galaxy 25.1.1

Galaxy server metapackage

The latest information about Galaxy can be found on the Galaxy Community Hub.

Community support is available at Galaxy Help.

Galaxy Quickstart

Galaxy requires Python 3.9 or higher. To check your Python version, run:

$ python -V
Python 3.9.21

Start Galaxy:

$ sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your browser at: http://localhost:8080

For more installation details please see: https://getgalaxy.org/

Documentation is available at: https://docs.galaxyproject.org/

Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/

Tools

Tools can be either installed from the Tool Shed or added manually. For details please see the tutorial. Note that not all dependencies for the tools provided in the tool_conf.xml.sample are included. To install them please visit “Manage dependencies” in the admin interface.

Issues and Galaxy Development

Please see CONTRIBUTING.md .

History

25.1.1 (2026-02-03)

Bug fixes

• Sample sheet column fix by @mvdbeek in #21446

• Record input parameter invocation inputs by @mvdbeek in #21452

• Remove ref and polish release-drafter workflow by @ahmedhamidawan in #21467

• Maintain column definitions on map over by @mvdbeek in #21468

• Add missing test file for sig datatype by @SaimMomin12 in #21473

• Remove release-drafter workflow and add a release config file to improve generated notes by @ahmedhamidawan in #21478

• Do not update a user’s update_time when an admin archives (and purges) a history by @natefoo in #21484

• Add missing ending newline to test.sig test data file by @nsoranzo in #21485

• Fix subworkflow runs for disconnected required inputs with defaults by @mvdbeek in #21488

• change locuszoom package version to 0.0.7 by @elmedjadjirayane in #21494

• Pin release prebuilt client package exactly by @dannon in #21498

• Usability fixes for sample sheet selection. by @jmchilton in #21503

• Fix exception message to enable debugging of missing dataset issue. by @jmchilton in #21504

• Fix type annotation for invocation report errors field by @mvdbeek in #21508

• Add missing dependencies to galaxy-files package by @nsoranzo in #21518

• Filter out failed_metadata HDAs from job cache by @mvdbeek in #21544

• Fix pulsar with rewrite_parameters: false by @mvdbeek in #21557

• Fix job cache collection copy by @mvdbeek in #21558

• Show “Expires today” instead of “Expires soon” in Expiration Warning by @mvdbeek in #21560

• Use quotes for Galaxy citation bibtex by @bernt-matthias in #21563

• Supports Dataverse file access via both persistent and database IDs by @davelopez in #21569

• Fix passing user id to preferences by @guerler in #21576

• Fix Pulsar with default_file_action: none by @mvdbeek in #21578

• Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by @jmchilton in #21584

• Add belated deprecation of Python 3.9 support by @nsoranzo in #21598

• Fix loading of credentials when associated tools are missing by @arash77 in #21599

• Fix race condition in workflow collection populated state check by @mvdbeek in #21613

• Harden Dataverse integration by @davelopez in #21624

• Add split paired or unpaired tool to sample tool conf by @bernt-matthias in #21647

• Fix secret credential editing and add clear button by @itisAliRH in #21650

• Fix condor typo by @gsaudade99 in #21651

• Fix HTCondor runner unwatching jobs when stopping containers by @kysrpex in #21656

• Fix data manager .loc file selection logic by @jdavcs in #21664

• Fixes storage management check for anonymous users by @davelopez in #21680

• Resets selection filter when loading dialog by @davelopez in #21681

• Fixes duplicated entries in “share with individual users” component by @davelopez in #21683

• Simplify docker build, use node as specified in requirements by @mvdbeek in #21695

• Remove Discover Tools button in the workflow tool panel by @ahmedhamidawan in #21697

• Fix option propagation for workflow inputs connected to multiple subworkflows by @mvdbeek in #21712

• Fix collection job state not preserved during history export/import by @mvdbeek in #21716

• Add missing filter_failed_collection_1.1.0.xml tool by @mvdbeek in #21719

• Strip inline comments in conditional requirements by @mvdbeek in #21720

• Exclude node_modules at all depths in Docker builds by @mvdbeek in #21721

Enhancements

• add new datatype for kmindex index data by @Smeds in #21429

• Add sample sheet support to many database operation tools by @mvdbeek in #21465

• Add Sourmash sig new datatype by @SaimMomin12 in #21469

• Add new jupyter version by @bgruening in #21531

• Adds object_expires_after_days example usage to sample config by @davelopez in #21547

• Add tool credentials system documentation and schema updates by @arash77 in #21561

• Add a few datatypes from the digital humanities domain by @bgruening in #21596

• Add new datatype pg and hg for pangenomics by @SaimMomin12 in #21620

• Add database operation tool to convert sample sheets to list collections by @mvdbeek in #21625

• Add new datatypes required for VG tool by @SaimMomin12 in #21644

• Document security considerations for using secrets by @bernt-matthias in #21654

Other changes

• Update 25.1 release notes with config changes by @ahmedhamidawan in #21444

• Fix 25.1 release month on user facing notes by @ahmedhamidawan in #21450

• Fix sample_sheet column display by @mvdbeek in #21457

• Merge 25.1 into master by @ahmedhamidawan in #21482

• Improve tempdir cleanup in integration tests by @mvdbeek in #21520

25.1.0 (2025-12-12)

Bug fixes

• Workaround to numeric sorting in the local portion of tool versions if they are galaxy “build” numbers by @natefoo in #13570

