gnu: Add bismark.
* gnu/packages/bioinformatics.scm (bismark): New variable.
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@ -9797,3 +9797,66 @@ such as transcription factor binding sites (ChIP-seq) or regions of open
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chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome
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Browser.")
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(license license:gpl3+))))
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(define-public bismark
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(package
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(name "bismark")
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(version "0.16.3")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://github.com/FelixKrueger/Bismark/"
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"archive/" version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
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(build-system perl-build-system)
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(arguments
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`(#:tests? #f ; there are no tests
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(delete 'build)
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((bin (string-append (assoc-ref outputs "out")
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"/bin"))
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(docdir (string-append (assoc-ref outputs "out")
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"/share/doc/bismark"))
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(docs '("Bismark_User_Guide.pdf"
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"RELEASE_NOTES.txt"))
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(scripts '("bismark"
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"bismark_genome_preparation"
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"bismark_methylation_extractor"
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"bismark2bedGraph"
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"bismark2report"
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"coverage2cytosine"
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"deduplicate_bismark"
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"bismark_sitrep.tpl"
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"bam2nuc"
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"bismark2summary")))
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(mkdir-p docdir)
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(mkdir-p bin)
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(for-each (lambda (file) (install-file file bin))
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scripts)
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(for-each (lambda (file) (install-file file docdir))
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docs)
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#t))))))
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(home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
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(synopsis "Map bisulfite treated sequence reads and analyze methylation")
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(description "Bismark is a program to map bisulfite treated sequencing
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reads to a genome of interest and perform methylation calls in a single step.
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The output can be easily imported into a genome viewer, such as SeqMonk, and
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enables a researcher to analyse the methylation levels of their samples
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straight away. Its main features are:
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@itemize
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@item Bisulfite mapping and methylation calling in one single step
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@item Supports single-end and paired-end read alignments
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@item Supports ungapped and gapped alignments
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@item Alignment seed length, number of mismatches etc are adjustable
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@item Output discriminates between cytosine methylation in CpG, CHG
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and CHH context
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@end itemize\n")
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(license license:gpl3+)))
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