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May 2021 Galaxy Release (v 21.05)

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Highlights

New development stack

Galaxy release 21.09 will ship with a new web framework (FastAPI), Celery task queue and process management using Circus. You can preview new stack now by running APP_WEBSERVER=dev ./run.sh.

Celery for background tasks

Galaxy can now run certain tasks in the background. The Celery workers are currently not required, but if activated can perform certain long-running tasks, such as creating history export archives. Celery tasks will bridge the gap between rapid requests that can be handled during a web request and jobs that require extensive and relatively slow setup. (Pull Request 11789, Pull Request 11772, Pull Request 11720)

More robust selection of job handlers

Job throughput can be increased by starting Galaxy with multiple external job handler processes. Jobs were traditionally assigned to a job handler process by the web handler or workflow handler process that created the job. Since Release 19.01 Galaxy has supported additional mechanisms that use database serialization techniques to let job handlers assign processes to themselves. This mechanism is more robust and doesn’t require that all job handler processes be alive and known by the web handler process. Galaxy now determines the best method for assigning jobs based on the database in use, if the assignment method is not set explicitly. Older job assignment methods will be removed in Galaxy release 21.09. For more details see the Job Handler Assignment Methods section of the Galaxy documentation. ( Pull Request 11792)

Also check out the 21.05 user release notes

Deprecation Notices

Deprecation of support for PostgreSQL < 9.5

When using PostgreSQL as database server, Galaxy now requires PostgreSQL 9.5 or newer. Instructions for updating PostgreSQL can be found in the official documentation.

Upcoming Deprecation Notices

Deprecation of support for Python 3.6 in Galaxy release 21.09

This Galaxy release (21.05) will be the last release that supports Python 3.6 or newer. We encourage updating to a newer Python if possible.

Deprecation of uwsgi and paste

This Galaxy release (21.05) will be the last release that supports the WSGI standard, and with it uwsgi and paste. From release 21.09 Galaxy will be an ASGI application. We will update documentation and playbooks during the upcoming development cycle to enable a smooth transition.

Configuration Changes

Added

The following configuration options are new

config/user_preferences_extra_conf.yml.sample

  • preferences.dropbox

  • preferences.owncloud

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.cache_dir

  • mapping.galaxy.mapping.enable_celery_tasks

  • mapping.galaxy.mapping.flush_per_n_datasets

  • mapping.galaxy.mapping.matomo_server

  • mapping.galaxy.mapping.matomo_site_id

  • mapping.galaxy.mapping.plausible_domain

  • mapping.galaxy.mapping.plausible_server

  • mapping.galaxy.mapping.statsd_mock_calls

Changed

The following configuration options have been changed

config/user_preferences_extra_conf.yml.sample

  • preferences.localization.inputs has changed from

    [{'label': 'Prefered language',
  'name': 'locale',
  'options': [['Navigator default', 'auto'],
              ['Chinese', 'zh'],
              ['English', 'en'],
              ['French', 'fr'],
              ['Japanese', 'ja']],
  'required': False,
  'type': 'select'}]

    to

    [{'label': 'Prefered language',
  'name': 'locale',
  'options': [['Navigator default', 'auto'],
              ['中文', 'zh'],
              ['English', 'en'],
              ['Español', 'es'],
              ['Français', 'fr'],
              ['日本語', 'ja']],
  'required': False,
  'type': 'select'}]

Removed

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.transfer_manager_port

New Configuration Files

The following files are new, or recently converted to yaml

  • config/file_sources_conf.yml.sample

Get Galaxy

The code lives at GitHub and you should have Git to obtain it.

To get a new Galaxy repository run:
$ git clone -b release_21.05 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_21.05 && git pull --ff-only origin release_21.05

See the community hub for additional details on source code locations.

Release Notes

Enhancements

Fixes

To stay up to date with Galaxy’s progress, watch our screencasts, visit our community Hub, and follow @galaxyproject@mstdn.science on Mastodon or @galaxyproject on Twitter.

You can always chat with us on Matrix.

Thanks for using Galaxy!

The Galaxy Team