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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 53daf4c2a7..47f5574eeb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13035,6 +13035,50 @@ storage format, called @code{cool}, used to store genomic interaction data, such as Hi-C contact matrices.") (license license:bsd-3))) +(define-public python-cooltools + (package + (name "python-cooltools") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "cooltools" version)) + (sha256 + (base32 + "08hyzd3kazr87nvv6rwp5i1g9rwj7jmrly925lqnvippz4wp7k4g")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v"))))))) + (native-inputs + (list python-cython + python-pytest)) + (propagated-inputs + (list python-bioframe + python-click + python-cooler + python-joblib + python-matplotlib + python-multiprocess + python-numba + python-numpy + python-pandas + python-scikit-image + python-scikit-learn + python-scipy)) + (home-page "https://github.com/open2c/cooltools") + (synopsis + "Analysis tools for genomic interaction data stored in .cool format") + (description + "This package provides necessary tools for the analysis of the genomic +interaction data stored in @code{.cool} format. This collection of tools +includes operations like compartment, insulation or peak calling.") + (license license:expat))) + (define-public python-hicmatrix (package (name "python-hicmatrix") |