms (i.e.,
-gene symbols) and over 300 drug addiction-related keywords that are organized
-into six categories. Data from @url{https://www.ebi.ac.uk/gwas/,
-@acronym{NHGRI-EBI GWAS, European Bioinformatics Institute Genome-Wide
-Association Studies}} catalog are also included in the search. These
-gene-keyword relationships are presented as an interactive graph and a table.")
- (license license:expat)))
-
(define use-corrected-inputs
(package-input-rewriting/spec
;; Tensorflow-native provides much improved speeds. python-h5py@2 provides
@@ -156,29 +27,6 @@ gene-keyword relationships are presented as an interactive graph and a table.")
`(("tensorflow" . ,(const tensorflow-native))
("python-h5py" . ,(const python-h5py-2)))))
-(define-public ratspub-with-tensorflow-native
- (package
- (inherit
- (tensowflow-native-instead-of-tensorflow ratspub))
- (name "ratspub-with-tensorflow-native")))
-
-;; We want a copy of python-keras with the AUC optimizer backported.
-;; We skip the tests because we "test in production".
-;; That's a lie. The test suite just takes a long time to run.
-(define-public python-keras-for-ratspub
- (hidden-package
- (package
- (inherit python-keras)
- (source
- (origin
- (inherit (package-source python-keras))
- (patches (search-patches "keras-auc-optimizer.patch"))))
- (arguments
- (substitute-keyword-arguments (package-arguments python-keras)
- ((#:phases phases)
- `(modify-phases ,phases
- (delete 'check))))))))
-
(define-public python-keras-no-tests
(hidden-package
(package