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authorEfraim Flashner2022-09-04 15:14:15 +0300
committerEfraim Flashner2022-09-20 14:20:48 +0300
commitc76d239f93e5bef315a719b3eee3cef5452e6bda (patch)
tree3c257dd2b5bf2fe52ba96b44d2bec1d19476881c /gn/packages
parent66c88ccd07c303af60494b110067ab0e5636931a (diff)
downloadguix-bioinformatics-c76d239f93e5bef315a719b3eee3cef5452e6bda.tar.gz
genecup: Update package.
Replace PYTHONPATH with GUIX_PYTHONPATH. Remove trailing #t from phases.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/ratspub.scm54
1 files changed, 19 insertions, 35 deletions
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index f298716..5f6f7b5 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -33,8 +33,7 @@
(modules '((guix build utils)))
(snippet
'(begin (substitute* "server.py"
- (("4201") "4200"))
- #t))
+ (("4201") "4200"))))
(sha256
(base32
"1y89rkqdxcnl2jjsy1wfp9p8qkgh6nzqs1r37wyhc8y7r3dva7kf"))))
@@ -51,8 +50,7 @@
(add-after 'unpack 'patch-datadir
(lambda _
(substitute* "server.py"
- (("^datadir.*") "datadir = \"/export/ratspub/\"\n"))
- #t))
+ (("^datadir.*") "datadir = \"/export/ratspub/\"\n"))))
(add-after 'unpack 'patch-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -71,13 +69,11 @@
(("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))
+ (("hostname") (string-append inetutils "/bin/hostname"))))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (copy-recursively "." out))
- #t))
+ (copy-recursively "." out))))
(add-after 'install 'install-javascript
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -111,19 +107,17 @@
(string-append out "/static/FileSaver.js"))
(symlink (string-append js-popper
"/share/javascript/popper.min.js")
- (string-append out "/static/popper.min.js")))
- #t))
+ (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 "PYTHONPATH")))
+ (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"))))
- `("PYTHONPATH" ":" prefix (,path))))
- #t)))))
+ `("GUIX_PYTHONPATH" ":" prefix (,path)))))))))
(inputs
`(("edirect" ,edirect)
("inetutils" ,inetutils)
@@ -208,8 +202,7 @@ gene-keyword relationships are presented as an interactive graph and a table.")
"/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")
- )
- #t))
+ )))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -226,8 +219,7 @@ if __name__ == '__main__':
app.run(debug=True, port=4222)~%"
python)))
(chmod "main.py" #o555)
- (copy-recursively "." out))
- #t))
+ (copy-recursively "." out))))
(add-after 'install 'install-javascript
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -247,15 +239,13 @@ if __name__ == '__main__':
;(symlink (string-append js-popper
; "/share/web/popper/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")))
+ (path (getenv "GUIX_PYTHONPATH")))
(wrap-program (string-append out "/main.py")
- `("PYTHONPATH" ":" prefix (,path))))
- #t)))))
+ `("GUIX_PYTHONPATH" ":" prefix (,path)))))))))
(inputs
`(("python" ,python)
("python-flask-sqlalchemy" ,python-flask-sqlalchemy)))
@@ -292,16 +282,14 @@ if __name__ == '__main__':
(add-after 'unpack 'use-different-port
(lambda _
(substitute* "server.py"
- (("4200") "4204"))
- #t))
+ (("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"))
- #t))
+ (("^datadir.*") "datadir = \"/export/ratspub/\"\n"))))
(add-after 'unpack 'patch-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -320,13 +308,11 @@ if __name__ == '__main__':
(("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))
+ (("hostname") (string-append inetutils "/bin/hostname"))))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (copy-recursively "." out))
- #t))
+ (copy-recursively "." out))))
(add-after 'install 'install-javascript
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
@@ -360,19 +346,17 @@ if __name__ == '__main__':
(string-append out "/static/FileSaver.js"))
(symlink (string-append js-popper
"/share/javascript/popper.min.js")
- (string-append out "/static/popper.min.js")))
- #t))
+ (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 "PYTHONPATH")))
+ (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"))))
- `("PYTHONPATH" ":" prefix (,path))))
- #t)))))
+ `("GUIX_PYTHONPATH" ":" prefix (,path)))))))))
(inputs
`(("edirect" ,edirect)
("inetutils" ,inetutils)