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authorPjotr Prins2021-08-24 08:19:09 +0000
committerPjotr Prins2021-08-24 08:19:09 +0000
commit82d0c5cc939f98adf597404adaef81ec0537d52a (patch)
tree9dc7a19470fce845c512b6180db319ee52f409a9 /gn/packages
parentc47ed182417cb6f8dd03478b54b0b7f99e703820 (diff)
downloadguix-bioinformatics-82d0c5cc939f98adf597404adaef81ec0537d52a.tar.gz
genenetwork[23]: updated git checkout and commented out DAG generation
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/genenetwork.scm137
1 files changed, 69 insertions, 68 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 1b9babc..3208c61 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -251,7 +251,7 @@ Graphical Fragment Assembly} files and related formats.")
(license license:expat)))
(define-public genenetwork3
- (let ((commit "487e50e8f8304a65e7af3759c13256f921efb8be"))
+ (let ((commit "c9ee473ff7797f6bbd7507eb55c772a3a646acee"))
(package
(name "genenetwork3")
(version (string-append "0.0.1-guix-" (string-take commit 7)))
@@ -264,7 +264,7 @@ Graphical Fragment Assembly} files and related formats.")
(file-name (git-file-name name version))
(sha256
(base32
- "1rm8pvl5x1350aivk7m2symdsf3iiacl4pnaz1q8fgxpr154qw93"))))
+ "1z25nr45kzy3vpk8gc1cq9r4j89dgpdmb83s1pgp75m9dcij5863"))))
(propagated-inputs `(("coreutils" ,coreutils)
("gemma-wrapper" ,gemma-wrapper)
("csvdiff" ,go-github-com-aswinkarthik-csvdiff)
@@ -292,7 +292,7 @@ Graphical Fragment Assembly} files and related formats.")
(license license:agpl3+))))
(define-public genenetwork2
- (let ((commit "84cbf35adbb15c79638372d108308edb05f12683"))
+ (let ((commit "fe345c9f2e99be748511f6889420d6560a553a37"))
(package
(name "genenetwork2")
(version (string-append "3.11-guix-" (string-take commit 7) ))
@@ -304,7 +304,7 @@ Graphical Fragment Assembly} files and related formats.")
(file-name (string-append name "-" version))
(sha256
(base32
- "1402g129ghfh0xwfxjj1i7gbib2yl9rahf55caj7b1psy24ys87x"))))
+ "1y6psmxpm3qn78dx6xfc11rdpf22vf807qb7grnp82gl19q6408w"))))
(native-inputs
`(("graphviz" ,graphviz)
;; And the graphs
@@ -331,6 +331,7 @@ Graphical Fragment Assembly} files and related formats.")
("plink-ng-gn" ,plink-ng-gn)
; ("pylmm-gn2" ,pylmm-gn2)
("rust-qtlreaper" ,rust-qtlreaper)
+ ("glibc-utf8-locales" ,glibc-utf8-locales)
("nginx" ,nginx)
("python" ,python-wrapper)
("python-pillow" ,python-pillow)
@@ -434,13 +435,13 @@ Graphical Fragment Assembly} files and related formats.")
(("rm") (which "rm"))
(("which") (which "which")))
#t))
- (add-after 'unpack 'patch-javascript
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((colorbox (assoc-ref inputs "javascript-colorbox"))
- (gn2 "/share/genenetwork2/javascript/"))
- (delete-file-recursively "wqflask/wqflask/static/packages/colorbox")
- (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox")
- #t)))
+ ; (add-after 'unpack 'patch-javascript
+ ; (lambda* (#:key inputs #:allow-other-keys)
+ ; (let ((colorbox (assoc-ref inputs "javascript-colorbox"))
+ ; (gn2 "/share/genenetwork2/javascript/"))
+ ; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox")
+ ; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox")
+ ; #t)))
(add-before 'install 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(let* (
@@ -457,63 +458,63 @@ Graphical Fragment Assembly} files and related formats.")
(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
)
)))
- (add-after 'install 'generate-graph
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (call-with-output-file
- (string-append
- (assoc-ref outputs "out")
- "/lib/python"
- (python-version (assoc-ref inputs "python"))
- "/site-packages"
- "/wqflask/dependency-graph.html")
- (lambda (port)
- (format
- port "~a"
- ,(call-with-output-string
- (lambda (p)
- (with-output-to-port p
- (lambda ()
- (run-with-store
- (open-connection)
- (export-graph
- (list this-package)
- p
- #:node-type %package-node-type
- #:backend %d3js-backend)))))))))))
- (add-after 'install 'generate-dag-svg-file
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((output-dir
- (string-append
- (assoc-ref outputs "out")
- "/lib/python"
- (python-version (assoc-ref inputs "python"))
- "/site-packages/wqflask/"))
- (dot-file
- (string-append
- output-dir
- "dependency-graph.dot"))
- (svg-file
- (string-append
- output-dir
- "dependency-graph.svg")))
- (begin
- (call-with-output-file
- dot-file
- (lambda (port)
- (format
- port "~a"
- ,(call-with-output-string
- (lambda (p)
- (with-output-to-port p
- (lambda ()
- (run-with-store
- (open-connection)
- (export-graph
- (list this-package)
- p
- #:node-type %package-node-type
- #:backend %graphviz-backend)))))))))
- (invoke "dot" "-Tsvg" "-o" svg-file dot-file)))))
+ ; (add-after 'install 'generate-graph
+ ; (lambda* (#:key inputs outputs #:allow-other-keys)
+ ; (call-with-output-file
+ ; (string-append
+ ; (assoc-ref outputs "out")
+ ; "/lib/python"
+ ; (python-version (assoc-ref inputs "python"))
+ ; "/site-packages"
+ ; "/wqflask/dependency-graph.html")
+ ; (lambda (port)
+ ; (format
+ ; port "~a"
+ ; ,(call-with-output-string
+ ; (lambda (p)
+ ; (with-output-to-port p
+ ; (lambda ()
+ ; (run-with-store
+ ; (open-connection)
+ ; (export-graph
+ ; (list this-package)
+ ; p
+ ; #:node-type %package-node-type
+ ; #:backend %d3js-backend)))))))))))
+ ;(add-after 'install 'generate-dag-svg-file
+ ; (lambda* (#:key inputs outputs #:allow-other-keys)
+ ; (let* ((output-dir
+ ; (string-append
+ ; (assoc-ref outputs "out")
+ ; "/lib/python"
+ ; (python-version (assoc-ref inputs "python"))
+ ; "/site-packages/wqflask/"))
+ ; (dot-file
+ ; (string-append
+ ; output-dir
+ ; "dependency-graph.dot"))
+ ; (svg-file
+ ; (string-append
+ ; output-dir
+ ; "dependency-graph.svg")))
+ ; (begin
+ ; (call-with-output-file
+ ; dot-file
+ ; (lambda (port)
+ ; (format
+ ; port "~a"
+ ; ,(call-with-output-string
+ ; (lambda (p)
+ ; (with-output-to-port p
+ ; (lambda ()
+ ; (run-with-store
+ ; (open-connection)
+ ; (export-graph
+ ; (list this-package)
+ ; p
+ ; #:node-type %package-node-type
+ ; #:backend %graphviz-backend)))))))))
+ ; (invoke "dot" "-Tsvg" "-o" svg-file dot-file)))))
;; TODO: Use this to replace the two previous phases.
;(add-after 'install 'install-generated-files