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| author | Efraim Flashner | 2022-03-20 08:56:33 +0200 |
|---|---|---|
| committer | Efraim Flashner | 2022-03-20 08:56:33 +0200 |
| commit | 7c78efdce60ca3c65a59c28ef806b4904e5ed6b5 (patch) | |
| tree | 97cb64359eb8f45dcc5307f5054e6acaba02fa5f /gn/packages | |
| parent | b923c80749dce8f78c623b3908618941c5305f03 (diff) | |
| download | guix-bioinformatics-7c78efdce60ca3c65a59c28ef806b4904e5ed6b5.tar.gz | |
gn: upstream python-scikit-allel
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 49 |
1 files changed, 0 insertions, 49 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 6dde766..01e4c59 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -3137,52 +3137,3 @@ from a VCF. In particular, pixy facilitates the use of VCFs containing invariant (monomorphic) sites, which are essential for the correct computation of π and dxy in the face of missing data (i.e. always).") (license license:expat))) - -(define-public python-scikit-allel - (package - (name "python-scikit-allel") - (version "1.3.5") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scikit-allel" version)) - (sha256 - (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "python" "setup.py" "build_ext" "--inplace") - (invoke "python" "-m" "pytest" "-v" "allel" - ;; AttributeError: 'Dataset' object has no attribute 'asstr' - ;; Perhaps need python-h5py@3? - "-k" (string-append - "not test_vcf_to_hdf5" - " and not test_vcf_to_hdf5_exclude" - " and not test_vcf_to_hdf5_rename" - " and not test_vcf_to_hdf5_group" - " and not test_vcf_to_hdf5_ann")))))))) - (propagated-inputs - (list python-dask - python-numpy)) - (native-inputs - (list python-cython - ;; The following are all needed for the tests - htslib - python-h5py - python-hmmlearn - python-numexpr - python-pytest - python-scipy - python-setuptools-scm - python-zarr)) - (home-page "https://github.com/cggh/scikit-allel") - (synopsis "Explore and analyze genetic variation data") - (description - "This package provides utilities for exploratory analysis of large scale -genetic variation data.") - (license license:expat))) |