gnu: Add scvelo.
* gnu/packages/bioinformatics.scm (scvelo): New variable.
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@ -15582,6 +15582,69 @@ (define-public python-bwapy
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;; bwa itself is licenced under GNU General Public License v3.0.
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;; bwa itself is licenced under GNU General Public License v3.0.
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(license license:mpl2.0)))
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(license license:mpl2.0)))
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(define-public scvelo
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(package
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(name "scvelo")
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(version "0.2.4")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scvelo" version))
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(sha256
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(base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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;; Numba needs a writable dir to cache functions.
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(add-before 'check 'set-numba-cache-dir
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(lambda _
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(setenv "NUMBA_CACHE_DIR" "/tmp")))
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(replace 'check
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(lambda* (#:key outputs tests? #:allow-other-keys)
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(when tests?
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;; The discovered test file names must match the names of the
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;; compiled files, so we cannot run the tests from
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;; /tmp/guix-build-*.
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(with-directory-excursion
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(string-append (assoc-ref outputs "out")
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"/lib/python3.9/site-packages/scvelo/core/tests/")
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(invoke "pytest" "-v"))))))))
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(propagated-inputs
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(list python-anndata
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python-hnswlib
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python-isort
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python-igraph
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python-loompy
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python-louvain
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python-matplotlib
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python-numba
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python-numpy
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python-pandas
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python-scanpy
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python-scikit-learn
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python-scipy
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python-umap-learn
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pybind11))
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(native-inputs
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(list python-black
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python-flake8
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python-hypothesis
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python-pre-commit
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python-pytest
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python-setuptools-scm
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python-wheel))
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(home-page "https://scvelo.org")
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(synopsis "RNA velocity generalized through dynamical modeling")
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(description "ScVelo is a scalable toolkit for RNA velocity analysis in
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single cells. RNA velocity enables the recovery of directed dynamic
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information by leveraging splicing kinetics. scVelo generalizes the concept of
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RNA velocity by relaxing previously made assumptions with a stochastic and a
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dynamical model that solves the full transcriptional dynamics. It thereby
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adapts RNA velocity to widely varying specifications such as non-stationary
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populations.")
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(license license:bsd-3)))
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(define-public scregseg
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(define-public scregseg
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(package
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(package
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(name "scregseg")
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(name "scregseg")
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