Running CyLinter

Step 1:

Ensure that the desired configurations for a given analysis have been set in CyLinter’s YAML configuration file. A copy of this file can be found in the virtual environment into which CyLinter was installed (.../miniconda3/envs/cylinter/lib/pythonXX/site-packages/cylinter/cylinter_config.yml)

Step 2:

Activate the CyLinter virtual environment:

conda activate cylinter

Step 3:

Execute the program from the beginning of the pipeline by passing the YAML configuration file (which should be stored at the top level of the CyLinter input directory) to the cylinter command:

cylinter <input_dir>/cylinter_config.yml

CyLinter bookmarks progress by automatically caching partially-redacted spatial feature tables in the checkpoints/ directory of the CyLinter output directory. To re-run any of the Modules, pass the --module flag followed by the name of a specific module:

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