docker-compose.yml

version: '3'
services:

  mrb-neo4j:
    image: neo4j:3.5
    restart: always
    ports:
    - "37474:7474"
    - "37687:7687"
    - "37473:7473"
    volumes:
    - /data/mrb_neo4j_v3/data:/data
    - /data/mrb_neo4j_v3/logs:/logs
    - /etc/timezone:/etc/timezone:ro
    environment:
      - NEO4J_AUTH=${NEO4J_AUTH}
      - NEO4J_dbms_memory_heap_max__size=20G
      - NEO4J_dbms_memory_heap_initial__size=5G
      - NEO4J_dbms_memory_pagecache_size=10G
      - NEO4J_dbms_shell_enabled=true
      - NEO4J_dbms_allow__upgrade=true
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:7474"]

  mr-base-api-v3-public:
    image: mr-base-api-v3:latest
    restart: always
    ports:
    - "8084:80"
    volumes:
    - /data/igd:/data/igd
    - /data/mrb_logs_pub:/data/mrb_logs
    - /etc/timezone:/etc/timezone:ro
    - /data/ref/ld_files:/app/ld_files
    environment:
      - NGINX_MAX_UPLOAD=750m
      - UWSGI_PROCESSES=20
      - UWSGI_THREADS=2
      - ENV=production
      - ACCESS=public
    depends_on:
      - mrb-neo4j
      - mr-base-api-cromwell
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost"]
  
  mr-base-api-v3-private:
    image: mr-base-api-v3:latest
    restart: always
    ports:
    - "8082:80"
    volumes:
    - /data/igd:/data/igd
    - /data/mrb_logs_priv:/data/mrb_logs
    - /etc/timezone:/etc/timezone:ro
    - /data/ref/ld_files:/app/ld_files
    environment:
      - NGINX_MAX_UPLOAD=750m
      - UWSGI_PROCESSES=20
      - UWSGI_THREADS=2
      - ENV=production
      - ACCESS=private
    depends_on:
      - mrb-neo4j
      - mr-base-api-cromwell
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost"]

  mr-base-api-cromwell:
    build: ./app/resources/workflow
    restart: always
    environment:
      - JAVA_OPTS=-Ddocker.hash-lookup.enabled=false -Dsystem.max-concurrent-workflows=12 -Dbackend.providers.Local.config.root=/data/cromwell-executions -Dworkflow-options.workflow-log-dir=/data/cromwell-workflow-logs -Ddatabase.profile=slick.jdbc.MySQLProfile$$ -Ddatabase.db.driver=com.mysql.cj.jdbc.Driver -Ddatabase.db.url=jdbc:mysql://mr-base-api-cromwell-mysql/cromwell?rewriteBatchedStatements=true -Ddatabase.db.user=${database_db_user} -Ddatabase.db.password=${database_db_password} -Ddatabase.db.connectionTimeout=5000
    ports:
    - "8001:8000"
    volumes:
    - /var/run/docker.sock:/var/run/docker.sock
    - /data:/data
    - /etc/timezone:/etc/timezone:ro
    - /data/ref/ld_files:/data/ld_files
    command: ["server"]
    depends_on:
      - mr-base-api-cromwell-mysql
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:8000"]

  mr-base-api-cromwell-mysql:
    image: mysql:5.7
    restart: always
    environment:
      - MYSQL_ROOT_PASSWORD=${database_db_password}
      - MYSQL_DATABASE=cromwell
      - MYSQL_USER=${database_db_user}
      - MYSQL_PASSWORD=${database_db_password}
    volumes:
        - /data/cromwell-mysql:/var/lib/mysql
        - /etc/timezone:/etc/timezone:ro
    healthcheck:
      test: ["CMD", "mysqladmin" ,"ping", "-h", "localhost"]