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Remove superfluous pulsar embedded config
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dometto committed Oct 1, 2024
1 parent aae625c commit 2046a52
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1 change: 0 additions & 1 deletion README.md
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Expand Up @@ -35,7 +35,6 @@ The component takes the following parameters:
* `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_pulsar_embedded`: Boolean (default: `true`). Runs any Docker jobs with the 'Pulsar Embedded' runner, which provides better data isolation (without it, [Docker containers have access to the entire data directory](https://training.galaxyproject.org/training-material/topics/admin/tutorials/interactive-tools/tutorial.html#securing-interactive-tools)). However, this causes another performance hit: job data needs to be copied to the container.
* `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_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:
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4 changes: 0 additions & 4 deletions vars/galaxy_vars.yml
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Expand Up @@ -31,10 +31,6 @@ postgresql_objects_users:
postgresql_objects_databases:
- name: galaxy
owner: galaxy
pulsar_embedded_runner:
load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
workers: 2
pulsar_config: "{{ galaxy_config_dir }}/pulsar_app.yml"
galaxy_configuration:
galaxy:
use_remote_user: true
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1 change: 0 additions & 1 deletion vars/src_galaxy_vars.yml
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Expand Up @@ -13,7 +13,6 @@ _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_pulsar_embedded: "{{ src_galaxy_pulsar_embedded | default(_galaxy_use_interactive_tools, true) | bool }}"

# 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 ['']
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