docker-compose.yml

secrets:
  GALAXY_STORAGE_PASSWORD:
    file: ./galaxy/secrets/GALAXY_STORAGE_PASSWORD

services:
  nginx:
    image: nginx
    container_name: ${PROJECT_NAME}-nginx
    restart: unless-stopped
    depends_on:
      - galaxy
    volumes:
      - galaxy-store:/galaxy/server/
      - ./nginx/galaxy.conf:/etc/nginx/conf.d/default.conf:ro
      - ./galaxy/config/welcome.html:/galaxy/server/static/welcome.html
    ports:
      - "80:80"
    networks:
      - galaxy
    
  galaxy:
    image: galaxy/galaxy-min:24.2.2
    restart: unless-stopped
    group_add:
      - ${DOCKER_GID}
    depends_on:
      galaxy-postgres:
        condition: service_healthy
      rabbitmq:
        condition: service_healthy
    container_name: ${PROJECT_NAME}-galaxy
    volumes:
      # Persistant storage for Galaxy
      - galaxy-store:/galaxy/server/
      - file-store:/file-store
      # TUSD binary
      - ./galaxy/tusd:/usr/local/sbin/tusd
      # Populate the instance
      - ./galaxy/init/bootstrap.py:/galaxy/server/bootstrap.py
      - ./galaxy/tools:/galaxy/server/tools/
      # Add custom configuration files
      - ./galaxy/config/galaxy.yml:/galaxy/server/config/galaxy.yml
      - ./galaxy/config/tool_conf.xml:/galaxy/server/config/tool_conf.xml.sample
      - ./galaxy/config/job_conf.xml:/galaxy/server/config/job_conf.xml 
      - ./galaxy/config/datatypes_conf.xml:/galaxy/server/config/datatypes_conf.xml
      - ./galaxy/config/file_sources_conf.yml:/galaxy/server/config/file_sources_conf.yml
      # Provide docker-in-docker
      - /usr/bin/docker:/usr/bin/docker
      - /var/run/docker.sock:/var/run/docker.sock:ro
    networks:
      - galaxy
    command: ["sh", "-c", "pip install --upgrade s3fs botocore boto3 && exec galaxy"]
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:8080"]
      interval: 30s
      timeout: 30s
      retries: 5

  galaxy-bootstrap:
    image: galaxy/galaxy-min:24.1.3
    container_name: ${PROJECT_NAME}-galaxy-bootstrap
    environment:
      - GALAXY_URL=http://${PROJECT_NAME}-galaxy:8080
      - GALAXY_API_KEY=${GALAXY_API_KEY}
      - GALAXY_ADMIN_USERNAME=${GALAXY_ADMIN_USER}
      - GALAXY_ADMIN_EMAIL=${GALAXY_ADMIN_EMAIL}
      - GALAXY_ADMIN_PASSWORD=${GALAXY_ADMIN_PASS}
    depends_on:
      galaxy:
        condition: service_healthy
    volumes:
      - ./galaxy/init/bootstrap.py:/bootstrap.py
      - ./galaxy/workflows:/galaxy-workflows
    networks:
      - galaxy
    entrypoint: ["python"]
    command: ["/bootstrap.py"]
    
  galaxy-postgres:
    container_name: ${PROJECT_NAME}-galaxy-postgres
    image: postgres
    restart: unless-stopped
    secrets: [GALAXY_STORAGE_PASSWORD]
    ports:
      - 5432:5432
    environment:
      POSTGRES_USER: galaxy
      POSTGRES_PASSWORD_FILE: /run/secrets/GALAXY_STORAGE_PASSWORD
      POSTGRES_DB: galaxy
    networks:
      - galaxy
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U galaxy"]
      interval: 5s
      timeout: 5s
      retries: 5

  rabbitmq:
    image: docker.io/bitnami/rabbitmq:3.12
    container_name: ${PROJECT_NAME}-rabbitmq
    restart: unless-stopped
    ports:
      - '1883:1883'
      - '5672:5672'
      - '15672:15672'
    environment:
      - RABBITMQ_SECURE_PASSWORD=yes
      - RABBITMQ_USERNAME=rabbitmq
      - RABBITMQ_PASSWORD=rabbitmq
      - RABBITMQ_MANAGEMENT_ALLOW_WEB_ACCESS=yes
      - RABBITMQ_PLUGINS=rabbitmq_mqtt,rabbitmq_management
      - RABBITMQ_DISK_FREE_RELATIVE_LIMIT=1.0
      - RABBITMQ_DISK_FREE_ABSOLUTE_LIMIT=500MB
      #- RABBITMQ_LOGS=-
    volumes:
      - rabbitmq_data:/bitnami/rabbitmq/mnesia
      #- ./config/rabbit/advanced.config:/bitnami/rabbitmq/conf/advanced.config:ro
    networks:
      - galaxy
    healthcheck:
      test: ["CMD", "rabbitmq-diagnostics", "ping"]
      interval: 10s
      timeout: 5s
      retries: 5

  minio:
    image: minio/minio
    container_name: ${PROJECT_NAME}-minio
    restart: unless-stopped
    ports:
      - "9000:9000"
      - "9001:9001"
    environment:
      MINIO_ROOT_USER: minioadmin
      MINIO_ROOT_PASSWORD: miniogalaxy
      MINIO_ACCESS_KEY: miniogalaxy
      MINIO_SECRET_KEY: miniogalaxy
    volumes:
      - minio-data:/data 
    command: server /data --console-address ":9001"
    networks:
      - galaxy
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:9000/minio/health/live"]
      interval: 30s
      timeout: 30s
      retries: 5

  minio-bootstrap:
    image: minio/mc
    container_name: ${PROJECT_NAME}-minio-bootstrap
    depends_on:
      minio:
        condition: service_healthy
    volumes:
      - ./minio/init/bootstrap.sh:/bootstrap.sh
    networks:
      - galaxy
    entrypoint: >-
      sh -c "
      echo 'Bootstraping Minio...';
      mc alias set minio http://minio:9000 minioadmin miniogalaxy;
      mc mb minio/galaxy;
      mc mb minio/galaxy-backend;
      exit 0;
      "
      
networks:
  galaxy:

volumes:
  galaxy-store:
    name: galaxy-store
  file-store:
    name: file-store
  rabbitmq_data:
    name: rabbitmq-data
  minio-data:
    name: minio-data