===========================================================
26.1 Galaxy Release (July 2026)
===========================================================

.. include:: _header.rst

Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v26.1.0>`__ for more details.

Highlights
===========================================================

Discover some of the exciting new features, enhancements, and improvements in Galaxy 26.1.

Galaxy Notebooks
----------------

Turn every Galaxy history into a living scientific notebook.

- **Unified workspace**. Combine narrative, datasets, visualizations, and AI-assisted writing in a single collaborative space.
- **Document as you go**. Capture the reasoning behind your analysis and record results while you work.
- **Reproducible reports**. Create rich reports that stay connected to the data they describe.
- **Assistant on hand**. GalaxyAI works inside a notebook with that notebook's own context, drafting and proposing content in place.

Galaxy Notebooks make it easy to capture, share, and reproduce the full story behind an analysis.
[`#22361 <https://github.com/galaxyproject/galaxy/pull/22361>`__]
[`#22807 <https://github.com/galaxyproject/galaxy/pull/22807>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/B7rQQ-4kjAk" title="Galaxy 26.1 - Galaxy Notebooks" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

GalaxyAI: Specialized Agents and Context-Aware Help
---------------------------------------------------

GalaxyAI now knows where you are and routes your question to the right specialist.

- **Context-aware panel**. A dockable assistant that knows which tool form, job, history, or notebook you are viewing.
- **Specialized agents**. Purpose-built agents for error analysis, tool recommendations, GTN tutorials, and IWC workflows.
- **Asks instead of guessing**. Ambiguous requests get a clarifying question with quick replies.
- **Report drafting**. Draft a workflow invocation report from the run itself.
- **Safer custom tools**. The custom tool agent resolves verified containers rather than inventing one.

Each answer is labeled with the agent that produced it.
[`#22096 <https://github.com/galaxyproject/galaxy/pull/22096>`__]
[`#22097 <https://github.com/galaxyproject/galaxy/pull/22097>`__]
[`#22791 <https://github.com/galaxyproject/galaxy/pull/22791>`__]
[`#21934 <https://github.com/galaxyproject/galaxy/pull/21934>`__]
[`#22981 <https://github.com/galaxyproject/galaxy/pull/22981>`__]

Connect Your Own AI Tools with MCP
----------------------------------

Galaxy now speaks the Model Context Protocol, so AI clients outside Galaxy can work with your data.

- **Bring your own client**. Any MCP-compatible client can connect to a Galaxy server.
- **Real Galaxy operations**. Search and run tools, inspect histories and datasets, invoke workflows, and monitor jobs.
- **Community workflows**. Find and import vetted Intergalactic Workflow Commission (IWC) workflows without leaving your client.
- **Same rules as any client**. External agents route through Galaxy's service layer, inheriting the same authorization and validation.
- **Administrator opt-in**. Disabled by default; enabled with ``enable_mcp_server``.

The same operations layer powers GalaxyAI in the application, so both surfaces stay in step.
[`#21942 <https://github.com/galaxyproject/galaxy/pull/21942>`__]
[`#22626 <https://github.com/galaxyproject/galaxy/pull/22626>`__]
[`#22906 <https://github.com/galaxyproject/galaxy/pull/22906>`__]

Bulk Dataset Storage Migration
------------------------------

Managing storage at scale just got much easier.

- **Bulk moves**. Move multiple datasets and collections between storage locations in a single operation.
- **Preview the impact**. Review what will change before you begin.
- **Progress tracking**. Follow migrations from start to finish with detailed status updates.
- **Optional notifications**. Get notified when large migrations complete.

These improvements make large storage migrations safer, simpler, and more transparent.
[`#22606 <https://github.com/galaxyproject/galaxy/pull/22606>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/1irTcAI4yW8" title="Galaxy 26.1 - Bulk Dataset Storage Migration" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

Modern Workflow Extraction Interface
------------------------------------

The history-to-workflow extraction interface has been rebuilt in Vue with a modern card-based design.

- **Clear step distinction**. Tool steps and workflow inputs are clearly separated.
- **Rename before extraction**. Give inputs meaningful names before the workflow is created.
- **Direct job access**. Open related jobs directly from the extraction view.
- **Immediate results**. The newly created workflow is displayed as soon as extraction finishes.

Extracting a workflow from your history is now clearer and more intuitive.
[`#21935 <https://github.com/galaxyproject/galaxy/pull/21935>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/NFUxEZeBnlw" title="Galaxy 26.1 - Modern Workflow Extraction Interface" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

Favorite and Recent Tools Panel
-------------------------------

Galaxy now includes an optional tool panel focused on faster access to the tools you use the most.

