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

.. include:: _header.rst

Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ for more details.

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

Discover some of the exciting new features, enhancements, and improvements in Galaxy 25.1.

A Fresh, Modern History List Interface
--------------------------------------

Galaxy 25.1 introduces a redesigned history list that makes managing your histories more intuitive and
visually appealing.

- **Card-based design**. Histories are now displayed as clean, modern cards that provide better visual
  organization in a grid vs list view, as you prefer.
- **Enhanced information display**. Each history card shows key details at a glance, including 
  creation date, size, update time, and status indicators in a more structured layout.
- **Improved responsive design**. The new interface adapts better to different screen sizes and 
  provides a more consistent experience across devices.
- **Advanced keyboard navigation and selection**. Navigate through histories using arrow keys, 
  select multiple histories with Shift+click for range selection, and use keyboard shortcuts 
  for efficient bulk operations — available across multiple Galaxy list interfaces.

This update modernizes one of Galaxy's core interfaces, providing a cleaner and more user-friendly 
way to navigate your analysis history collection while adding powerful selection capabilities.
[`#20744 <https://github.com/galaxyproject/galaxy/pull/20744>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/1kPTyiEr3ks?si=OYLxFeyA82bZ13Xd" title="Galaxy 25.1 - A Fresh, Modern History List Interface" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

Smart Sample Sheets for Complex Workflow Inputs
-----------------------------------------------

Galaxy now supports **Sample Sheets** to simplify complex workflow inputs and data organization. This
feature allows you to import data from external spreadsheets (CSV, TSV, or Excel) and use them to
configure workflow parameters and organize datasets.

- **Spreadsheet-style data entry**. Define your experimental data using familiar spreadsheet interfaces
  with customizable columns for sample names, treatments, conditions, and file locations — whether
  datasets or remote URLs.
- **Workflow author-defined templates**. Workflow creators can pre-configure sample sheet templates
  with specific columns, validation rules, and helpful descriptions, guiding users through proper data
  organization.
- **Built into the Apply Rules tool**. Advanced users can leverage sample sheet data within the Apply
  Rules tool for sophisticated data manipulation and collection operations.
- **Integration within the Workflow Editor**. Configure workflows to accept sample sheet inputs
  directly from the Workflow Editor.

Sample Sheets are particularly useful for workflows that require multiple related inputs or when you
need to process batches of samples with associated metadata in a structured format.
[`#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/5sAjEABPh8M?si=sxIX6RV1LtUkH4xW" title="Galaxy 25.1 - Smart Sample Sheets for Complex Workflow Inputs" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

An Enhanced Tool Discovery View
-------------------------------

Galaxy 25.1 introduces a redesigned **Tool Discovery View** that replaces the previous advanced tool
search with a more powerful and intuitive tool exploration interface.

- **Dedicated Discovery Interface**. Advanced tool search has moved from the tool panel to a rich,
  dedicated center-panel view optimized for finding the right tools for your analysis.
- **Card-based Tool Display**. Tools are presented as visually appealing cards with key information,
  including EDAM ontology tags, descriptions, and links.
- **Tool Favorites and Sharing**. Easily add tools to your favorites for quick access, and share useful
  tools with colleagues via the copyable link feature.
- **EDAM Ontology Integration**. Browse and filter tools by EDAM (EMBRACE Data and Methods) ontologies
  to discover tools based on scientific domains and data types.

This new interface makes tool discovery more efficient and helps users find the most appropriate tools
for their specific analysis needs.
[`#20747 <https://github.com/galaxyproject/galaxy/pull/20747>`__]

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   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/7L_QjcwyBiw?si=gD8tGTr0BTzgv7rw" title="Galaxy 25.1 - Tool Discovery View" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

New Galaxy Charts Visualization Framework
-----------------------------------------

This release also introduces the **Galaxy Charts** framework, bringing enhanced visualizations and a
more powerful visualization experience to Galaxy users.

