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gnu: bismark: Update to 0.24.1. 

* gnu/packages/bioinformatics.scm (bismark): Update to 0.24.1.
[source]: Delete bundled plot.ly.
[arguments]: Use plain list; remove trailing #T from build phases; adjust
'replace-plotly.js phase to account for use of script tags; adjust 'install
phase to install documentation in markdown format; add 'configure phase for
replacing references to tools.
[inputs]: Add bowtie, hisat2, minimap2, and samtools.
Ricardo Wurmus 2023-07-05 16:38:24 +02:00
parent 961ffca1c7
commit df5bf65f26
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GPG Key ID: 197A5888235FACAC
1 changed files with 78 additions and 57 deletions
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@ -12300,7 +12300,7 @@ Browser.")
(define-public bismark (define-public bismark
(package (package
(name "bismark") (name "bismark")
(version "0.20.1") (version "0.24.1")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -12310,69 +12310,90 @@ Browser.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9")))) "0j4dy33769f0jr2w1brb710zxwpg3zwjlnvlcpi5pr6mqc8dkg8n"))
(snippet '(delete-file "plotly/plot.ly"))))
(build-system perl-build-system) (build-system perl-build-system)
(arguments (arguments
`(#:tests? #f ; there are no tests (list
#:modules ((guix build utils) #:tests? #f ; there are no tests
#:modules '((guix build utils)
(ice-9 popen) (ice-9 popen)
(srfi srfi-26) (srfi srfi-26)
(guix build perl-build-system)) (guix build perl-build-system))
#:phases #:phases
(modify-phases %standard-phases #~(modify-phases %standard-phases
;; The bundled plotly.js is minified. (add-after 'unpack 'replace-plotly.js
(add-after 'unpack 'replace-plotly.js (lambda* (#:key inputs #:allow-other-keys)
(lambda* (#:key inputs #:allow-other-keys) (let* ((share (string-append #$output "/share/bismark"))
(let* ((file (assoc-ref inputs "plotly.js")) (file (assoc-ref inputs "plotly.js"))
(installed "plotly/plotly.js")) (installed "plotly/plotly.js"))
(let ((minified (open-pipe* OPEN_READ "uglifyjs" file))) ;; The bundled plotly.js is minified.
(call-with-output-file installed (let ((minified (open-pipe* OPEN_READ "uglifyjs" file)))
(cut dump-port minified <>)))) (call-with-output-file installed
#t)) (cut dump-port minified <>)))
(delete 'configure) (substitute* "bismark2report"
(delete 'build) (("plotly_template.tpl")
(replace 'install (string-append share "/plotly/plotly_template.tpl"))
(lambda* (#:key inputs outputs #:allow-other-keys) (("my \\$plotly_code = read_report_template\\('plot.ly'\\);")
(let* ((out (assoc-ref outputs "out")) (string-append "\
(bin (string-append out "/bin")) my $plotly_code = read_report_template('" share "/plotly/plotly.js');
(share (string-append out "/share/bismark")) $plotly_code = \"<script>\" . $plotly_code . \"</script>\";"))))))
(docdir (string-append out "/share/doc/bismark")) (replace 'configure
(docs '("Docs/Bismark_User_Guide.html")) (lambda* (#:key inputs #:allow-other-keys)
(scripts '("bismark" (substitute* "bismark"
"bismark_genome_preparation" (("\\(\\!system \"which samtools >/dev/null 2>&1\"\\)")
"bismark_methylation_extractor" "(\"true\")")
"bismark2bedGraph" (("\\$samtools_path = `which samtools`;")
"bismark2report" (string-append "$samtools_path = '"
"coverage2cytosine" (search-input-file inputs "/bin/samtools")
"deduplicate_bismark" "';"))
"filter_non_conversion" (("\\$path_to_bowtie2 = 'bowtie2'")
"bam2nuc" (string-append "$path_to_bowtie2 = '"
"bismark2summary" (search-input-file inputs "/bin/bowtie2")
"NOMe_filtering"))) "'"))
(substitute* "bismark2report" (("\\$path_to_hisat2 = 'hisat2'")
(("\\$RealBin/plotly") (string-append "$path_to_hisat2 = '"
(string-append share "/plotly"))) (search-input-file inputs "/bin/hisat2")
(mkdir-p share) "'"))
(mkdir-p docdir) (("\\$path_to_minimap2 = 'minimap2'")
(mkdir-p bin) (string-append "$path_to_minimap2 = '"
(for-each (lambda (file) (install-file file bin)) (search-input-file inputs "/bin/minimap2")
scripts) "'")))))
(for-each (lambda (file) (install-file file docdir)) (delete 'build)
docs) (replace 'install
(copy-recursively "Docs/Images" (string-append docdir "/Images")) (lambda* (#:key inputs outputs #:allow-other-keys)
(copy-recursively "plotly" (let* ((bin (string-append #$output "/bin"))
(string-append share "/plotly")) (share (string-append #$output "/share/bismark"))
(docdir (string-append #$output "/share/doc/bismark"))
(scripts '("bismark"
"bismark_genome_preparation"
"bismark_methylation_extractor"
"bismark2bedGraph"
"bismark2report"
"coverage2cytosine"
"deduplicate_bismark"
"filter_non_conversion"
"bam2nuc"
"bismark2summary"
"NOMe_filtering")))
(mkdir-p share)
(mkdir-p docdir)
(mkdir-p bin)
(for-each (lambda (file) (install-file file bin))
scripts)
(copy-recursively "docs" docdir)
(copy-recursively "plotly"
(string-append share "/plotly"))
;; Fix references to gunzip ;; Fix references to gunzip
(substitute* (map (lambda (file) (substitute* (map (lambda (file)
(string-append bin "/" file)) (string-append bin "/" file))
scripts) scripts)
(("\"gunzip -c") (("\"gunzip -c")
(string-append "\"" (assoc-ref inputs "gzip") (string-append "\"" (assoc-ref inputs "gzip")
"/bin/gunzip -c"))) "/bin/gunzip -c")))))))))
#t))))))
(inputs (inputs
(list gzip perl-carp perl-getopt-long)) (list bowtie gzip hisat2 minimap2 perl-carp perl-getopt-long samtools))
(native-inputs (native-inputs
`(("plotly.js" `(("plotly.js"
,(origin ,(origin