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authorEfraim Flashner2019-12-22 03:49:03 -0600
committerEfraim Flashner2019-12-22 03:49:03 -0600
commit5856fb3878e69a2091afbfdd3b15268e310f82e3 (patch)
treea4bd7cf668275279bcbf01ede37954f8087d7172 /gn/packages
parent3035ea5144af76b6ff260b1bceef3feafec8a177 (diff)
downloadguix-bioinformatics-5856fb3878e69a2091afbfdd3b15268e310f82e3.tar.gz
gn: Update bnw service
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bnw.scm12
1 files changed, 10 insertions, 2 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index f7e95e3..5b7131b 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -44,6 +44,9 @@
(substitute* (find-files "." "\\.php")
(("HTTP_POST_VARS") "_POST")
(("HTTP_POST_FILES") "_FILES"))
+ ;; change $dir to a writable directory
+ ;(substitute* (find-files "sourcecodes" "\\.php$")
+ ; (("\\$dir=\"./data") "$dir=\"./data/tmp"))
#t))
(add-after 'patch-source-shebangs 'patch-more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
@@ -84,6 +87,11 @@
(substitute* '("sourcecodes/build.sh"
"downloads/BNW/src/build.sh")
(("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so")))
+ (substitute* "sourcecodes/run.sh"
+ (("rm ") (string-append (which "rm") " "))
+ (("rmdir ") (string-append (which "rmdir") " "))
+ (("mkdir ") (string-append (which "mkdir") " "))
+ (("dirname ") (string-append (which "dirname")" ")))
;(substitute* "sourcecodes/layout_cyto.php"
; (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js")
; (string-append cyto js-path "cytoscape/cytoscape.min.js"))
@@ -127,8 +135,8 @@
(lambda (file)
(chmod file #o555))
(append (find-files out "\\.(sh|py)$")
- (find-files (string-append out "/sourcecodes/run_scripts" ".*"))
- ))
+ (find-files (string-append out "/sourcecodes/run_scripts/" "."))))
+ (chmod (string-append out "/sourcecodes/data") #o777) ; needs to be writable
#t)))
(replace 'build
(lambda _