Loading config/job_conf.yml.interactivetools 0 → 100644 +58 −0 Original line number Diff line number Diff line ## 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 No newline at end of file config/job_conf.yml.interactivetools.podman 0 → 100644 +38 −0 Original line number Diff line number Diff line ## 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 No newline at end of file Loading
config/job_conf.yml.interactivetools 0 → 100644 +58 −0 Original line number Diff line number Diff line ## 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 No newline at end of file
config/job_conf.yml.interactivetools.podman 0 → 100644 +38 −0 Original line number Diff line number Diff line ## 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 No newline at end of file