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01/02: gnu: bismark: Update to 0.24.1.
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From: |
guix-commits |
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Subject: |
01/02: gnu: bismark: Update to 0.24.1. |
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Date: |
Thu, 6 Jul 2023 17:29:50 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit df5bf65f261dfd1e09096b014d5dfef052be994a
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Jul 5 16:38:24 2023 +0200
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.
---
gnu/packages/bioinformatics.scm | 137 +++++++++++++++++++++++-----------------
1 file changed, 79 insertions(+), 58 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 62bb0074b2..09cd606b8b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12300,7 +12300,7 @@ Browser.")
(define-public bismark
(package
(name "bismark")
- (version "0.20.1")
+ (version "0.24.1")
(source
(origin
(method git-fetch)
@@ -12310,69 +12310,90 @@ Browser.")
(file-name (git-file-name name version))
(sha256
(base32
- "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9"))))
+ "0j4dy33769f0jr2w1brb710zxwpg3zwjlnvlcpi5pr6mqc8dkg8n"))
+ (snippet '(delete-file "plotly/plot.ly"))))
(build-system perl-build-system)
(arguments
- `(#:tests? #f ; there are no tests
- #:modules ((guix build utils)
+ (list
+ #: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 "uglifyjs" file)))
- (call-with-output-file installed
- (cut dump-port minified <>))))
- #t))
- (delete 'configure)
- (delete 'build)
- (replace 'install
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (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"
- "NOMe_filtering")))
- (substitute* "bismark2report"
- (("\\$RealBin/plotly")
- (string-append share "/plotly")))
- (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"))
- (copy-recursively "plotly"
- (string-append share "/plotly"))
-
- ;; Fix references to gunzip
- (substitute* (map (lambda (file)
- (string-append bin "/" file))
- scripts)
- (("\"gunzip -c")
- (string-append "\"" (assoc-ref inputs "gzip")
- "/bin/gunzip -c")))
- #t))))))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'replace-plotly.js
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((share (string-append #$output "/share/bismark"))
+ (file (assoc-ref inputs "plotly.js"))
+ (installed "plotly/plotly.js"))
+ ;; The bundled plotly.js is minified.
+ (let ((minified (open-pipe* OPEN_READ "uglifyjs" file)))
+ (call-with-output-file installed
+ (cut dump-port minified <>)))
+ (substitute* "bismark2report"
+ (("plotly_template.tpl")
+ (string-append share "/plotly/plotly_template.tpl"))
+ (("my \\$plotly_code = read_report_template\\('plot.ly'\\);")
+ (string-append "\
+my $plotly_code = read_report_template('" share "/plotly/plotly.js');
+$plotly_code = \"<script>\" . $plotly_code . \"</script>\";"))))))
+ (replace 'configure
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "bismark"
+ (("\\(\\!system \"which samtools >/dev/null 2>&1\"\\)")
+ "(\"true\")")
+ (("\\$samtools_path = `which samtools`;")
+ (string-append "$samtools_path = '"
+ (search-input-file inputs "/bin/samtools")
+ "';"))
+ (("\\$path_to_bowtie2 = 'bowtie2'")
+ (string-append "$path_to_bowtie2 = '"
+ (search-input-file inputs "/bin/bowtie2")
+ "'"))
+ (("\\$path_to_hisat2 = 'hisat2'")
+ (string-append "$path_to_hisat2 = '"
+ (search-input-file inputs "/bin/hisat2")
+ "'"))
+ (("\\$path_to_minimap2 = 'minimap2'")
+ (string-append "$path_to_minimap2 = '"
+ (search-input-file inputs "/bin/minimap2")
+ "'")))))
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((bin (string-append #$output "/bin"))
+ (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
+ (substitute* (map (lambda (file)
+ (string-append bin "/" file))
+ scripts)
+ (("\"gunzip -c")
+ (string-append "\"" (assoc-ref inputs "gzip")
+ "/bin/gunzip -c")))))))))
(inputs
- (list gzip perl-carp perl-getopt-long))
+ (list bowtie gzip hisat2 minimap2 perl-carp perl-getopt-long samtools))
(native-inputs
`(("plotly.js"
,(origin