- **Improved Visualization Performance**. Enjoy faster loading times, smoother interactions, and more
  responsive visualizations built with modern web technologies for a better user experience.
- **Enhanced IGV.js Genome Browser**. Galaxy now includes a complete IGV.js (Integrative Genome Browser)
  integration for comprehensive genomic data visualization with multi-track support for BAM, VCF,
  BigWig, BED, GFF, GTF, and CRAM files.
- **Automatic Data Integration**. Visualizations now automatically connect to your Galaxy datasets and
  match reference genomes, eliminating manual configuration steps and making it easier to explore your
  data.
- **Expanded Visualization Library**. The new framework enables rapid deployment of cutting-edge
  visualizations, meaning Galaxy users will see more powerful visualization options in future releases.

*See the Admin Notes and Deprecation Notices sections* :doc:`here <25.1_announce>` *for more details on
the visualization framework and the removal of Trackster.*

**Featured Implementation: IGV.js Genome Browser**

Galaxy 25.1 ships with a complete IGV.js (Integrative Genome Browser) implementation built on the
Galaxy Charts framework, showcasing the platform's capabilities:

- **Multi-track Genomic Visualization**. View multiple tracks in various formats including BAM, VCF,
  BigWig, BED, GFF, GTF, and CRAM files with full support for indexed data and byte-range requests.
- **Automatic Genome Matching**. Automatically matches dataset database keys against available genomes,
  supporting both IGV-provided reference genomes and Galaxy-served genomes in 2bit and FASTA formats.
- **Interactive Exploration**. Full IGV.js functionality including zooming, panning, dynamic track
  configuration, and multi-sample comparisons for comprehensive genomic data analysis.

The Galaxy Charts framework represents a major advancement in Galaxy's visualization capabilities, 
making it easier than ever to create sophisticated, interactive visualizations while maintaining full
integration with Galaxy's data management and analysis ecosystem. Here's a look at the IGV.js addition:
[`#20943 <https://github.com/galaxyproject/galaxy/pull/20943>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/VC05IvZGPiU?si=tMVdiHS1d5yTOX06" title="Galaxy 25.1 - New Galaxy Charts Visualization Framework" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

A Place to Find your Recent Downloads in Galaxy
-----------------------------------------------

Galaxy 25.1 introduces a dedicated "Recent Exports & Downloads" page that lists your recent
exports/downloads.

- **Re-download available items**. Easily access and download files still available in the short-term
  storage cache.
- **Navigate to source objects**. Jump directly to the details page of the originating item (e.g.
  workflow invocation, history, etc.).

This improves the discoverability and accessibility of recent downloads without needing to track links
manually.
[`#20585 <https://github.com/galaxyproject/galaxy/pull/20585>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/NMeH_HWuMwA?si=ly9gCTQksghLwRf0" title="Galaxy 25.1 - A Place to Find your Recent Downloads in Galaxy" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

Visual Indicators for Short-Term Storage Expiration
---------------------------------------------------

Galaxy 25.1 introduces visual expiration indicators that help users identify when datasets and
collections are stored in temporary or short-term storage that will be automatically cleaned up.

- **Expiration warnings in history**. Datasets and collections now display countdown timers showing
  when they will expire, helping users plan data management and downloads before automatic cleanup.
- **Collection-aware indicators**. Smart detection across dataset collections shows the earliest
  expiration time when collections contain datasets from mixed storage types.
- **Admin-configurable expiration periods**. Administrators can set `object_expires_after_days` in
  object store configurations to match their actual cleanup schedules and inform users appropriately.

*Note that Galaxy instance administrators must set `object_expires_after_days` in their object store
configurations for these indicators to function correctly.*

This feature is particularly valuable for instances using scratch storage or temporary
high-performance storage tiers, as it gives users clear visibility into data lifecycle and helps
prevent unexpected data loss due to automatic cleanup processes.
[`#20332 <https://github.com/galaxyproject/galaxy/pull/20332>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/CytCTixQTY8?si=taaSIrbl_gM2QhUC" title="Galaxy 25.1 - Visual Indicators for Short-Term Storage Expiration" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

Galaxy Tools Now Handle Secrets and Authentication
--------------------------------------------------

Galaxy 25.1 implements a comprehensive tool credentials system, allowing tools to securely access
external services by defining authentication credentials (variables and secrets) in tool requirements
while keeping sensitive information separate from tool definitions.

