Setting up

To run this demo, you'll need to have Docker (minimum version 27) and Docker Compose (minimum version 2.17.0) installed, as well as jq.

We also recommend a Node.js package manager (such as npm or yarn) to make things a easier, but we will provide directions for doing everything without one that you can follow if you prefer.

Getting the data

First download the demo data used for this guide and put it in a directory where you can also put a couple other files. For example:

mkdir apollo-demo/
cd apollo-demo/
wget https://s3.us-east-1.amazonaws.com/jbrowse.org/apollo/data.zip
unzip data.zip
rm data.zip

You'll now have two directories called data/ and jbrowse_data/.

Running Apollo

Create a file called compose.yml and paste the following contents into the file:

compose.yml

name: apollo-local-testing
services:
  apollo-collaboration-server:
    image: 'ghcr.io/gmod/apollo-collaboration-server'
    depends_on:
      db:
        condition: service_healthy
    environment:
      NAME: My Local Testing Server
      URL: 'http://localhost/apollo/'
      MONGODB_URI: 'mongodb://db:27017/apolloDb?replicaSet=rs0'
      FILE_UPLOAD_FOLDER: /data/uploads
      ALLOW_GUEST_USER: true
      GUEST_USER_ROLE: admin
      ALLOW_ROOT_USER: true
      ROOT_USER_PASSWORD: password
      JWT_SECRET: local_testing_only
      SESSION_SECRET: local_testing_only
    ports:
      - '3999:3999'
    volumes:
      - 'uploads:/data/uploads'

  client:
    build:
      context: .
      dockerfile_inline: |
        FROM httpd:alpine
        COPY <<EOF /usr/local/apache2/conf/httpd.conf.append
        LogLevel debug
        LoadModule proxy_module modules/mod_proxy.so
        LoadModule proxy_http_module modules/mod_proxy_http.so
        LoadModule proxy_wstunnel_module modules/mod_proxy_wstunnel.so
        ProxyPass "/config.json" "http://apollo-collaboration-server:3999/jbrowse/config.json"
        ProxyPassReverse "/config.json" "http://apollo-collaboration-server:3999/jbrowse/config.json"
        ProxyPassMatch "^/apollo/(.*)$" "http://apollo-collaboration-server:3999/\$1" upgrade=websocket connectiontimeout=3600 timeout=3600
        ProxyPassReverse "/apollo/" "http://apollo-collaboration-server:3999/"
        EOF
        WORKDIR /usr/local/apache2/htdocs/
        RUN <<EOF
        set -o errexit
        set -o nounset
        set -o pipefail
        cat /usr/local/apache2/conf/httpd.conf.append >> /usr/local/apache2/conf/httpd.conf
        wget https://github.com/GMOD/jbrowse-components/releases/download/v2.18.0/jbrowse-web-v2.18.0.zip --output-document=jbrowse-web.zip
        unzip -o jbrowse-web.zip
        rm jbrowse-web.zip
        wget --output-document=- --quiet https://registry.npmjs.org/@apollo-annotation/jbrowse-plugin-apollo/-/jbrowse-plugin-apollo-0.3.1.tgz | \
        tar --extract --gzip --file=- --strip=2 package/dist/jbrowse-plugin-apollo.umd.production.min.js
        mv jbrowse-plugin-apollo.umd.production.min.js apollo.js
        wget --quiet https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/refs/heads/master/Ontology_Files/so.json
        mv so.json sequence_ontology.json
        EOF
    depends_on:
      - apollo-collaboration-server
    ports:
      - '80:80'
    volumes:
      - './jbrowse_data:/usr/local/apache2/htdocs/data'

  db:
    image: 'mongo:7'
    command:
      - '--replSet'
      - rs0
      - '--bind_ip_all'
      - '--port'
      - '27017'
    healthcheck:
      interval: 30s
      retries: 3
      start_period: 2m
      test: |
        mongosh --port 27017 --quiet --eval "
        try {
          rs.status()
          console.log('replica set ok')
        } catch {
          rs.initiate()
          console.log('replica set initiated')
        }
        "
      timeout: 10s
    ports:
      - '27017:27017'
    volumes:
      - 'db_data:/data/db'
      - 'db_config:/data/configdb'

volumes:
  db_config: null
  db_data: null
  uploads: null

Now in the terminal, run docker compose up. You should see a stream of logs from the Docker containers. If you do, Apollo is now running! You can use Ctrl + C in the terminal to stop Apollo when you are done.