- **Favorites at hand**. Highlight and quickly access your favorite tools.
- **Automatic recents**. Recently executed tools are automatically tracked.
- **Keyboard navigation**. Move through the panel without leaving the keyboard.
- **Integrated search**. Search tools with quick favorite and unfavorite actions.
- **Guided discovery**. When no favorites are configured, the panel helps you discover and organize tools through the redesigned tool discovery interface.

The result is faster, more personalized access to your everyday tools.
[`#21600 <https://github.com/galaxyproject/galaxy/pull/21600>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/LWiEQpuNJFY" title="Galaxy 26.1 - Favorite and Recent Tools Panel" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

View Workflow Step Configuration During Execution
-------------------------------------------------

No more switching back to the workflow editor to inspect a running workflow.

- **In-context inspection**. View the full configuration of any workflow step directly from the invocation graph.
- **Understand settings at a glance**. See tool settings, inputs, and parameters while an analysis runs.
- **Stay in the monitor**. Review step details without interrupting execution.

Monitoring a running workflow is now more transparent and informative.
[`#22144 <https://github.com/galaxyproject/galaxy/pull/22144>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/k8O4JAbmB50" title="Galaxy 26.1 - View Workflow Step Configuration During Execution" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

----

Visualizations Updates
===========================================================

.. visualizations
* Update locuszoom package version to 0.0.9
  (thanks to `@elmedjadjirayane <https://github.com/elmedjadjirayane>`__).
  `Pull Request 21658`_
* Update Vintent
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 22660`_
* Update tiffviewer to v0.0.5
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 22866`_
* Fix table header column handling in plotly and tabulator
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 22893`_

Datatypes Updates
===========================================================

.. datatypes
* Add bwa_index datatype
  (thanks to `@Delphine-L <https://github.com/Delphine-L>`__).
  `Pull Request 22310`_
* adding egapx_local_cache, a subclass of Directory
  (thanks to `@richard-burhans <https://github.com/richard-burhans>`__).
  `Pull Request 22268`_
* Show file size for CRAM datasets and in download tooltip
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 22273`_
* Merge 26.0 into dev
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 22368`_
* Added file type ascii raster .asc
  (thanks to `@tStehling <https://github.com/tStehling>`__).
  `Pull Request 21937`_
* Fix display of BAMs with large headers
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 22516`_
* Speed up integration tests
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 22538`_
* add TEI XML datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 22718`_
* Harden access control for user-defined tools
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 22704`_
* Add sheet_names metadata to XLSX datatype
  (thanks to `@Anthony96pi <https://github.com/Anthony96pi>`__).
  `Pull Request 22327`_
* update the binary.py for spatialdata so it also works if the file has…
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 22802`_
* Migrate Python packages to \`src\` layout and pure namespace packages
  (thanks to `@mr-c <https://github.com/mr-c>`__).
  `Pull Request 21977`_
* Add new datatypes for the tool vg giraffe
  (thanks to `@Maed0x <https://github.com/Maed0x>`__).
  `Pull Request 22935`_
* update spatialdata datatype
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 23087`_
* Bound memory use in h5grove structured content endpoint
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 23089`_
* Add new datatypes for the tool vg
  (thanks to `@Maed0x <https://github.com/Maed0x>`__).
  `Pull Request 23111`_
* Add PAGE XML, AbbyyXML, hOCR, mlmodel, Apache Arrow IPC datatype support in datatypes_conf.xml.sample
  (thanks to `@IvoLeist <https://github.com/IvoLeist>`__).
  `Pull Request 23088`_
* Hide generated headers for tabular previews
  (thanks to `@qchiujunhao <https://github.com/qchiujunhao>`__).
  `Pull Request 22947`_

Builtin Tool Updates
===========================================================

.. tools
* First pass in unifying and clarifying collection operation interfaces and help sections
  (thanks to `@nekrut <https://github.com/nekrut>`__).
  `Pull Request 21939`_
* Fix tool id handling for shed-installed tools
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 22553`_
* Update label for invert parameter in grep.xml for clarity
  (thanks to `@Sch-Da <https://github.com/Sch-Da>`__).
  `Pull Request 22550`_
* patch bar_chart
  (thanks to `@gsaudade99 <https://github.com/gsaudade99>`__).
  `Pull Request 22597`_
* Fix recent tools for My Tools default panel
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 23075`_
* Fix discover tool count fallback for My Tools default panels
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 23074`_
* Fix Markdown help rendering in tools list
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 23106`_

Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v26.1.0>`__ for more details.
The admin-facing release notes are available :doc:`here <26.1_announce>`.

.. include:: 26.1_prs.rst

----

.. include:: _thanks.rst