docker-compose.override.yml-exomiser

# Docker Compose Override YAML fragment that provides a Exomiser REST
# Prioritiser.
#
# Quick Manual:
#
# - merge with docker-compose.override.yml
# - place configuration (from utils/exomiser) in the right plase
# - place data in the right place

# == Re-useable Definitions ==================================================

# Default service definition for all (incl. postgres/redis/...)
x-service-default: &service_default
  networks:
    - varfish
  restart: unless-stopped

# == Overide Definitions =====================================================

services:
  # -- Exomiser --------------------------------------------------------------
  #
  # We use the Exomiser REST Prioritizer for phenotype-based prioritization

  exomiser-rest-prioritiser:
    <<: *service_default
    image: "${image_exomiser__name-quay.io/biocontainers/exomiser-rest-prioritiser}:\
      ${image_exomiser__version-13.3.0--hdfd78af_0}"
    command:
      - "exomiser-rest-prioritiser"
      - "-Xmx6G"
      - "-Xms2G"
      - "-Dserver.address=0.0.0.0"
      - "-Dserver.port=80"
    volumes:
      - type: bind
        source: ${config_basedir:-./.dev/config}/exomiser/application.properties
        target: /application.properties
        read_only: true
      - type: bind
        source: ${volumes_basedir:-./.dev/volumes}/exomiser
        target: /data
        read_only: true