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authorEfraim Flashner2019-10-24 09:51:00 +0300
committerEfraim Flashner2019-10-24 09:51:00 +0300
commitb23e20d0d292f59b117aee197566eece3ead4f53 (patch)
tree39b0e9a23774b6738fadc4ac59199fd3563c966f /gn/packages/bnw.scm
parent0af2186e2fa99f96ec3fa96e60cdd7eaba9caf8c (diff)
downloadguix-bioinformatics-b23e20d0d292f59b117aee197566eece3ead4f53.tar.gz
gn: Update bnw to 1.22-2.eb6b002.
* gn/packages/bnw.scm (bnw)[arguments]: Patch more files. [inputs]: Add python2-plotly-3.2.1.
Diffstat (limited to 'gn/packages/bnw.scm')
-rw-r--r--gn/packages/bnw.scm36
1 files changed, 31 insertions, 5 deletions
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index db30a84..036fe2b 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -4,16 +4,17 @@
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages gcc)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages statistics)
#:use-module (gn packages graphviz)
#:use-module (gn packages javascript)
#:use-module (gn packages maths)
- #:use-module (gnu packages python)
- #:use-module (gnu packages statistics)
+ #:use-module (gn packages python)
#:use-module (gn packages web))
(define-public bnw
(let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04")
- (revision "1"))
+ (revision "2"))
(package
(name "bnw")
(version (git-version "1.22" revision commit)) ; June 28, 2019
@@ -32,7 +33,12 @@
#:phases
(modify-phases %standard-phases
(delete 'configure)
- (add-after 'patch-source-shebangs 'patch--more-shebangs
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "sourcecodes/header_batchsearch.inc"
+ (("my_style.css") "my_new_style.css"))
+ #t))
+ (add-after 'patch-source-shebangs 'patch-more-shebangs
(lambda* (#:key inputs #:allow-other-keys)
(let* ((bash (assoc-ref inputs "bash"))
(graphviz (assoc-ref inputs "graphviz"))
@@ -58,6 +64,10 @@
(string-append octave "/bin")
(string-append python "/bin"))))
(find-files "." ".*"))
+ (substitute* '("sourcecodes/examplefilecopy.sh"
+ "sourcecodes/filecopy.sh")
+ (("rm") (which "rm"))
+ (("cp") (which "cp")))
(substitute*
(append '("home.php")
(find-files "sourcecodes" ".php")
@@ -101,17 +111,33 @@
(delete-file "sourcecodes/localscore/libRmath.so")
(copy-recursively "." out))
#t))
+ (add-after 'install 'make-files-executable
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (for-each
+ (lambda (file)
+ (chmod file #o555))
+ (find-files out "\\.sh$"))
+ #t)))
(replace 'build
(lambda _
(with-directory-excursion "sourcecodes"
(substitute* "build.sh"
(("./localscore") "localscore"))
(chmod "k-best/src/buildk_poster.sh" #o755)
- (invoke "sh" "build.sh")))))))
+ (invoke "sh" "build.sh")
+ ;; from info_files/plotly_notes.txt
+ ;(with-directory-excursion "data"
+ ; (setenv "HOME" "/tmp")
+ ; (invoke "python" "../cv_plotly.py" "LvQ")
+ ; (invoke "sh" "../plotly_loo.sh"))
+ ;(invoke "./run_loo" "LvQ Weight")
+ ))))))
(inputs
`(("graphviz" ,graphviz-2.26)
("octave" ,octave-3.4.3)
("python" ,python-2)
+ ("plotly" ,python2-plotly-3.2.1)
("rmath" ,rmath-standalone) ; Should this be r-minimal? Which version?
("jquery" ,web-jquery)
("awesome" ,web-font-awesome)