BioAPI/docker-compose_dist.yml at master · omics-datascience/BioAPI · GitHub

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services:
    # MongoDB Server
    mongo_bioapi:
        image: mongo:8.3.2
        restart: always
        container_name: bio_api_mongo_db
        volumes:
            - mongo_data:/data/db
            - mongo_config:/data/configdb
            # Uncomment if you want custom MongoDB config
            # - ./config/mongo/mongod.conf:/etc/mongo/mongod.conf
        environment:
            MONGO_INITDB_ROOT_USERNAME: '' # Complete
            MONGO_INITDB_ROOT_PASSWORD: '' # Complete
            MONGO_INITDB_DATABASE: bio_api # Don't change this value!
        deploy:
            resources:
                limits:
                    memory: 6g

    # BioAPI server
    web_bioapi:
        image: omicsdatascience/bio-api:1.5.0
        restart: always
        volumes:
            - bioapi_logs:/logs
        depends_on:
            - mongo_bioapi
        environment:
            DEBUG: 'false'
            # MongoDB's credentials must be the same as 'mongo' service above
            MONGO_HOST: 'mongo_bioapi' # Change if needed
            MONGO_PORT: '27017' # Change if needed
            MONGO_USER: '' # Complete
            MONGO_PASSWORD: '' # Complete
            MONGO_DB: bio_api # Don't change this value!
        healthcheck:
            test: ["CMD", "curl", "--fail", "--silent", "--show-error", "http://127.0.0.1:8000/ping"]
            interval: 30s
            timeout: 10s
            retries: 5
            start_period: 60s

    # BioAPI MCP server
    mcp_bioapi:
        image: omicsdatascience/bio-api:1.5.0
        restart: always
        depends_on:
            - web_bioapi
        entrypoint: ["/usr/local/bin/python3", "-m", "bioapi_sdk.mcp_server"]
        command:
            - "--transport"
            - "streamable-http"
            - "--host"
            - "0.0.0.0"
            - "--port"
            - "8001"
            - "--path"
            - "/mcp"
        environment:
            PYTHONPATH: '/app/sdk/src'
            BIOAPI_BASE_URL: 'http://web_bioapi:8000'
            BIOAPI_TIMEOUT: '30'
            MCP_PUBLIC_BASE_URL: 'https://bioapi.multiomix.org/mcp'
            MCP_ALLOWED_HOSTS: 'bioapi.multiomix.org,bioapi.multiomix.org:*,localhost,localhost:*,127.0.0.1,127.0.0.1:*,[::1],[::1]:*'
            MCP_ALLOWED_ORIGINS: 'https://bioapi.multiomix.org,http://localhost,http://localhost:*,http://127.0.0.1,http://127.0.0.1:*,http://[::1],http://[::1]:*'
        healthcheck:
            test: ["CMD", "curl", "--fail", "--silent", "--show-error", "http://127.0.0.1:8001/health"]
            interval: 30s
            timeout: 10s
            retries: 5
            start_period: 30s

    # NGINX server
    nginx_bioapi:
        image: nginx:1.31
        restart: always
        ports:
            - '80:8000'
        depends_on:
            web_bioapi:
                condition: service_healthy
            mcp_bioapi:
                condition: service_healthy
        volumes:
            - ./config/nginx/conf.d:/etc/nginx/conf.d
        healthcheck:
            test: ["CMD-SHELL", "curl --fail --silent --show-error http://127.0.0.1:8000/ping || exit 1"]
            interval: 30s
            timeout: 10s
            retries: 5
            start_period: 30s

volumes:
    mongo_data:
        external: true
        name: 'bio_api_mongo_data'
    mongo_config:
        external: true
        name: 'bio_api_mongo_config'
    bioapi_logs:
        external: true
        name: 'bio_api_logs'