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Running CyLinter

Step 1:

Ensure that the desired configurations for a given analysis have been set in the YAML configuration file.

Step 2:

Activate the dedicated CyLinter virtual environment:

# on Mac:
source ~/cylinter/bin/activate

# on PC
cd C:\Users\<username>\cylinter\scripts
activate

Step 3:

Execute the program from the beginning of the pipeline by passing the YAML configuration file to the cylinter command:

cylinter <input_dir>/config.yml

Step 3.1:

CyLinter bookmarks progress by automatically caching partially-redacted feature tables as .parquet files in the checkpoints/ directory of the CyLinter output directory. To re-start the program at a desired module or re-run any of the Modules, pass the --module flag followed by a module name:

cylinter --module <module-name> <input_dir>/config.yml