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Teichlab / celltypist

A tool for semi-automatic cell type classification
https://www.celltypist.org/
MIT License
278 stars 44 forks source link

Support custom .celltypist dir? #11

Closed bbimber closed 2 years ago

bbimber commented 2 years ago

Hello,

By default, celltypist makes a folder in the user's home dir to cache data. It would be convenient if celltypist supported either an environment variable or argument to directly specify this path. Our scenario is that we're running in docker on a cluster as a non-root user and the default home is non-writable. I'm fixing this, but having flexibility over the save location would still be a nice feature.

Thanks, Ben

ChuanXu1 commented 2 years ago

@bbimber , this option has been added 1c8f21852a932b651b268421c5346e2aa765aa20

Also copied some text from the README

By default, a folder .celltypist/ will be created in the user's home directory to store model files. A different path/folder can be specified by exporting the environment variable CELLTYPIST_FOLDER in your configuration file (e.g. in ~/.bash_profile).

  #In the shell configuration file.
  export CELLTYPIST_FOLDER='/path/to/model/folder/'

Does this suffice?

(Btw, I also pushed a new version (0.2.0), you can pip install celltypist)

bbimber commented 2 years ago

very helpful, thank you