Commit 42743743 authored by Sveinung Gundersen's avatar Sveinung Gundersen Committed by Cage, Gregory
Browse files

Added simple job_conf.yml files for interactive tools, including config for Podman

parent 41d96c94
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## A sample job config for InteractiveTools using local runner. ##

runners:
  local:
    load: galaxy.jobs.runners.local:LocalJobRunner
    workers: 4

# Uncomment if dynamic handlers are defined in "gravity:handlers" section in galaxy.yml
#
#handling:
#  assign:
#    - db-skip-locked

execution:
  default: docker_dispatch
  environments:
    local:
      runner: local

    docker_local:
      runner: local
      docker_enabled: true
      #docker_volumes: $defaults,/mnt/galaxyData/libraries:ro,/mnt/galaxyData/indices:ro
      #docker_volumes_from: parent_container_name
      #docker_memory: 24G
      #docker_sudo: false
      #docker_sudo_cmd: /usr/bin/sudo -extra_param
      #docker_net: bridge
      #docker_auto_rm: true
      #docker_set_user: $UID
      docker_set_user:

      # InteractiveTools do need real hostnames or URLs to work - simply specifying IPs will not work.
      # If you develop interactive tools on your 'localhost' and don't have a proper domain name
      # you need to tell all Docker containers a hostname where Galaxy is running.
      # This can be done via the add-host parameter during the `docker run` command.
      # 'localhost' here is an arbitrary hostname that matches the IP address of your
      # Galaxy host. Make sure this hostname ('localhost') is also set in your galaxy.yml file, e.g.
      # `galaxy_infrastructure_url: http://localhost:8080`.
      #docker_run_extra_arguments: add-host localhost:host-gateway

      #docker_cmd: /usr/local/custom_docker/docker
      #docker_host:
      #docker_container_id_override: busybox:ubuntu-14.04
      #docker_default_container_id: busybox:ubuntu-14.04
      #require_container: true
      #container_monitor: true
      #container_monitor_result: file
      #container_monitor_command: python /path/to/galaxy/lib/galaxy_ext/container_monitor/monitor.py
      #container_monitor_get_ip_method: null
      #container_resolvers_config_file: null
      #container_resolvers:

    docker_dispatch:
      runner: dynamic
      type: docker_dispatch
      docker_destination_id: docker_local
      default_destination_id: local
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## A sample job config for InteractiveTools using local runner, configured for Podman ##

runners:
  local:
    load: galaxy.jobs.runners.local:LocalJobRunner
    workers: 4

# Uncomment if dynamic handlers are defined in "gravity:handlers" section in galaxy.yml
#
#handling:
#  assign:
#    - db-skip-locked

execution:
  default: docker_dispatch
  environments:
    local:
      runner: local

    docker_local:
      runner: local
      docker_enabled: true

      docker_set_user:

      # For containers running as root (on the inside)
      docker_run_extra_arguments: --security-opt label=disable
      # Should work for containers with non-root user (on the inside)
      #docker_run_extra_arguments:  --userns=keep-id --security-opt label=disable

      # Change to home directory of the galaxy user, not the directory of the galaxy installation
      docker_cmd: HOME="/home/galaxy"; podman

    docker_dispatch:
      runner: dynamic
      type: docker_dispatch
      docker_destination_id: docker_local
      default_destination_id: local
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