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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 37 |
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8aa21c4fd6..6aaee38295 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14600,3 +14600,40 @@ modified nucleotides from nanopore sequencing data. Tombo also provides tools for the analysis and visualization of raw nanopore signal.") ;; Some parts may be BSD-3-licensed. (license license:mpl2.0))) + +(define-public python-pyvcf + (package + (name "python-pyvcf") + (version "0.6.8") + ;; Use git, because the PyPI tarballs lack test data. + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jamescasbon/PyVCF.git") + ;; Latest release is not tagged. + (commit "bfcedb9bad1a14074ac4526ffdb610611e073810"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'remove-installed-tests + ;; Do not install test files. + (lambda* (#:key inputs outputs #:allow-other-keys) + (delete-file-recursively (string-append + (site-packages inputs outputs) + "vcf/test")) + #t))))) + (native-inputs `(("python-cython" ,python-cython))) + (propagated-inputs + `(("python-pysam" ,python-pysam) + ("python-rpy2" ,python-rpy2))) + (home-page "https://github.com/jamescasbon/PyVCF") + (synopsis "Variant Call Format parser for Python") + (description "This package provides a @acronym{VCF,Variant Call Format} +parser for Python.") + (license license:expat))) |