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gnu: python-pyvcf: Update to 0.6.8-0.476169c.

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* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c.
This commit is contained in:
Ricardo Wurmus 2022-09-20 14:26:15 +02:00
parent 9ed635cd9a
commit 8084e3bdb3
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GPG key ID: 197A5888235FACAC
1 changed files with 37 additions and 35 deletions
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72
gnu/packages/bioinformatics.scm
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@ -15541,47 +15541,49 @@ (define-public tombo
(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
(let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
(revision "0"))
(package
(name "python-pyvcf")
(version (git-version "0.6.8" revision commit))
;; 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
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-sample-script
(lambda _
;; Add Python 3 compatibility to this sample script.
(substitute* "scripts/vcf_sample_filter.py"
(("print (.*)\n" _ arg)
(string-append "print(" arg ")\n")))))
(add-after 'install 'remove-installed-tests
;; Do not install test files.
(lambda* (#:key inputs outputs #:allow-other-keys)
(delete-file-recursively (string-append
"0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-sample-script
(lambda _
;; Add Python 3 compatibility to this sample script.
(substitute* "scripts/vcf_sample_filter.py"
(("print (.*)\n" _ arg)
(string-append "print(" arg ")\n")))))
(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")))))))
(native-inputs
;; Older setuptools is needed for use_2to3.
(list python-cython python-setuptools-for-tensorflow))
(propagated-inputs
(list python-pysam 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}
(native-inputs
;; Older setuptools is needed for use_2to3.
(list python-cython python-setuptools-for-tensorflow))
(propagated-inputs
(list python-pysam 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)))
(license license:expat))))
(define-public nanosv
(package