3
5
Fork 0
mirror of git://git.savannah.gnu.org/guix.git synced 2023-12-14 03:33:07 +01:00

gnu: Add scvelo.

* gnu/packages/bioinformatics.scm (scvelo): New variable.
This commit is contained in:
Ricardo Wurmus 2022-01-31 16:06:39 +01:00
parent 9686c828ed
commit 7fc8a6faf6
No known key found for this signature in database
GPG key ID: 197A5888235FACAC

View file

@ -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")