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| author | Efraim Flashner | 2019-12-22 03:49:03 -0600 |
|---|---|---|
| committer | Efraim Flashner | 2019-12-22 03:49:03 -0600 |
| commit | 5856fb3878e69a2091afbfdd3b15268e310f82e3 (patch) | |
| tree | a4bd7cf668275279bcbf01ede37954f8087d7172 /gn/packages/bnw.scm | |
| parent | 3035ea5144af76b6ff260b1bceef3feafec8a177 (diff) | |
| download | guix-bioinformatics-5856fb3878e69a2091afbfdd3b15268e310f82e3.tar.gz | |
gn: Update bnw service
Diffstat (limited to 'gn/packages/bnw.scm')
| -rw-r--r-- | gn/packages/bnw.scm | 12 |
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 _ |