Dispatch only interactive tools to docker by default

README.md

@@ -34,8 +34,8 @@ The component takes the following parameters:
 * `src_galaxy_version`: String. Set to e.g. `23.2` (default) to control the version of Galaxy that will be installed.
 * `src_galaxy_api_exposed`: Boolean. if `true` (default), the `/api` route does not require authentication via Single Sign-On.
 * `src_ibridges`: Boolean (default: `true`). Whether to enable support for the [iBridges](https://github.com/UtrechtUniversity/galaxy-tools-ibridges) tool for connecting to Yoda and iRODS instances. Implies `src_galaxy_bootstrap`, and adds iBridges to the list of tools to be installed automatically.
-* `src_galaxy_jobs_docker`: Boolean. Enables Galaxy support for running jobs in Docker containers. Any jobs that *can* be run in a docker container will be---jobs that cannot will be run in the default manner (in a `conda` env). Runnings jobs in a container may be slower than running them locally, so consider turning this feature off if not needed.
-* `src_galaxy_interactive_tools`: if `true` (default), support for [interactive tools](https://docs.galaxyproject.org/en/master/admin/special_topics/interactivetools.html) is enabled. **Note**: this implies *src_galaxy_jobs_docker*, and the accompanying performance hits.
+* `src_galaxy_jobs_default`: String. What runner to use for jobs by default. Valid values: `singularity`, `docker`, `local`.
+* `src_galaxy_interactive_tools`: if `true` (default), support for [interactive tools](https://docs.galaxyproject.org/en/master/admin/special_topics/interactivetools.html) is enabled.
 * `src_galaxy_co_admin_group`: String group corresponding to an SRAM group. Members of this SRAM group will be made Galaxy admin users.
 * `src_galaxy_bootstrap`: if `true` (default), will attempt to install workflows, dataproviders and tools as configured by the following options:
     * `src_galaxy_tool_files`: String of comma-separated paths to YAML files (in this repo) containing tool specifications.

galaxysrv.yml

@@ -26,7 +26,7 @@
 
   roles:
     - role: geerlingguy.docker
-      when: not _molecule_active and _galaxy_jobs_docker
+      when: not _molecule_active and _galaxy_enable_docker
     - role: uusrc.general.nginx_reverse_proxy
       vars:
         nginx_reverse_proxy_locations: "{{ galaxy_nginx_vhost_config }}"

tasks/interactive_tools.yml

@@ -14,3 +14,8 @@
     path: "{{ galaxy_config_dir }}/tool_conf.xml"
     regexp: '\s*<!--\s*\n.*(<section id="interactivetools" name="Interactive tools">[\d\D\n]*</section>)\n\s*-->'
     replace: '\n  \1'
+
+- name: Copy script to dynamically determine if a job should use Docker
+  ansible.builtin.template:
+    src: default_dispatch.py.j2
+    dest: "{{ galaxy_server_dir }}/lib/galaxy/jobs/rules/{{ _galaxy_default_dispatcher }}.py"

tasks/set_config.yml

@@ -5,6 +5,13 @@
 - name: Load component variables
   ansible.builtin.include_vars: vars/src_galaxy_vars.yml
 
+- name: Sanity check
+  block:
+    - name: Assert default handler is valid
+      ansible.builtin.assert:
+        that:
+          - "['singularity', 'docker', 'local'] is contains(_galaxy_jobs_default)"
+
 - name: Load interactive tools variables
   ansible.builtin.include_vars: vars/interactive_tools_vars.yml
 

templates/default_dispatch.py.j2

@@ -0,0 +1,8 @@
+from galaxy.jobs import JobDestination
+import os
+
+def {{ _galaxy_default_dispatcher }}(tool):
+  if tool.tool_type == 'interactive':
+    return 'docker'
+  else:
+    return '{{ _galaxy_jobs_default }}'

templates/galaxy/config/job_conf.yml.j2

@@ -4,23 +4,23 @@ runners:
     workers: 4
 
 execution:
-  default: docker_dispatch
+  default: {{ _galaxy_default_dispatcher if _galaxy_use_interactive_tools else _galaxy_jobs_default }}
   environments:
     local:
       runner: local
 
-    docker_local:
+    docker:
       runner: local
       docker_enabled: true
       docker_set_user:
       docker_sudo: false
 
-    docker_dispatch:
+{% if _galaxy_use_interactive_tools %}
+    {{ _galaxy_default_dispatcher }}:
       runner: dynamic
-      type: docker_dispatch
-      docker_destination_id: docker_local
-      default_destination_id: local
-
+      type: python
+      function: {{ _galaxy_default_dispatcher }}
+{% endif %}
 tools:
   - class: local # these special tools that aren't parameterized for remote execution - expression tools, upload, etc
     environment: local

vars/internal_vars.yml

@@ -20,6 +20,8 @@ _galaxy_local_address: localhost:8080
 
 galaxy_src_documentation: https://github.com/UtrechtUniversity/vre-docs
 
+_galaxy_default_dispatcher: default_dispatcher # function and file name for the dynamic job handler used by interactive tools
+
 # Variables for the docker role
 
 docker_install_compose: false

vars/src_galaxy_vars.yml

@@ -12,7 +12,8 @@ _galaxy_custom_repo_branch: "{{ src_galaxy_custom_repo_branch | default('main',
 _galaxy_api_exposed: "{{ src_galaxy_api_exposed | default(true, true) }}"
 _galaxy_use_interactive_tools: "{{ src_galaxy_interactive_tools | default(true, true) | bool }}"
 _galaxy_server_fqdn: "{{ workspace_fqdn | default('localhost', true) }}"
-_galaxy_jobs_docker: "{{ _galaxy_use_interactive_tools or (src_galaxy_jobs_docker | default(true, false) | bool )  }}"
+_galaxy_jobs_default: "{{ src_galaxy_jobs_default | default('local', true) }}"
+_galaxy_enable_docker: "{{ _galaxy_use_interactive_tools or (_galaxy_jobs_default == 'docker' )  }}"
 
 # Build the final lists of tool and workflow installation files
 _galaxy_tool_files: "{{ src_galaxy_tool_files | default('', true) | split(',') | select() + _galaxy_default_tool_files_list }}"  # select() necessary because split on the default '' yields ['']