From 9634804890a811f65267f273835b001cc087c23f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 9 Aug 2017 19:40:23 +0200
Subject: gnu: Add bismark.

* gnu/packages/bioinformatics.scm (bismark): New variable.
---
 gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

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+)))
-- 
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