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author | Ricardo Wurmus <rekado@elephly.net> | 2022-01-31 16:06:39 +0100 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-01-31 16:07:40 +0100 |
commit | 7fc8a6faf6269fd6417e3ed4794504f66899432b (patch) | |
tree | 6ae035ea7609098eeeb87c63b25000463d4e6a6e | |
parent | 9686c828ed330a23357a8fd53e62ef9cdb7288ef (diff) | |
download | guix-7fc8a6faf6269fd6417e3ed4794504f66899432b.tar.gz |
gnu: Add scvelo.
* gnu/packages/bioinformatics.scm (scvelo): New variable.
-rw-r--r-- | gnu/packages/bioinformatics.scm | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9eefc64184..92a299634f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15582,6 +15582,69 @@ aligner.") ;; bwa itself is licenced under GNU General Public License v3.0. (license license:mpl2.0))) +(define-public scvelo + (package + (name "scvelo") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scvelo" version)) + (sha256 + (base32 "0h5ha1459ljs0qgpnlfsw592i8dxqn6p9bl08l1ikpwk36baxb7z")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (replace 'check + (lambda* (#:key outputs tests? #:allow-other-keys) + (when tests? + ;; The discovered test file names must match the names of the + ;; compiled files, so we cannot run the tests from + ;; /tmp/guix-build-*. + (with-directory-excursion + (string-append (assoc-ref outputs "out") + "/lib/python3.9/site-packages/scvelo/core/tests/") + (invoke "pytest" "-v")))))))) + (propagated-inputs + (list python-anndata + python-hnswlib + python-isort + python-igraph + python-loompy + python-louvain + python-matplotlib + python-numba + python-numpy + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-umap-learn + pybind11)) + (native-inputs + (list python-black + python-flake8 + python-hypothesis + python-pre-commit + python-pytest + python-setuptools-scm + python-wheel)) + (home-page "https://scvelo.org") + (synopsis "RNA velocity generalized through dynamical modeling") + (description "ScVelo is a scalable toolkit for RNA velocity analysis in +single cells. RNA velocity enables the recovery of directed dynamic +information by leveraging splicing kinetics. scVelo generalizes the concept of +RNA velocity by relaxing previously made assumptions with a stochastic and a +dynamical model that solves the full transcriptional dynamics. It thereby +adapts RNA velocity to widely varying specifications such as non-stationary +populations.") + (license license:bsd-3))) + (define-public scregseg (package (name "scregseg") |