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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-02-20 17:43:08 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-03-02 11:32:10 +0100
commita2fb1492afe9e22102ee2404f1b546ee655ec7ac (patch)
treeb2d32b02228d8f226e9b8a3470dd6e4b102ea1a4
parent8d12be1eb1226d795e260558168a9756b6900259 (diff)
gnu: Add pybedtools.
* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm33
1 files changed, 33 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b64dab73cd..a919da8b51 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -141,6 +141,39 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
(license license:gpl2)))
+(define-public python2-pybedtools
+ (package
+ (name "python2-pybedtools")
+ (version "0.6.9")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
+ (build-system python-build-system)
+ (arguments `(#:python ,python-2)) ; no Python 3 support
+ (inputs
+ `(("python-cython" ,python2-cython)
+ ("python-matplotlib" ,python2-matplotlib)))
+ (propagated-inputs
+ `(("bedtools" ,bedtools)
+ ("samtools" ,samtools)))
+ (native-inputs
+ `(("python-pyyaml" ,python2-pyyaml)
+ ("python-nose" ,python2-nose)
+ ("python-setuptools" ,python2-setuptools)))
+ (home-page "https://pythonhosted.org/pybedtools/")
+ (synopsis "Python wrapper for BEDtools programs")
+ (description
+ "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
+which are widely used for genomic interval manipulation or \"genome algebra\".
+pybedtools extends BEDTools by offering feature-level manipulations from with
+Python.")
+ (license license:gpl2+)))
+
(define-public bowtie
(package
(name "bowtie")