- **Credential Definition in Tools**. Tools can define credential requirements using `<credentials>`
  elements within `<requirements>` with support for both variables (non-sensitive config like URLs,
  usernames) and secrets (sensitive data like passwords, API keys).
- **Secure Storage & Management**. Integration with Galaxy's vault system provides secure secret
  storage with user-specific credential isolation by tool and service, plus credential groups for
  organizing multiple credential sets.
- **REST API**. Complete CRUD operations enable credential management with user credential listing,
  group-based credential organization, and secure deletion with vault cleanup.
- **Frontend Integration**. Unified credential management UI appears for every tool with workflow-level
  credential status display, multi-tool credential coordination, and real-time credential validation
  and feedback.
- **Tool Execution Integration**. Automatic credential injection as environment variables with job
  context tracking for credential usage, supporting tool proxies and various tool types while
  maintaining backward compatibility.

This system provides secure credential management for tools that need to access external APIs,
databases, or cloud services, ensuring sensitive authentication information is properly protected
while making it easy for users to configure and manage their credentials across different tools and
workflows.
[`#19084 <https://github.com/galaxyproject/galaxy/pull/19084>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/2xEFtTS3DSk?si=TvG5EUBy96Otrt9T" title="Galaxy 25.1 - Tools Now Handle Secrets and Authentication" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

Search for Steps, Tools and Subworkflows within the Workflow Editor
-------------------------------------------------------------------

As with many improvements to the Workflow Editor in recent releases, Galaxy 25.1 adds the ability to
search for several properties of all elements in the workflow graph, displays the search results in a
list, and highlights them when clicked.
[`#20390 <https://github.com/galaxyproject/galaxy/pull/20390>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/Guma5nPqZ_8?si=BuQ2xkiCCULhV_Q5" title="Galaxy 25.1 - A Search in the Workflow Editor" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

A Redesign of your User Preferences
-----------------------------------

The User Preferences interface has been redesigned to enhance user experience through improved
navigation and a modernised interface.
[`#19658 <https://github.com/galaxyproject/galaxy/pull/19658>`__]

.. raw:: html

   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/vTjJtStlf9w?si=98P65gcBJP0xNDZA" title="Galaxy 25.1 - A Redesign of your User Preferences" 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
* [igv] Allow selection of genomes from history fasta/2bit
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21269`_
* Add Hyphy Vision Result Viewer
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21196`_
* Enable drag-and-drop of collection elements in IGV
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21173`_
* Update Javascript package licenses to MIT
  (thanks to `@mr-c <https://github.com/mr-c>`__).
  `Pull Request 20264`_
* Install Visualization plugins as self-contained packages
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20348`_
* Restore Nora
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20387`_
* Install visualizations directly to static path, avoid duplication
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20372`_
* Add rerun.io web viewer
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20202`_
* Update tiffviewer visualization to version 0.0.3
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20658`_
* Consolidate visualization mako, avoid user agent styles
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20760`_
* Enable data label column selection in basic Plotly plots and add heatmap
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20813`_
* Update JupyterLite version to 0.6.4
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20877`_
* Add Multiple Sequence Alignment Viewer 2.0
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20907`_
* Make jupyterlite default visualization for ipynb
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20931`_
* Fix JupyterLite History Identifier Retrieval Without Dataset
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20971`_
* Save IGV locus and improve error handling
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20996`_
* Bump vitessce to 3.8.2
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21003`_
* Fix and migrate HIV-TRACE to Charts Visualization Framework
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21006`_
* Add README and update the minimal visualization example
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21007`_
* Allow creation of visualizations without dataset
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20914`_
* Adds IGV.js Visualization
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20943`_

