diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 72 |
1 files changed, 37 insertions, 35 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d35e86cd3e..f54ac6ffab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15541,47 +15541,49 @@ for the analysis and visualization of raw nanopore signal.") (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 |