Standalone Docker Image

In order to build a standalone Docker image for a BioCypher KG, you only need small modifications to the Docker image of the template. We will render the data that ususally is stored in the biocypher_neo4j_volume to our local disk by exchanging biocypher_neo4j_volume with a local directory, ./biocypher_neo4j_volume. Then, we use a Dockerfile to build an image that contains the final database. This image can be used to deploy the database anywhere, without the need to run the BioCypher code. This process is demonstrated in the drug-interactions example repository.

  1. Clone the example repository

git clone https://github.com/biocypher/drug-interactions.git
cd drug-interactions

  1. Attach volumes to disk by modifying the docker-compose.yml. In the example repository, we have created a dedicated compose file for the standalone image. You can see the differences between the standard and standalone compose files here. IMPORTANT: only run the standalone compose file once, as the data in the ./biocypher_neo4j_volume directory is persistent and interferes with subsequent runs. If you want to run it again, you need to delete the ./biocypher_neo4j_volume directory.

  2. Run the standalone compose file. This will create the ./biocypher_neo4j_volume directory and store the data in it. You can stop the container after the database has been created.

docker compose -f docker-compose-local-disk.yml up -d
docker compose -f docker-compose-local-disk.yml down

  1. Create standalone Dockerfile (example here):

# Dockerfile
FROM neo4j:4.4-enterprise
COPY ./biocypher_neo4j_volume /data
RUN chown -R 7474:7474 /data
EXPOSE 7474
EXPOSE 7687

  1. Build the standalone image.

docker build -t drug-interactions:latest .

This image can be deployed anywhere, without the need to run the BioCypher code. For example, you can add it to a Docker Compose file (example here):

# docker-compose.yml
version: '3.9'
services:
  [other services ...]

  biocypher:
    container_name: biocypher
    image: biocypher/drug-interactions:latest
    environment:
      NEO4J_dbms_security_auth__enabled: "false"
      NEO4J_dbms_databases_default__to__read__only: "false"
      NEO4J_ACCEPT_LICENSE_AGREEMENT: "yes"
    ports:
      - "0.0.0.0:7474:7474"
      - "0.0.0.0:7687:7687"