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| author | Janneke Nieuwenhuizen <janneke@gnu.org> | 2025-08-22 23:02:21 +0200 |
|---|---|---|
| committer | Janneke Nieuwenhuizen <janneke@gnu.org> | 2025-08-22 23:02:21 +0200 |
| commit | 49b0066100d2033a98cea728503ddfdba0cb26ec (patch) | |
| tree | 25e465f6dabb77069a08a1a132ef2b49da3099f7 /gnu | |
| parent | c6db3916fa6191a1a55d103a0bf18bc3da153435 (diff) | |
gnu: Add python-circe.
* gnu/packages/bioinformatics.scm (python-circe): New variable.
Change-Id: Ie250a044da02d2a2c8d2113d2331e37c6b3e46b0
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 46 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6ec3ea23001..3801e827c64 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4868,6 +4868,52 @@ consensus sequences.") long-read sequencing data.") (license license:expat))) +(define-public python-circe + (package + (name "python-circe") + (version "0.3.8") + (home-page "https://github.com/cantinilab/circe") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "050zwg6qvd6sa4xd41sn4gigwmyfn0v6r93j5kvpbxklq4144q15")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-anndata + python-dask + python-distributed + python-joblib + python-numpy + python-pandas + python-rich + python-scanpy + python-scikit-learn)) + (inputs + (list lapack openblas)) + (native-inputs + (list python-cython + python-setuptools + python-pybiomart + python-wheel)) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (synopsis "Cis-regulatory interactions between chromatin regions") + (description "Circe is a Python package for inferring co-accessibility +networks from single-cell ATAC-seq data, using skggm for the graphical lasso +and python-scanpy for data processing.") + (license license:gpl3))) + (define-public qtltools (package (name "qtltools") |