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Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 38 |
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")) |