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

.. datatypes
* New datatype addition: HAL
  (thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
  `Pull Request 21379`_
* Add PNTS datatype for 3D Tiles Point Cloud
  (thanks to `@kgerb <https://github.com/kgerb>`__).
  `Pull Request 21414`_
* Backport fix anndata datatype update
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 21111`_
* Fix MIME type for LAZ datatype
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 21202`_
* Add SpatialData datatype
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 21000`_
* support ZARR v3 for  Spatialdata dt
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 21265`_
* Fix forward merge
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 21307`_
* Fix tool-provided metadata for CONVERTER_tar_to_directory
  (thanks to `@mr-c <https://github.com/mr-c>`__).
  `Pull Request 20260`_
* Pin isa-rwval 0.10.11, drop conditional import handling
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20527`_
* Remove ``num_unique_values`` tiff metadata element
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20464`_
* Add LocusZoom Visualization
  (thanks to `@elmedjadjirayane <https://github.com/elmedjadjirayane>`__).
  `Pull Request 20354`_
* Add mzMLb and MBI datatypes
  (thanks to `@chambm <https://github.com/chambm>`__).
  `Pull Request 20632`_
* Pairtool updated format and sniffers
  (thanks to `@Smeds <https://github.com/Smeds>`__).
  `Pull Request 20634`_
* Add `num_unique_values` tiff metadata element, fixed
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 20669`_
* add fasta.bz2 as auto_compressed type
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 20496`_
* Add support for M4A audio files
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 20667`_
* Add datatype for LexicMap index
  (thanks to `@Smeds <https://github.com/Smeds>`__).
  `Pull Request 20586`_
* Bump requirement of directory converters
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 20834`_
* Undo accidental push
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 20854`_
* Fix Ipynb datatype sniffer and add unit tests
  (thanks to `@ksuderman <https://github.com/ksuderman>`__).
  `Pull Request 20811`_
* Add axt and maf to auto_compressed_types
  (thanks to `@richard-burhans <https://github.com/richard-burhans>`__).
  `Pull Request 20875`_
* Add HiC datatype
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 20874`_
* Fix DOCX detection and add PPTX support
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 20827`_
* Fix anndata metadata
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 20778`_
* Use a streaming based parser (ijson) when setting metadata for biom1 files
  (thanks to `@ksuderman <https://github.com/ksuderman>`__).
  `Pull Request 20851`_
* Add support for picking ``from_work_dir`` directory
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20916`_
* Skip sam metadata if we have too many references
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20820`_
* Extract: do not use common prefix dir
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 20929`_
* Add Auspice JSON datatype
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 20466`_
* Clean up code from pyupgrade
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20642`_
* Add safetensors datatype
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 20754`_
* Add freq.json datatype subclass
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21012`_
* Merge 25.0 into dev
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 21018`_
* New datatype addition: beast.trees datatype
  (thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
  `Pull Request 21055`_
* New datatype addition: gam for vg toolkit
  (thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
  `Pull Request 21096`_
* Prefix download link
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 21112`_
* Add LAS and LAZ file format
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 21049`_
* Add display_in_upload to LAZ and LAS
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 21060`_
* Type annotation fixes for mypy 1.16.0
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20424`_

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

.. tools
* Set minimum profile version for expression tools
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 21151`_
* Drop ucsc test server from sample build sites
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20723`_
* Drop Python helper script from sort1 tool
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20876`_
* Update requirements of sort1 tool
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20892`_
* Update maf tools with profiles, required_files, and requirements
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20865`_
* Modernize tools in the filters/ dir
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20840`_
* Add special case for BAM files in RStudio
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20692`_
* Fix comp1 / test_subworkflow_map_over_data_column
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20992`_

Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ for more details.
The admin-facing release notes are available :doc:`here <25.1_announce>`.

.. include:: 25.1_prs.rst

----

.. include:: _thanks.rst