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[bug#71670] [PATCH 2/2] bioinformatics: Add python-muon
From: |
guix |
Subject: |
[bug#71670] [PATCH 2/2] bioinformatics: Add python-muon |
Date: |
Thu, 20 Jun 2024 08:51:12 +0000 |
Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d
---
gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 37fa1727cb..b3fe67cae7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4481,6 +4481,61 @@ (define-public python-mofapy2
(description "Multi-omics factor analysis.")
(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
+ #: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")))
+ (add-before 'check 'disable-failing-tests
+ (lambda _
+ ;; even providing a random seed, scipy.sparse.rand
+ ;; produces inconsistent results across scipy versions
+ (substitute* "tests/test_atac_preproc.py"
+ (("^class TestTFIDFSparse.*" m)
+ (string-append "@unittest.skip(reason=\"\")\n" m))))))))
+ (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-bootstrap
+ python-pytest
+ python-pytest-flake8))
+ (home-page "https://github.com/scverse/muon")
+ (synopsis "Multimodal omics analysis framework")
+ (description "Multimodal omics analysis framework.")
+ (license license:bsd-3)))
+
(define-public python-pyega3
(deprecated-package "python-pyega3" python-ega-download-client))
--
2.45.1