this is repository contains a Flask application dashboard designed to show the results of the analysis done by the monitoring pipeline available here
To run the dashboard app, activate the conda environment you have created for the monitoring pipeline and run
python3 ./dashboard.py \
--summary_path /<path to the summary dir created by the pipeline>/summary/ \
--config_path /<path to the pipeline config dir>/config/ \
--run_name "<anything>"
Options for the script are:
usage: dashboard.py [-h] --summary_path SUMMARY_PATH --config_path CONFIG_PATH --run_name RUN_NAME
[--smoothing_window_size SMOOTHING_WINDOW_SIZE]
[--smoothing_window_step SMOOTHING_WINDOW_STEP] [--low_cutoff LOW_CUTOFF]
[--high_cutoff HIGH_CUTOFF] [--coverage_cutoff] [--port PORT] [--debug]
Flask-app dashboard for pande-mic.
optional arguments:
-h, --help show this help message and exit
--summary_path SUMMARY_PATH
full path to summary directory
--config_path CONFIG_PATH
full path to config directory
--run_name RUN_NAME run name or ID
--smoothing_window_size SMOOTHING_WINDOW_SIZE
window size used for smoothing of coverage graphs
--smoothing_window_step SMOOTHING_WINDOW_STEP
step between smoothing windows for coverage graphs (calculating madians for each
position might be slow)
--low_cutoff LOW_CUTOFF
coverage value that is considered too low
--high_cutoff HIGH_CUTOFF
coverage value that is considered too high
--coverage_cutoff cut values higher than high_cutoff from the graph
--port PORT
--debug run app in debug mode
To test the dashboard app on the sample output from the pipeline, run
python3 ./dashboard.py --summary_path ./sample_pipeline_output/SARS-CoV-2/ --config_path ./sample_pipeline_output/SARS-CoV-2-config/ --run_name "SARS-CoV-2"
in case of any errors, you can try:
python3 ./dashboard.py --summary_path ./sample_pipeline_output/SARS-CoV-2/ --config_path ./sample_pipeline_output/SARS-CoV-2-config/ --run_name "SARS-CoV-2" --debug
this will run the dashboard app with the Flask development server