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-rw-r--r--gn/packages/bioinformatics.scm38
1 files changed, 38 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index de66599..3ee2934 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1246,6 +1246,44 @@ runApp(launch.browser=0, port=4206)~%\n"
"")
(license #f)))
+(define-public python-whatshap
+ (package
+ (name "python-whatshap")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "whatshap" version))
+ (sha256
+ (base32 "0vxv6y8sg25yii106j6k55vc5z7n1l1y1nax49dgbarbrvk8cr2f"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "setup.py"
+ (("~=.*\"") "\"")
+ ((">=1.73") ""))
+ #t)))))
+ (inputs
+ `(("python-biopython" ,python-biopython)
+ ("python-networkx" ,python-networkx)
+ ("python-pyfaidx" ,python-pyfaidx)
+ ("python-pysam" ,python-pysam)
+ ("python-scipy" ,python-scipy)
+ ("python-xopen" ,python-xopen)))
+ (native-inputs
+ `(("python-cython" ,python-cython)
+ ("python-setuptools-scm" ,python-setuptools-scm)))
+ (home-page "https://github.com/whatshap/whatshap/")
+ (synopsis "Read-based phasing of genomic variants")
+ (description
+ "WhatsHap is a software for phasing genomic variants using DNA sequencing
+reads, also called read-based phasing or haplotype assembly. It is especially
+suitable for long reads, but works also well with short reads.")
+ (license license:expat)))
+
(define-public bh20-seq-resource
(let ((commit "ae4cb3c2cf7103bbc84f52618bb755d7ce25775b")
(revision "3"))