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author | Ricardo Wurmus <rekado@elephly.net> | 2022-06-16 15:19:44 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-06-16 15:20:59 +0200 |
commit | f700223c3bb7e80104c7c011edcd09479145bb26 (patch) | |
tree | a48b51a3c85f8135f6958d514d78c32cbc657f41 /gnu/packages/bioinformatics.scm | |
parent | 3535d8dc5ae3116d8c3bedf0d5c920b19ba41cc5 (diff) | |
download | guix-f700223c3bb7e80104c7c011edcd09479145bb26.tar.gz guix-f700223c3bb7e80104c7c011edcd09479145bb26.zip |
gnu: Add pyscenic.
* gnu/packages/bioinformatics.scm (pyscenic): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-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 e6b14069ec..75973b0dd8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13457,6 +13457,69 @@ pycisTarget and SCENIC.") tree-based ensemble regressors.") (license license:bsd-3))) +(define-public pyscenic + (package + (name "pyscenic") + (version "0.11.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/pySCENIC") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pbmmr1zdb1vbbs6wx357s59d13pna6x03wq8blj6ckjws8bbq73")))) + (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 _ + (invoke "pytest" "-v")))))) + (propagated-inputs + (list python-ctxcore + python-cytoolz + python-multiprocessing-on-dill + python-llvmlite + python-numba + python-attrs + python-frozendict + python-numpy + python-pandas + python-cloudpickle + python-dask + python-distributed + python-arboreto + python-boltons + python-setuptools + python-pyyaml + python-tqdm + python-interlap + python-umap-learn + python-loompy + python-networkx + python-scipy + python-fsspec + python-requests + python-aiohttp + python-scikit-learn)) + (native-inputs + (list python-pytest)) + (home-page "https://scenic.aertslab.org/") + (synopsis "Single-Cell regulatory network inference and clustering") + (description + "pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell +rEgulatory Network Inference and Clustering) which enables biologists to infer +transcription factors, gene regulatory networks and cell types from +single-cell RNA-seq data.") + (license license:gpl3+))) + (define-public vbz-compression (package (name "vbz-compression") |