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25.1 Galaxy Release (October 2025)

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Please see the full release notes 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]

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]

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]

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 here 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]

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]

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]

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]

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]

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]

Visualizations Updates

Datatypes Updates

Builtin Tool Updates

Please see the full release notes for more details. The admin-facing release notes are available here.

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Thanks for using Galaxy!

The Galaxy Team