MedGen ingest

Prerequisites

On macOS, Perl should be available without the need for installation. Python and Perl are also dev dependencies. They're not needed to run the docker containers, but they are needed for local development situations / debugging.

1. Python 3.9+
2. Perl
3. Docker
4. Docker images
   One or both of the following, depending on if you want to run the stable build latest or dev:
   • a. docker pull obolibrary/odkfull:latest
   • b. docker pull obolibrary/odkfull:dev

Local development setup

1. Give permission to run Perl: chmod +x ./bin/*.pl
2. Install Python dependencies: pip install -r requirements.txt

Running

sh run.sh make all