FAQ

Do I need to upload Phenofhy manually to the TRE?

Yes. Phenofhy is currently a beta package and must be uploaded to the OFH TRE manually (using the Airlock process). There is no automated installer yet, as OFH doesn't yet allow access to package repositories like PyPI.

Where does config.json live?

Phenofhy expects config.json at /mnt/project/helpers/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?

config.json controls cohort keys under COHORTS. Add or update the key for your study before running extraction.

Where are metadata dictionaries stored?

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