From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: 28030@debbugs.gnu.org
Cc: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: [bug#28030] [PATCH 2/2] gnu: Add bismark.
Date: Wed, 9 Aug 2017 19:40:23 +0200 [thread overview]
Message-ID: <20170809174023.23455-2-ricardo.wurmus@mdc-berlin.de> (raw)
In-Reply-To: <20170809174023.23455-1-ricardo.wurmus@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (bismark): New variable.
---
gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 63 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 478a756fb..debe32961 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9794,3 +9794,66 @@ 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+)))
--
2.13.0
next prev parent reply other threads:[~2017-08-09 17:42 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-08-09 17:40 [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Ricardo Wurmus
2017-08-09 17:40 ` Ricardo Wurmus [this message]
2017-08-16 8:51 ` bug#28030: [PATCH 2/2] gnu: Add bismark Ricardo Wurmus
2017-08-09 18:04 ` [bug#28029] [PATCH 1/2] gnu: Add r-dexseq Roel Janssen
2017-08-14 10:03 ` bug#28029: " Ricardo Wurmus
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