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-rw-r--r--gnu/packages/bioinformatics.scm35
1 files changed, 35 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc0ce4a166..744f8c2a4a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -285,6 +285,41 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for
70-100bp Illumina reads.")
(license license:gpl3+)))
+(define-public python2-bx-python
+ (package
+ (name "python2-bx-python")
+ (version "0.7.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/b/bx-python/bx-python-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* "setup.py"
+ ;; remove dependency on outdated "distribute" module
+ (("^from distribute_setup import use_setuptools") "")
+ (("^use_setuptools\\(\\)") "")))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ;tests fail because test data are not included
+ #:python ,python-2))
+ (inputs
+ `(("python-numpy" ,python2-numpy)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("python-nose" ,python2-nose)
+ ("python-setuptools" ,python2-setuptools)))
+ (home-page "http://bitbucket.org/james_taylor/bx-python/")
+ (synopsis "Tools for manipulating biological data")
+ (description
+ "bx-python provides tools for manipulating biological data, particularly
+multiple sequence alignments.")
+ (license license:expat)))
+
(define-public clipper
(package
(name "clipper")