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HTS Bioinf - Update external reference data


This procedure explains how to update the external reference data used by the gene panel builder service.


A bioinformatician from GDx is responsible for performing these tasks.

The gene panel builder service

An instance of the gene panel builder service database must be running on the computer the update is to be performed on.


Hereafter, we will assume that the name of the directory holding the local gene panel builder code repository is stored in a variable called GPBHOME. Before performing the update, make sure that a valid OMIM API key is available; we will assume one is stored in the OMIM_API_KEY variable.

On the computer running the gene panel builder service, run

docker compose -f "${GPBHOME}/docker-compose-prod.yml" \
    exec -e OMIM_API_KEY="${OMIM_API_KEY}" -w /tmp gpbuilder gpb update all