Merge branch 'update-dev-with-upstream-interactive-tool-updates' into 'dev'

  gx_it_proxy:

    enable: true

    port: 4002

  #handlers:

  #  handler:

  #    processes: 3

  #    pools:

  #      - job-handlers

  #      - workflow-schedulers

galaxy:

  interactivetools_enable: true

  interactivetools_map: database/interactivetools_map.sqlite

  # outputs_to_working_directory will provide you with a better level of isolation. It is highly recommended to set

  # this parameter with InteractiveTools.

  outputs_to_working_directory: true

  interactivetools_map: database/interactivetools_map.sqlite

  # `galaxy_infrastructure_url` needs to be reachable from IT containers.

  # For local development you can map arbitrary hostnames. See `job_conf.xml.interactivetools`

  # For local development you can map arbitrary hostnames. See `job_conf.yml.interactivetools`

  # for an example.

  # In the local development case you should use the `http` protocol (e.g http://localhost:8080) to access

  # your Galaxy, so saving notebooks doesn't fail due to invalid certificates.

  galaxy_infrastructure_url: http://localhost:8080

  # Do not set the following 2 options if you are using an upstream proxy server like nginx

  interactivetools_upstream_proxy: false

  interactivetools_proxy_host: localhost:4002

## 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

## 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

:Type: str

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

``interactivetools_shorten_url``

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

:Description:

    Shorten the uuid portion of the subdomain or path for interactive

    tools. Especially useful for avoiding the need for wildcard

    certificates by keeping subdomain under 63 chars

:Default: ``false``

:Type: bool

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

``retry_interactivetool_metadata_internally``

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

```

In this example 4 processes will be started in total:

3 processes will act as job handlers and workflow schedulers, and one process will be dedicated to handling jobs for the `special` tag only. With the `job_conf.xml` configuration above these would be jobs created by the `test1` tool.

You can omit the `pools` argument, this will then default to:

```yaml

        ...

        pools:

          - job-handlers

          - workflow-schedulers

        ...

```

3 processes will act as job handlers and workflow schedulers, and one process will be dedicated to handling jobs for the 

`special` tag only. With the `job_conf.xml` configuration above these would be jobs created by the `test1` tool.

If you omit the `processes` argument this will default to a single process.

You can further customize the handler names using the `name_template` section,