
===========================================================
25.1 Galaxy Release (December 2025)
===========================================================

.. include:: _header.rst

Please see the `25.1 user release notes <25.1_announce_user.html>`__ for a summary of new user features.
The `GitHub Release Notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ provide a comprehensive overview of all changes.

Get Galaxy
===========================================================

The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.

To get a new Galaxy repository run:
  .. code-block:: shell

      $ git clone -b release_25.1 https://github.com/galaxyproject/galaxy.git

To update an existing Galaxy repository run:
  .. code-block:: shell

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

See the `community hub <https://galaxyproject.org/develop/source-code/>`__ 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 <https://github.com/galaxyproject/galaxy/pull/20974>`__. 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 <https://github.com/galaxyproject/galaxy/pull/21133>`__.
  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:

  * `Galaxy Monitoring with Telegraf and Grafana <https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html>`__
  * `Galaxy Monitoring with gxadmin <https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/tutorial.html>`__

**Deprecation of Python 3.9 support in Galaxy release 26.0**
  Since Python 3.9 reached its end-of-life in October 2025, support for it will
  be removed in Galaxy 26.0.
  Administrators should upgrade their Python environment to version 3.10 or
  higher to avoid security vulnerabilities and ensure a smooth transition to
  Galaxy 26.0 and beyond.

Release Team
===========================================================

Release manager:  `Ahmed Awan <https://github.com/ahmedhamidawan>`__, `Aysam Guerler <https://github.com/guerler>`__

Release testing:

* `Tyler Collins <https://github.com/tcollins2011>`__
* `Arash Kadkhodaei <https://github.com/arash77>`__
* `John Chilton <https://github.com/jmchilton>`__
* `Keith Suderman <https://github.com/ksuderman>`__
* `Aysam Guerler <https://github.com/guerler>`__
* `Alireza Heidari <https://github.com/itisAliRH>`__
* `Jennifer Hillman-Jackson <https://github.com/jennaj>`__

Communications:

* `Natalie Whitaker-Allen <https://github.com/natalie-wa>`__
* `Scott Cain <https://github.com/scottcain>`__

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

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.. include:: _thanks.rst
