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ImagingDataCommons / CloudSegmentator

Medical imaging segmentation workflows for FireCloud (Terra) and Seven Bridges Cancer Genomics Cloud
Apache License 2.0
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Add explanation of using Papermill parameterized notebooks #5

Closed fedorov closed 9 months ago

fedorov commented 1 year ago

For the key notebooks we are using, we should have documentation/preamble describing how they are parameterized, and some basic instructions on how to use them (e.g., example papermill command line), in the opening text cell of the notebook.

vkt1414 commented 1 year ago

Sure. There are three ways one can use a notebook.

  1. Colab..just need to uncomment some cells to install some packages
  2. as a Jupyter notebook: Steps for Colab+install more packages that are pre-installed in colab env
  3. Inside a docker container/terra/sb-cgc: papermill command

I can add these instructions to all notebooks

fedorov commented 1 year ago

and the instructions on what should be the format of the input parameters (ie, provide a snippet of a sample input CSV).

vkt1414 commented 10 months ago

I think we can close this issue now that #35 is merged.