docker-compose.yml

#  Postgres backend for the legacy OmniPath server (omnipath-server).
#
#  The legacy API loads the build's `omnipath_webservice_*.tsv[.gz]` outputs plus
#  `licenses.tsv` into this database and serves them over HTTP. This compose
#  brings up only the database; the Sanic app is run separately (e.g. via
#  `scripts/run-in-production.py`, pointed at this DB).
#
#  All settings are overridable from a `.env` file next to this compose; the
#  defaults below are generous so the ~2 GB interactions / annotations tables
#  load and serve comfortably.
#
#    cp .env.example .env   # then edit POSTGRES_PORT / password as needed
#    docker compose up -d

services:
  db:
    image: postgres:16
    container_name: ${COMPOSE_PROJECT_NAME:-omnipath-server}-db
    restart: unless-stopped
    environment:
      POSTGRES_DB: ${POSTGRES_DB:-omnipath}
      POSTGRES_USER: ${POSTGRES_USER:-omnipath}
      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:-omnipath123}
    ports:
      - "127.0.0.1:${POSTGRES_PORT:-5486}:5432"
    #  Docker defaults /dev/shm to 64 MB, too small for large parallel-query
    #  shared-memory segments; bump it.
    shm_size: ${POSTGRES_SHM_SIZE:-2gb}
    #  Generous memory tuning for loading + serving the large interactions and
    #  annotations tables. Override per host via .env.
    command:
      - postgres
      - -c
      - shared_buffers=${POSTGRES_SHARED_BUFFERS:-4GB}
      - -c
      - effective_cache_size=${POSTGRES_EFFECTIVE_CACHE_SIZE:-12GB}
      - -c
      - work_mem=${POSTGRES_WORK_MEM:-512MB}
      - -c
      - maintenance_work_mem=${POSTGRES_MAINTENANCE_WORK_MEM:-2GB}
      - -c
      - max_wal_size=${POSTGRES_MAX_WAL_SIZE:-8GB}
      - -c
      - min_wal_size=1GB
      - -c
      - checkpoint_timeout=15min
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U ${POSTGRES_USER:-omnipath} -d ${POSTGRES_DB:-omnipath}"]
      interval: 5s
      timeout: 5s
      retries: 20
    volumes:
      - pgdata:/var/lib/postgresql/data

volumes:
  pgdata: