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authorRicardo Wurmus <rekado@elephly.net>2019-03-15 11:36:56 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-15 11:36:56 +0100
commit07c8b558e32f3fca27d20152f6b8f5569f11c960 (patch)
treec0333f806e4b7bd4c13e8dfab2f42074fa00431d
parent963dfd3a06a1a9906706ea6bad34f89cc617d905 (diff)
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patches-07c8b558e32f3fca27d20152f6b8f5569f11c960.tar.gz
gnu: Add bwa-meth.
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm41
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9b0a4314b9..3364a357fb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1570,6 +1570,47 @@ the original BWA alignment program and shares the genome index structure as
well as many of the command line options.")
(license license:gpl3+)))
+(define-public bwa-meth
+ (package
+ (name "bwa-meth")
+ (version "0.2.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/brentp/bwa-meth.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "17j31i7zws5j7mhsq9x3qgkxly6mlmrgwhfq0qbflgxrmx04yaiz"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'keep-references-to-bwa
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "bwameth.py"
+ (("bwa mem")
+ (string-append (which "bwa") " mem"))
+ ;; There's an ill-advised check for "samtools" on PATH.
+ (("^checkX.*") ""))
+ #t)))))
+ (inputs
+ `(("bwa" ,bwa)))
+ (native-inputs
+ `(("python-toolshed" ,python-toolshed)))
+ (home-page "https://github.com/brentp/bwa-meth")
+ (synopsis "Fast and accurante alignment of BS-Seq reads")
+ (description
+ "BWA-Meth works for single-end reads and for paired-end reads from the
+directional protocol (most common). It uses the method employed by
+methylcoder and Bismark of in silico conversion of all C's to T's in both
+reference and reads. It recovers the original read (needed to tabulate
+methylation) by attaching it as a comment which BWA appends as a tag to the
+read. It performs favorably to existing aligners gauged by number of on and
+off-target reads for a capture method that targets CpG-rich region.")
+ (license license:expat)))
+
(define-public python-bx-python
(package
(name "python-bx-python")