diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 61 |
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)) |