January 2022 Galaxy Release (v 22.01)

Get Galaxy

Highlights

Galaxy starts as FastAPI application by default

Starting Galaxy via run.sh will use the new gravity process manager. The new configuration uses gunicorn and FastAPI to drive Galaxy’s web process and starts job handler and Celery processes automatically. For more details and instructions please consult the Migrating to Gunicorn documentation. (Pull Request 13224).

User Preferences can be encrypted in Galaxy Vault

Galaxy can now be configured to store secrets in an external vault, which is useful for secure handling and centralization of secrets management. In particular, information fields in the “Manage information” section of the user profile, such as dropbox keys, can be configured to be encrypted at rest in a vault (Hashicorp, Custos or database) instead of being stored as plain text in the user preferences table. For detailed information on configuration, refer to the vault section of the admin documentation. (Pull Request 12940).

Resumable uploads via tus.io, improved upload provenance

Galaxy now supports chunked and resumable uploads via the tus protocol. This is more performant and easier to setup than the current nginx-based solutions. For detailed configuration instructions, see the documentation. Galaxy now displays all manipulations that were performed during an upload, such as newline conversions, converting spaces to tabs or dataset grooming. (Pull Request 12656, Pull Request 12861, Pull Request 13313, Pull Request 12912).

Also check out the 22.01 user release notes

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_22.01 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_22.01 && git pull --ff-only origin release_22.01

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

Deprecation Notices

PostgreSQL 9.x is now EOL and is no longer supported. Please upgrade to PostgreSQL 10 or higher. Python 3.6 is officially EOL and Galaxy no longer tests or maintains compatibility. This release will be the last Galaxy release that can run under Paste or uWSGI. Please consult the Migrating to Gunicorn documentation for . instructions on how to upgrade.

Configuration Changes

Added

The following configuration options are new

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.enable_tool_source_display

  • mapping.galaxy.mapping.galaxy_url_prefix

  • mapping.galaxy.mapping.load_tool_shed_datatypes

  • mapping.galaxy.mapping.max_discovered_files

  • mapping.galaxy.mapping.maximum_upload_file_size

  • mapping.galaxy.mapping.tool_evaluation_strategy

  • mapping.galaxy.mapping.tus_upload_store

  • mapping.galaxy.mapping.vault_config_file

Changed

The following configuration options have been changed

config/galaxy.yml.sample:galaxy

  • mapping.reports.mapping.file_path.default has changed from

    database/files
    

    to

    database/objects
    

Removed

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.check_migrate_tools

  • mapping.galaxy.mapping.enable_openid

  • mapping.galaxy.mapping.force_beta_workflow_scheduled_for_collections

  • mapping.galaxy.mapping.force_beta_workflow_scheduled_min_steps

  • mapping.galaxy.mapping.openid_consumer_cache_path

Release Notes

Enhancements

Fixes

To stay up to date with Galaxy’s progress watch our screencasts, visit our community hub, and follow @galaxyproject on Twitter.

You can always reach us on Gitter or IRC.

Thanks for using Galaxy!

The Galaxy Team