docker-compose.yml

name: predomics

services:
  db:
    image: postgres:16-alpine
    container_name: predomics-db
    environment:
      POSTGRES_USER: predomics
      POSTGRES_PASSWORD: predomics
      POSTGRES_DB: predomics
    volumes:
      - pg-data:/var/lib/postgresql/data
    ports:
      - "5433:5432"
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U predomics"]
      interval: 5s
      timeout: 3s
      retries: 5

  app:
    container_name: predomics-web
    build:
      context: .
      dockerfile: Dockerfile
    ports:
      - "8001:8000"
    volumes:
      - app-data:/app/data
    environment:
      - PREDOMICS_DATA_DIR=/app/data
      - PREDOMICS_UPLOAD_DIR=/app/data/uploads
      - PREDOMICS_PROJECT_DIR=/app/data/projects
      - PREDOMICS_SAMPLES_DIR=/app/samples
      - PREDOMICS_SAMPLE_DIR=/app/samples/qin2014_cirrhosis
      - PREDOMICS_DATABASE_URL=postgresql+asyncpg://predomics:predomics@db:5432/predomics
      - PREDOMICS_SECRET_KEY=change-me-in-production
    depends_on:
      db:
        condition: service_healthy
    restart: unless-stopped

  # ---------------------------------------------------------------------------
  # Optional: scitq distributed task queue (uncomment to enable)
  # Set PREDOMICS_SCITQ_SERVER=scitq-server:5000 in the app environment above
  # ---------------------------------------------------------------------------
  # scitq-server:
  #   image: gmtscience/scitq-server:latest
  #   container_name: predomics-scitq-server
  #   ports:
  #     - "5000:5000"
  #   restart: unless-stopped
  #
  # scitq-worker:
  #   image: predomics-app:latest
  #   container_name: predomics-scitq-worker
  #   volumes:
  #     - app-data:/app/data
  #   environment:
  #     - SCITQ_SERVER=scitq-server
  #   depends_on:
  #     - scitq-server
  #   restart: unless-stopped

volumes:
  app-data:
  pg-data: