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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2017-08-09 19:40:23 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-08-14 12:00:56 +0200 |
| commit | 9634804890a811f65267f273835b001cc087c23f (patch) | |
| tree | 80fa3471f067fae2c4ab71f9d1a0a959c995e120 | |
| parent | 86763fdd70b48df5e4be5f2df6ac4335d9f7abe5 (diff) | |
| download | patches-9634804890a811f65267f273835b001cc087c23f.tar patches-9634804890a811f65267f273835b001cc087c23f.tar.gz | |
gnu: Add bismark.
* gnu/packages/bioinformatics.scm (bismark): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c5a4dcad93..9d64294e48 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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+))) |