Running Bedboss in Docker

To run bedboss in docker, go through the following steps:

1. Clone the bedboss repository:

   git clone [email protected]:databio/bedboss.git
   

2. Go to the bedboss directory.

3. Build the docker image:

   docker build -t my_bedboss .
   

4. source the environment variables:

   source production/production.env
   

5. Run the docker container with setting limit of the files that have to be processed:

   docker run --rm -it \
       --env POSTGRES_DB=$POSTGRES_DB \
       --env POSTGRES_HOST=$POSTGRES_HOST \
       --env POSTGRES_USER=$POSTGRES_USER \
       --env POSTGRES_PASSWORD=$POSTGRES_PASSWORD \
       --env QDRANT_API_KEY=$QDRANT_API_KEY \
       --env QDRANT_API_HOST=$QDRANT_API_HOST \
       --env AWS_ACCESS_KEY_ID=$AWS_ACCESS_KEY_ID \
       --env AWS_SECRET_ACCESS_KEY=$AWS_SECRET_ACCESS_KEY \
       --env AWS_ENDPOINT_URL=$AWS_ENDPOINT_URL \
       --env UPLOAD_LIMIT=1 \
       -t my_bedboss
   

If everything is set up correctly, you should see the bedboss prompt.