pepkit / pephub.databio.org

Data stores for pephub PEPs

pephub.databio.org

This is the publically available instance of PEPhub provided by the Sheffield lab. You can view the deployed instance at https://pephub.databio.org

Development

Build the container

docker build -t pephub.databio.org .

Run

PEPhub requires many parameters to run. You can read more about those here. These must be injected as environment variables. You can manually do this and inject one-by-one. There is an example script in this repo called launch_docker.sh.

launch_docker.sh

The basic steps are:

1. Initialize env vars

source /home/nsheff/code/pephub/environment/production.env

2. Run with docker:

docker run --rm -p 80:80 \
    --env POSTGRES_HOST=$POSTGRES_HOST \
    --env POSTGRES_DB=$POSTGRES_DB \
    --env POSTGRES_USER=$POSTGRES_USER \
    --env POSTGRES_PASSWORD=$POSTGRES_PASSWORD \
    --env QDRANT_HOST=$QDRANT_HOST \
    --env QDRANT_PORT=$QDRANT_PORT \
    --env QDRANT_ENABLED=$QDRANT_ENABLED \
    --env QDRANT_API_KEY=$QDRANT_API_KEY \
    --env HF_MODEL=$HF_MODEL \
    --env GH_CLIENT_ID=$GH_CLIENT_ID \
    --env GH_CLIENT_SECRET=$GH_CLIENT_SECRET \
    --env REDIRECT_URI=$REDIRECT_URI \
    --env SERVER_ENV=$SERVER_ENV \
    --name pephub pephub

3. Visit http://localhost:80 to view the server.