gnu: Add python-celltypist.

* gnu/packages/bioinformatics.scm (python-celltypist): New variable.

Change-Id: I196b7a07955224fe4c641d79729f0facb6367adb
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Ricardo Wurmus 2024-05-30 23:18:28 +02:00
parent 8144c587f8
commit 01de17143c
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@ -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")