diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 34 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 196c563625..4481235c78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -84,6 +84,7 @@ #:use-module (gnu packages jemalloc) #:use-module (gnu packages dlang) #:use-module (gnu packages linux) + #:use-module (gnu packages lisp) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) @@ -11673,7 +11674,7 @@ Browser.") (define-public bismark (package (name "bismark") - (version "0.19.1") + (version "0.20.1") (source (origin (method git-fetch) @@ -11683,18 +11684,25 @@ Browser.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "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)))) + "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9")))) (build-system perl-build-system) (arguments `(#:tests? #f ; there are no tests + #:modules ((guix build utils) + (ice-9 popen) + (srfi srfi-26) + (guix build perl-build-system)) #:phases (modify-phases %standard-phases + ;; The bundled plotly.js is minified. + (add-after 'unpack 'replace-plotly.js + (lambda* (#:key inputs #:allow-other-keys) + (let* ((file (assoc-ref inputs "plotly.js")) + (installed "plotly/plotly.js")) + (let ((minified (open-pipe* OPEN_READ "uglify-js" file))) + (call-with-output-file installed + (cut dump-port minified <>)))) + #t)) (delete 'configure) (delete 'build) (replace 'install @@ -11713,10 +11721,11 @@ Browser.") "deduplicate_bismark" "filter_non_conversion" "bam2nuc" - "bismark2summary"))) + "bismark2summary" + "NOMe_filtering"))) (substitute* "bismark2report" - (("\\$RealBin/bismark_sitrep") - (string-append share "/bismark_sitrep"))) + (("\\$RealBin/plotly") + (string-append share "/plotly"))) (mkdir-p share) (mkdir-p docdir) (mkdir-p bin) @@ -11725,8 +11734,8 @@ Browser.") (for-each (lambda (file) (install-file file docdir)) docs) (copy-recursively "Docs/Images" (string-append docdir "/Images")) - (copy-recursively "bismark_sitrep" - (string-append share "/bismark_sitrep")) + (copy-recursively "plotly" + (string-append share "/plotly")) ;; Fix references to gunzip (substitute* (map (lambda (file) @@ -11737,7 +11746,18 @@ Browser.") "/bin/gunzip -c"))) #t)))))) (inputs - `(("gzip" ,gzip))) + `(("gzip" ,gzip) + ("perl-carp" ,perl-carp) + ("perl-getopt-long" ,perl-getopt-long))) + (native-inputs + `(("plotly.js" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/" + "v1.39.4/dist/plotly.js")) + (sha256 + (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr")))) + ("uglify-js" ,uglify-js))) (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") (synopsis "Map bisulfite treated sequence reads and analyze methylation") (description "Bismark is a program to map bisulfite treated sequencing |