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author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2022-10-15 00:52:18 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-11-04 13:50:20 +0100 |
commit | 49e1a3a04b7aac1a5046f243f1320fef93effcf7 (patch) | |
tree | 3001f75e29f4fc58f31b177f92ac5dd5c0ebf666 | |
parent | 14cbaac69c142b9e45c4ff111668bf187994bab8 (diff) | |
download | guix-49e1a3a04b7aac1a5046f243f1320fef93effcf7.tar guix-49e1a3a04b7aac1a5046f243f1320fef93effcf7.tar.gz |
gnu: Add python-cooltools.
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
-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") |