docker-compose.yml

version: "3.9"

services:

  nextflow:
    image: nextflow/nextflow:${NEXTFLOW_TAG}
    container_name: ${PROJECT_NAME}-nextflow
    hostname: nextflow
    env_file: .env
    working_dir: ${PWD}
    environment:
      PROJECT_NAME: $PROJECT_NAME
      USER: $USER
      HOME: $HOME
      NXF_ASSETS: $NXF_ASSETS
      AWS_ACCESS_KEY_ID: $AWS_ACCESS_KEY_ID
      AWS_SECRET_ACCESS_KEY: $AWS_SECRET_ACCESS_KEY
      MLFLOW_S3_ENDPOINT_URL: $MLFLOW_S3_ENDPOINT_URL
      ARANGO_ROOT_PASSWORD: $ARANGO_ROOT_PASSWORD
    volumes:
      - ${PWD}:${PWD}:Z
      - /var/run/docker.sock:/var/run/docker.sock
      - ${HOME}:${HOME}:ro,Z
      - ${NXF_ASSETS}:${NXF_ASSETS}:Z

  mlflow:
    image: $GITHUB_CONTAINER_REPO
    container_name: ${PROJECT_NAME}-mlflow
    hostname: mlflow
    restart: unless-stopped
    stop_grace_period: 10s
    env_file: .env
    environment:
      MLFLOW_BACKEND_STORE_URI: $MLFLOW_BACKEND_STORE_URI
      MLFLOW_S3_ENDPOINT_URL: $MLFLOW_S3_ENDPOINT_URL
      AWS_ACCESS_KEY_ID: $AWS_ACCESS_KEY_ID
      AWS_SECRET_ACCESS_KEY: $AWS_SECRET_ACCESS_KEY
    ports:
      - ${MLFLOW_PORT}:5000
    command: >
      mlflow server --serve-artifacts --host 0.0.0.0 --port 5000 
      --backend-store-uri "${MLFLOW_BACKEND_STORE_URI}" --default-artifact-root s3://mlflow/

  minio:
    image: minio/minio:${MINIO_TAG}
    container_name: ${PROJECT_NAME}-minio
    hostname: minio
    restart: unless-stopped
    stop_grace_period: 10s
    env_file: .env
    working_dir: /data
    volumes:
      - minio-data:/data
    ports:
      - ${MINIO_PORT}:9000
      - ${MINIO_CONSOLE_PORT}:9001
    environment:
      MINIO_ACCESS_KEY: $MINIO_ACCESS_KEY
      MINIO_SECRET_KEY: $MINIO_SECRET_KEY
      MINIO_ROOT_USER: $MINIO_ROOT_USER
      MINIO_ROOT_PASSWORD: $MINIO_ROOT_PASSWORD
      MINIO_STORAGE_USE_HTTPS: $MINIO_STORAGE_USE_HTTPS
    command: server /data --console-address ':9001' --address ':9000'

  mc:
    image: minio/mc:${MINIO_MC_TAG}
    container_name: ${PROJECT_NAME}-mc
    hostname: mc
    env_file: .env
    environment:
      MINIO_PORT: $MINIO_PORT
      MINIO_ACCESS_KEY: $MINIO_ACCESS_KEY
      MINIO_SECRET_KEY: $MINIO_SECRET_KEY
    depends_on:
      - minio
    entrypoint: >
      /bin/sh -c ' sleep 5; 
      /usr/bin/mc config host add s3 http://minio:9000 ${MINIO_ACCESS_KEY} ${MINIO_SECRET_KEY} --api S3v4;  
      [[ ! -z "`/usr/bin/mc ls s3 | grep challenge`" ]] || /usr/bin/mc mb s3/mlflow;  /usr/bin/mc policy download s3/mlflow;  
      [[ ! -z "`/usr/bin/mc ls s3 | grep challenge`" ]] || /usr/bin/mc mb s3/data;  /usr/bin/mc policy download s3/data; exit 0; '

  postgres:
    image: postgres:${POSTGRES_TAG}
    container_name: ${PROJECT_NAME}-postgres
    hostname: postgres
    restart: unless-stopped
    stop_grace_period: 10s
    env_file: .env
    environment:
      POSTGRES_PASSWORD: $DB_PASSWORD
      POSTGRES_DB: $DB_NAME
      POSTGRES_USER: $DB_USER
    ports:
      - ${DB_PORT}:5432
    volumes:
      - postgres-data:/var/lib/postgresql/data

