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Change-Id: I8a4f2293bde59b10e7b673025bbb4c5a8420738b --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) base-commit: 49a113e3fc618d6f6bd5000c164a1d33701a30c4 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 317c15817e..7566346df1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2581,6 +2581,49 @@ (define-public python-cmseq and sequence consensus.") (license license:expat))) +(define-public python-cnmf + (package + (name "python-cnmf") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cnmf" version)) + (sha256 + (base32 "0aic8cwj6riykcfgl6v2x3si5z04gaknkh5a8lcyv1qh4s1gx3d3")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f ;There are no tests + #:phases '(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + (setenv "MPLCONFIGDIR" "/tmp"))) + ;; 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-fastcluster + python-matplotlib + python-numba + python-numpy + python-palettable + python-pandas + python-pyyaml + python-scanpy + python-scikit-learn + python-scipy)) + (native-inputs (list python-setuptools python-wheel)) + (home-page "https://github.com/dylkot/cNMF") + (synopsis "Consensus NMF for scRNA-Seq data") + (description + "This tool offers a pipeline for inferring gene expression programs from scRNA-Seq. +It takes a count matrix (N cells X G genes) as input and produces a (K x G) matrix of +gene expression programs (GEPs) and a (N x K) matrix specifying the usage of each +program for each cell in the data.") + (license license:expat))) + (define-public python-cyvcf2 (package (name "python-cyvcf2")