gnu: Add bismark.

* gnu/packages/bioinformatics.scm (bismark): New variable.
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Ricardo Wurmus 2017-08-09 19:40:23 +02:00 committed by Ricardo Wurmus
parent 86763fdd70
commit 9634804890
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@ -9797,3 +9797,66 @@ such as transcription factor binding sites (ChIP-seq) or regions of open
chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
Browser.")
(license license:gpl3+))))
(define-public bismark
(package
(name "bismark")
(version "0.16.3")
(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"))
(sha256
(base32
"1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
(build-system perl-build-system)
(arguments
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key 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")))
(mkdir-p docdir)
(mkdir-p bin)
(for-each (lambda (file) (install-file file bin))
scripts)
(for-each (lambda (file) (install-file file docdir))
docs)
#t))))))
(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
reads to a genome of interest and perform methylation calls in a single step.
The output can be easily imported into a genome viewer, such as SeqMonk, and
enables a researcher to analyse the methylation levels of their samples
straight away. Its main features are:
@itemize
@item Bisulfite mapping and methylation calling in one single step
@item Supports single-end and paired-end read alignments
@item Supports ungapped and gapped alignments
@item Alignment seed length, number of mismatches etc are adjustable
@item Output discriminates between cytosine methylation in CpG, CHG
and CHH context
@end itemize\n")
(license license:gpl3+)))