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-rw-r--r--gnu/packages/bioinformatics.scm126
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