diff options
| author | guix@mawumag.com <guix@mawumag.com> | 2024-06-20 08:51:12 +0000 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-07-01 16:18:34 +0200 |
| commit | ddce6b2303dc6064ca50b4fbd53389e50faa115d (patch) | |
| tree | ebafe59dc0acabc0c57e960624f0f01547b9b0a8 /gnu/packages | |
| parent | 58ead4baf9596bafbfe1299c48795c9d54af671e (diff) | |
gnu: Add python-muon.
* gnu/packages/bioinformatics.scm (python-muon): New variable.
Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 52 |
1 files changed, 52 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0484ea3b0d..063017a8aa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4535,6 +4535,58 @@ thus facilitating the identification of cellular states or disease subgroups.") (license license:lgpl3))) +(define-public python-muon + (package + (name "python-muon") + (version "0.1.6") + (source + (origin + ;; The tarball from PyPi doesn't include tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/scverse/muon") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1kd3flgy41dc0sc71wfnirh8vk1psxgyjxkbx1zx9yskkh6anbgw")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; Even providing a random seed, scipy.sparse.rand produces inconsistent + ;; results across scipy versions. + '(list "-k" "not test_tfidf") + #: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")))))) + (propagated-inputs (list python-anndata + python-h5py + python-matplotlib + python-mofapy2 + python-mudata + python-numba + python-numpy + python-pandas + python-protobuf + python-pybedtools + python-pysam + python-scanpy + python-scikit-learn + python-seaborn + python-tqdm + python-umap-learn)) + (native-inputs (list python-flit-core + python-pytest + python-pytest-flake8)) + (home-page "https://github.com/scverse/muon") + (synopsis "Multimodal omics analysis framework") + (description "muon is a multimodal omics Python framework.") + (license license:bsd-3))) + (define-public python-pyega3 (deprecated-package "python-pyega3" python-ega-download-client)) |