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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.
This commit is contained in:
Ricardo Wurmus 2018-05-09 18:36:23 +02:00
parent f895a7a4d4
commit 126c9e3ff7
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1 changed files with 38 additions and 23 deletions
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@ -11568,47 +11568,62 @@ Browser.")
(define-public bismark (define-public bismark
(package (package
(name "bismark") (name "bismark")
(version "0.16.3") (version "0.19.1")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/FelixKrueger/Bismark/" (uri (git-reference
"archive/" version ".tar.gz")) (url "https://github.com/FelixKrueger/Bismark.git")
(file-name (string-append name "-" version ".tar.gz")) (commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (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) (build-system perl-build-system)
(arguments (arguments
`(#:tests? #f ; there are no tests `(#:tests? #f ; there are no tests
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure) (delete 'configure)
(delete 'build) (delete 'build)
(replace 'install (replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") (let* ((out (assoc-ref outputs "out"))
"/bin")) (bin (string-append out "/bin"))
(docdir (string-append (assoc-ref outputs "out") (share (string-append out "/share/bismark"))
"/share/doc/bismark")) (docdir (string-append out "/share/doc/bismark"))
(docs '("Bismark_User_Guide.pdf" (docs '("Docs/Bismark_User_Guide.html"))
"RELEASE_NOTES.txt")) (scripts '("bismark"
(scripts '("bismark" "bismark_genome_preparation"
"bismark_genome_preparation" "bismark_methylation_extractor"
"bismark_methylation_extractor" "bismark2bedGraph"
"bismark2bedGraph" "bismark2report"
"bismark2report" "coverage2cytosine"
"coverage2cytosine" "deduplicate_bismark"
"deduplicate_bismark" "filter_non_conversion"
"bismark_sitrep.tpl" "bam2nuc"
"bam2nuc" "bismark2summary")))
"bismark2summary"))) (mkdir-p share)
(mkdir-p docdir) (mkdir-p docdir)
(mkdir-p bin) (mkdir-p bin)
(for-each (lambda (file) (install-file file bin)) (for-each (lambda (file) (install-file file bin))
scripts) scripts)
(for-each (lambda (file) (install-file file docdir)) (for-each (lambda (file) (install-file file docdir))
docs) 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 ;; Fix references to gunzip
(substitute* (map (lambda (file) (substitute* (map (lambda (file)
(string-append bin "/" file)) (string-append bin "/" file))