diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b7e8e54de2..cecd94bbb7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1967,6 +1967,53 @@ (define-public python-cellbender from high-throughput single-cell RNA sequencing (scRNA-seq) data.") (license license:bsd-3))) +(define-public python-celltypist + (package + (name "python-celltypist") + (version "1.6.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Teichlab/celltypist") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0c42cx01zkxr0dk5f1d7q71qdi18v2smlc3wpvwyjlzplya7k2iy")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + '(modify-phases %standard-phases + (add-before 'check 'set-home + ;; The sanity check requires a HOME directory, because celltypist + ;; wants to write settings. + (lambda _ (setenv "HOME" "/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-click + python-leidenalg + python-numpy + python-openpyxl + python-pandas + python-scanpy + python-scikit-learn + python-requests)) + (home-page "https://github.com/Teichlab/celltypist") + (synopsis "Tool for semi-automatic cell type classification") + (description + "CellTypist is an automated cell type annotation tool for scRNA-seq +datasets on the basis of logistic regression classifiers optimised by the +stochastic gradient descent algorithm. CellTypist allows for cell prediction +using either built-in (with a current focus on immune sub-populations) or +custom models, in order to assist in the accurate classification of different +cell types and subtypes.") + (license license:expat))) + (define-public python-cmseq (package (name "python-cmseq")