Improve Docker images usability #249
Merged
Commits on Mar 10, 2024
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Address import error encountered in annotation.ipynb
When trying to run `sc.pp.highly_variable_genes()` in docs/tutorials/annotation.ipynb the following ImportError is encountered: ImportError: Please install skmisc package via `pip install --user scikit-misc Looking at the pyproject.toml for the `scanpy` project it looks like the `scikit-misc` package can be co-installed by specifying `scanpy[skmisc]` (see: https://github.com/scverse/scanpy/blob/a956fa781a8406fc5030093356c0372456d9184b/pyproject.toml#L142)
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Make recommend-interactive docker image even more user friendly
User friendliness improvements: - Added short guide on how to make use of Nvidia GPU with Docker image - Updated recommend-interactive image and example command so that downloaded datasets can be shared with local machine (and vice versa) - This commit also bumps the default `SnapATAC2` version that will be built when following the README to v2.6.0.
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