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authorEfraim Flashner2022-09-04 15:04:33 +0300
committerEfraim Flashner2022-09-20 14:20:48 +0300
commit66c88ccd07c303af60494b110067ab0e5636931a (patch)
tree42eb937b78c3f643e54cfa325ab0a5040b4d3eed
parentc380c2cdedfa0a20a2b731f081443b963ab3b97f (diff)
downloadguix-bioinformatics-66c88ccd07c303af60494b110067ab0e5636931a.tar.gz
bnw: Update package
Remove trailing #t from phases Replace PYTHONPATH with GUIX_PYTHONPATH
-rw-r--r--gn/packages/bnw.scm26
1 files changed, 9 insertions, 17 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index b545b84..1e2c86e 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -56,8 +56,7 @@
;"fontawesome-webfont.woff" ; sha256 mismatch
;"jquery.min.js" ; sha256 mismatch
;"lodash.js" ; sha256 mismatch
- ))
- #t))))
+ ))))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no test suite
@@ -68,8 +67,7 @@
(lambda _
;; sourcecodes/matrix.php hardcodes $dir=/tmp/bnw
(substitute* "sourcecodes/matrix.php"
- (("/tmp/bnw") "/var/lib/genenet/bnw/"))
- #t))
+ (("/tmp/bnw") "/var/lib/genenet/bnw/"))))
(add-after 'patch-source-shebangs 'patch-more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
(let ((graphviz (assoc-ref inputs "graphviz"))
@@ -91,8 +89,7 @@
(("/usr/bin/dot") (string-append graphviz "/bin/dot")))
(substitute* "var_lib_genenet_bnw/build.sh"
(("./localscore/libRmath.so")
- (string-append rmath "/lib/libRmath.so")))
- #t)))
+ (string-append rmath "/lib/libRmath.so"))))))
(add-after 'patch-source-shebangs 'replace-javascript
(lambda* (#:key inputs #:allow-other-keys)
(let ((jquery (assoc-ref inputs "jquery"))
@@ -140,13 +137,11 @@
; "sourcecodes/network_layout_inv.php"
; "sourcecodes/network_layout_inv_2.php")
; (("https://www.google.com/jsapi") "https://www.gstatic.com/charts/loader.js"))
- )
- #t))
+ )))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- (copy-recursively "." out))
- #t))
+ (copy-recursively "." out))))
(add-after 'install 'install-javascript-libraries
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@@ -212,8 +207,7 @@
(string-append scripts "canvas-toBlob.js")))
(unless (file-exists? (string-append scripts "FileSaver.min.js"))
(symlink (string-append filesaver js-path2 "filesaver/FileSaver.min.js")
- (string-append scripts "FileSaver.min.js")))
- #t)))
+ (string-append scripts "FileSaver.min.js"))))))
(add-after 'install 'make-files-executable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
@@ -222,15 +216,14 @@
(chmod file #o555))
(append (find-files out "\\.(sh|py)$")
(find-files
- (string-append out "/sourcecodes/run_scripts/") "^run")))
- #t)))
+ (string-append out "/sourcecodes/run_scripts/") "^run"))))))
(add-after 'make-files-executable 'wrap-executables
(lambda* (#:key outputs #:allow-other-keys)
(for-each
(lambda (script)
(wrap-program script
`("PATH" prefix (,(dirname (which "cp"))))
- `("PYTHONPATH" prefix (,(getenv "PYTHONPATH")))))
+ `("GUIX_PYTHONPATH" prefix (,(getenv "GUIX_PYTHONPATH")))))
(find-files (string-append (assoc-ref outputs "out")
"/sourcecodes/run_scripts") "^run"))
(for-each
@@ -241,8 +234,7 @@
(find-files (string-append (assoc-ref outputs "out")
"/sourcecodes") "\\.sh$")
(find-files (string-append (assoc-ref outputs "out")
- "/var_lib_genenet_bnw") "\\.sh$")))
- #t))
+ "/var_lib_genenet_bnw") "\\.sh$")))))
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "var_lib_genenet_bnw"