MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Apache License 2.0
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Graphviz error with `maxatac train` #100

Closed tacazares closed 2 years ago

tacazares commented 2 years ago

I had an error when saving the graph representation of the model at the end of training.

[2022-05-29 14:01:28,329]
Plot and save results
Traceback (most recent call last):
  File "/users/caz3so/.conda/envs/maxatac_train/bin/maxatac", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/users/caz3so/repo/miraldilab/maxATAC/maxatac/bin/maxatac", line 24, in <module>
    sys.exit(main(sys.argv[1:]))
  File "/users/caz3so/repo/miraldilab/maxATAC/maxatac/bin/maxatac", line 20, in main
    args.func(args)
  File "/users/caz3so/repo/miraldilab/maxATAC/maxatac/analyses/train.py", line 143, in run_training
    export_model_structure(maxatac_model.nn_model, maxatac_model.results_location)
  File "/users/caz3so/repo/miraldilab/maxATAC/maxatac/utilities/plot.py", line 11, in export_model_structure
    plot_model(
  File "/users/caz3so/.conda/envs/maxatac_train/lib/python3.9/site-packages/keras/utils/vis_utils.py", line 421, in plot_model
    dot = model_to_dot(
  File "/users/caz3so/.conda/envs/maxatac_train/lib/python3.9/site-packages/keras/utils/vis_utils.py", line 163, in model_to_dot
    raise ImportError(message)
ImportError: You must install pydot (`pip install pydot`) and install graphviz (see instructions at https://graphviz.gitlab.io/download/) for plot_model/model_to_dot to work.

We need to add instructions to the readme on how to make sure graphviz is installed.