FAQ

How do I install Phenofhy?

Install it from PyPI when the TRE permits package installation:

python -m pip install phenofhy

If the TRE cannot access PyPI, transfer the wheel through the Airlock process.

Where does config.json live?

Run phenofhy.init() once. It creates a local config in the notebook working directory and uploads the project copy to phenofhy/config.json.

Do I need the dx CLI?

Yes. Phenofhy relies on DNAnexus tools for dataset access and metadata downloads. But note dx comes preinstalled on the OFH tre.

What if my cohort key is missing?

The generated config.json controls cohort keys under COHORTS. The default dataset is available as COHORTS["FULL_SAMPLE"]; pass another cohort key when using a custom configuration.

Where are metadata dictionaries stored?

Phenofhy downloads them into ./metadata in your working directory when needed.