25.1 Galaxy Release (December 2025)

Please see the 25.1 user release notes for a summary of new user features. The GitHub Release Notes provide a comprehensive overview of all changes.

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_25.1 https://github.com/galaxyproject/galaxy.git

To update an existing Galaxy repository run:

$ git fetch origin && git checkout release_25.1 && git pull --ff-only origin release_25.1

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

Admin Notes

Database Migrations will require stopping the Galaxy instance: This release includes database migrations that require the Galaxy instance to be stopped before applying the update. Please plan accordingly to minimize downtime for users.

Configuration Changes

Added

The following configuration options are new

config/galaxy.yml.sample:galaxy

mapping.galaxy.mapping.allow_local_account_creation
mapping.galaxy.mapping.citation_bibtex
mapping.galaxy.mapping.disable_local_accounts
mapping.galaxy.mapping.enable_tool_generated_tours
mapping.galaxy.mapping.oidc_auth_pipeline
mapping.galaxy.mapping.oidc_auth_pipeline_extra

Removed

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy

mapping.galaxy.mapping.allow_user_creation
mapping.galaxy.mapping.enable_tool_document_cache

Deprecation Notices

Deprecation of the Trackster Visualization in Galaxy release 26.0

The legacy Trackster genome browser visualization has been deprecated and will be completely removed in Galaxy 26.0. This includes the removal of special handling for Trackster across tool execution, toolbox filtering, visualization framework features, controller endpoints, client code, and other conditional logic. With the removal of Trackster, the era of Mako-based visualizations served from controller endpoints ends. Galaxy now provides the modern IGV (Integrative Genomics Viewer) as the primary genome browser visualization, offering superior functionality and performance for genomic data exploration.

Deprecation of Mako-based visualizations in Galaxy release 26.0

With the removal of Trackster in 26.0, the remaining legacy Mako-based visualization framework and controller endpoints are deprecated and will be completely removed in Galaxy 26.0. Any remaining Mako-based visualizations should be migrated to the modern script-based visualization plugin framework. Users and administrators are encouraged to transition to supported visualization plugins to ensure continued functionality and access to new features.

Deprecation of the Galaxy Reports application in Galaxy release 26.0

The standalone Galaxy Reports application, which provides administrative usage statistics and analytics for Galaxy instances, is deprecated and will be removed in Galaxy 26.0. The Reports app was a separate web application that connected to the Galaxy database to display information about jobs, workflows, users, and system usage. Administrators currently using the Reports app should plan to migrate to alternative monitoring and analytics solutions before Galaxy 26.0 is released next year. The following GTN tutorials provide guidance on alternative monitoring approaches:

Release Team

Release manager: Ahmed Awan, Aysam Guerler

Release testing:

Communications:

A special thank you goes to everyone who helped test the new release after its deployment on usegalaxy.org.

To stay up to date with Galaxy’s progress, watch our screencasts; visit our community Hub; and follow us on Bluesky, Mastodon, and LinkedIn.

You can always chat with us on Matrix.

Thanks for using Galaxy!

The Galaxy Team