diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 126 |
1 files changed, 68 insertions, 58 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37cc08c8fe..2546454acd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18066,67 +18066,77 @@ 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 + ;; Latest commit from the update-pyarrow branch + (let ((commit "5f170fdf474548c37ab381d1849c662820d658ee") + (revision "1")) + (package + (name "pyscenic") + (version (git-version "0.11.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/pySCENIC") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03qkvy400rjndg2ds6bhcaprir71mqr2v3yv9vd77lcnzxgw3s0z")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; The cli modules referenced here have been removed, so this + ;; breaks the sanity check. + (add-after 'unpack 'do-not-reference-deleted-modules + (lambda _ + (substitute* "setup.py" + (("'db2feather = .*',") "") + (("'invertdb = .*',") "") + (("'gmt2regions = pyscenic.cli.gmt2regions:main'") "")))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (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-pyarrow ;XXX for 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+))) + (license license:gpl3+)))) (define-public python-ikarus (package |