  arangodb:
    image: arangodb:${ARANGODB_TAG}
    container_name: ${PROJECT_NAME}-arangodb
    hostname: arangodb
    restart: unless-stopped
    stop_grace_period: 10s
    env_file: .env
    environment:
      ARANGO_ROOT_PASSWORD: $ARANGO_ROOT_PASSWORD
    ports:
      - ${ARANGODB_PORT}:8529
    volumes:
      - arangodb-data:/var/lib/arangodb3
      - arangodb-app-data:/var/lib/arangodb3-apps

  adminer:
    image: adminer:${ADMINER_TAG}
    container_name: ${PROJECT_NAME}-adminer
    hostname: adminer
    restart: unless-stopped
    stop_grace_period: 10s
    env_file: .env
    ports:
      - ${ADMINER_PORT}:8080

  portainer:
    image: portainer/portainer-ce:${PORTAINER_TAG}
    container_name: ${PROJECT_NAME}-portainer
    hostname: portainer
    command: -H unix:///var/run/docker.sock
    restart: unless-stopped
    stop_grace_period: 10s
    env_file: .env
    ports:
      - ${PORTAINER_PORT}:9000
    volumes:
      - /var/run/docker.sock:/var/run/docker.sock
      - portainer-data:/data

  cloudbeaver:
    image: dbeaver/cloudbeaver:${CLOUDBEAVER_TAG}
    container_name: ${PROJECT_NAME}-cloudbeaver
    hostname: cloudbeaver
    restart: always
    stop_grace_period: 10s
    ports:
      - ${CLOUDBEAVER_PORT}:8978
    volumes:
      - cloudbeaver-data:/opt/cloudbeaver/workspace

  metabase:
    image: metabase/metabase:${METABASE_TAG}
    container_name: ${PROJECT_NAME}-metabase
    hostname: metabase
    restart: unless-stopped
    stop_grace_period: 10s
    env_file: .env
    environment:
      MB_DB_TYPE: postgres
      MB_DB_HOST: postgres
      MB_DB_PORT: 5432
      MB_DB_PASS: $DB_PASSWORD
      MB_DB_DBNAME: $DB_NAME
      MB_DB_USER: $DB_USER
      MB_DB_FILE: /metabase-data/metabase.db
    ports:
      - ${METABASE_PORT}:3000
    volumes:
      - metabase-data:/metabase-data

  redis:
    image: redis:${REDIS_TAG}
    container_name: ${PROJECT_NAME}-redis
    hostname: redis
    restart: always
    stop_grace_period: 10s
    ports:
      - ${REDIS_PORT}:6379

  mailhog:
    image: mailhog/mailhog:${MAILHOG_TAG}
    container_name: ${PROJECT_NAME}-mailhog
    hostname: mailhog
    restart: always
    stop_grace_period: 10s
    ports:
      - ${MAILHOG_SMTP_PORT}:1025
      - ${MAILHOG_HTTP_PORT}:8025

  elasticsearch:
    image: elasticsearch:${ELASTICSEARCH_TAG}
    container_name: ${PROJECT_NAME}-elasticsearch
    hostname: elasticsearch
    restart: always
    stop_grace_period: 10s
    environment:
      discovery.type: single-node
      ES_JAVA_OPTS: -Xms1g -Xmx1g
      xpack.security.enabled: false
    volumes:
      - elasticsearch-data:/usr/share/elasticsearch/data
    ports:
      - ${ELASTICSEARCH_PORT}:9200

  kibana:
    image: kibana:${KIBANA_TAG}
    container_name: ${PROJECT_NAME}-kibana
    hostname: kibana
    restart: always
    stop_grace_period: 10s
    ports:
      - ${KIBANA_PORT}:5601
      
networks:
  default:
    name: $PROJECT_NAME
    driver: bridge
    
volumes:
  postgres-data: {}
  minio-data: {}
  portainer-data: {}
  arangodb-data: {}
  arangodb-app-data: {}
  cloudbeaver-data: {}
  metabase-data: {}
  elasticsearch-data: {}