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authorRicardo Wurmus <rekado@elephly.net>2018-05-09 18:36:23 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-05-09 18:37:33 +0200
commit126c9e3ff798d06a8398337bb8c3bb09b3da3d35 (patch)
treea511478a4348f8385ddc776d3500a525cd3a5302 /gnu
parentf895a7a4d41a37871b044e48984d460bc896db68 (diff)
downloadpatches-126c9e3ff798d06a8398337bb8c3bb09b3da3d35.tar
patches-126c9e3ff798d06a8398337bb8c3bb09b3da3d35.tar.gz
gnu: bismark: Update to 0.19.1.
* gnu/packages/bioinformatics.scm (bismark): Update to 0.19.1. [source]: Fetch from git; remove non-free software in snippet. [arguments]: Update install phase.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm61
1 files changed, 38 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bba7056db2..1996cfa3b3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11568,47 +11568,62 @@ Browser.")
(define-public bismark
(package
(name "bismark")
- (version "0.16.3")
+ (version "0.19.1")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/FelixKrueger/Bismark/"
- "archive/" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/FelixKrueger/Bismark.git")
+ (commit version)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
+ "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
+ (snippet
+ '(begin
+ ;; highcharts.js is non-free software. The code is available under
+ ;; CC-BY-NC or proprietary licenses only.
+ (delete-file "bismark_sitrep/highcharts.js")
+ #t))))
(build-system perl-build-system)
(arguments
- `(#:tests? #f ; there are no tests
+ `(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out")
- "/bin"))
- (docdir (string-append (assoc-ref outputs "out")
- "/share/doc/bismark"))
- (docs '("Bismark_User_Guide.pdf"
- "RELEASE_NOTES.txt"))
- (scripts '("bismark"
- "bismark_genome_preparation"
- "bismark_methylation_extractor"
- "bismark2bedGraph"
- "bismark2report"
- "coverage2cytosine"
- "deduplicate_bismark"
- "bismark_sitrep.tpl"
- "bam2nuc"
- "bismark2summary")))
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (share (string-append out "/share/bismark"))
+ (docdir (string-append out "/share/doc/bismark"))
+ (docs '("Docs/Bismark_User_Guide.html"))
+ (scripts '("bismark"
+ "bismark_genome_preparation"
+ "bismark_methylation_extractor"
+ "bismark2bedGraph"
+ "bismark2report"
+ "coverage2cytosine"
+ "deduplicate_bismark"
+ "filter_non_conversion"
+ "bam2nuc"
+ "bismark2summary")))
+ (mkdir-p share)
(mkdir-p docdir)
(mkdir-p bin)
(for-each (lambda (file) (install-file file bin))
scripts)
(for-each (lambda (file) (install-file file docdir))
docs)
+ (copy-recursively "Docs/Images" (string-append docdir "/Images"))
+
+ (substitute* "bismark2report"
+ (("\\$RealBin/bismark_sitrep")
+ (string-append share "/bismark_sitrep")))
+ (copy-recursively "bismark_sitrep"
+ (string-append share "/bismark_sitrep"))
+
;; Fix references to gunzip
(substitute* (map (lambda (file)
(string-append bin "/" file))