• Change wording of the client side storage handling by @bgruening in #19815

• Check for format="input" as well as format="auto" in datatype linter by @bernt-matthias in #20177

• Add missing galaxy slots and memory tool by @mvdbeek in #20262

• Fix a transiently failing API test. by @jmchilton in #20278

• Fix test timeout in k8s test_slots_and_memory test by @mvdbeek in #20284

• Fix memory and slots test by @mvdbeek in #20291

• Add built visualizations path to .gitignore by @guerler in #20355

• Remove 8 year old note that points at a non-existent subdomain by @scottcain in #20361

• Restore Nora by @guerler in #20387

• Bump requests from 2.32.3 to 2.32.4 in /lib/galaxy/dependencies by @dependabot[bot] in #20422

• Fix client build, set create_time by @mvdbeek in #20445

• Update mulled_containers.rst by @ccoulombe in #20446

• Fix transient selenium error when adding collection input. by @jmchilton in #20460

• Collection API related spelling fix. by @jmchilton in #20470

• Fix alembic down_revision for trigger replacement migration by @mvdbeek in #20501

• Add a merge migration, revert previous edit by @jdavcs in #20507

• Update core.history tour by @pavanvidem in #20576

• Add missing cleanup table by @jdavcs in #20594

• Fix UI Bug - don’t allow checking deferred for local files. by @jmchilton in #20609

• Require user for visualizations create endpoint by @guerler in #20615

• Use store to cache step jobs summary by @ahmedhamidawan in #20638

• Fix typo in lib/galaxy/config/sample/job_conf.sample.yml: enviroment –> environment by @blankenberg in #20652

• Remove select and deselect labels from visualization select field by @guerler in #20665

• Fix assertion on python version by @ccoulombe in #20696

• Remove decoded ids from job/dataset error report email by @ahmedhamidawan in #20714

• Fix various collection descriptions in history panel. by @jmchilton in #20736

• Various client unit test fixes and cleanup. by @jmchilton in #20752

• More client unit test clean up. by @jmchilton in #20755

• More cleanup for Jest output. by @jmchilton in #20769

• Fix anndata metadata by @nilchia in #20778

• Fix Switch to history link click actions and add extensive jests by @ahmedhamidawan in #20783

• Fix visualization installs by @dannon in #20788

• Only show breadcrumb when on history permissions route (not in sharing view) by @ahmedhamidawan in #20800

• Fix Ipynb datatype sniffer and add unit tests. by @ksuderman in #20811

• Ignore yaml and json in prettier pre-commit hook by @mvdbeek in #20823

• Bump requirement of directory converters by @bernt-matthias in #20834

• Fix lint error in WorkflowRunSuccess by @ahmedhamidawan in #20837

• Fix multiple=”true” data collection map over for shell_command tools by @mvdbeek in #20859

• Fix test in configfile_user_defined.yml by @nsoranzo in #20873

• Likely fix for transiently failing published histories test. by @jmchilton in #20890

• Update requirements of sort1 tool by @nsoranzo in #20892

• Avoid overscroll behavior by @guerler in #20908

• Bump codecov/codecov-action from 3 to 5 by @dependabot[bot] in #20920

• Extract: do not use common prefix dir by @bernt-matthias in #20929

• Fix default conditional test parameters… by @jmchilton in #20942

• Fix JupyterLite History Identifier Retrieval Without Dataset by @guerler in #20971

• Apply overscroll behavior setting to html by @guerler in #20975

• Ensure that conversion_key is defined by @guerler in #20984

• Tsc fixes and pin by @dannon in #20985

• Fix jest tests – wait for async calls in grid list by @dannon in #20986

• Fix comp1 / test_subworkflow_map_over_data_column by @mvdbeek in #20992

• Save IGV locus and improve error handling by @guerler in #20996

• Fix content wrapping in cards and preference title by @guerler in #21009

• Fix horizontal scrolling w/ GButton in input-group-append by @dannon in #21025

• Fix GCS file source to handle virtual directories without marker objects by @dannon in #21051

• Fix Huggingface timestamp parsing when last_commit is missing by @davelopez in #21072

• Allow cors on data and tool landing pages by @mvdbeek in #21078

• Fix invocation export dataset exclusion by @davelopez in #21091

• Fix copy export download link for old exports by @davelopez in #21094

• Test and fix CORS on exceptions by @mvdbeek in #21105

• Fix invalid invocation tab handling and unify disabled tab components by @ahmedhamidawan in #21115

• Fix shift+click range select not working in history list by @ahmedhamidawan in #21117

• Restore job.get_param_values by @mvdbeek in #21130

• Improve _touch_collection_update_time_cte performance by @mvdbeek in #21134

• Fix type annotation in test_run_workflow_use_cached_job_implicit_conv… by @mvdbeek in #21138

• Use corepack to link yarn into $VIRTUALENV/bin by @mvdbeek in #21140

• Pin Ansible version by @ksuderman in #21141

• Remove invocation view connection animations by @ahmedhamidawan in #21145

• Mark user creation API endpoint as admin-only by @mvdbeek in #21149

• Set minimum profile version for expression tools by @mvdbeek in #21151

• Fix subworkflow editing by @mvdbeek in #21159

• Add Convert characters1 to workflow safe updates by @mvdbeek in #21160

• Use yarn instead of npx to use pinned openapi-typescript by @mvdbeek in #21164

• Bump up minimal tpv version by @mvdbeek in #21166

• Fix proxy endpoint encoding by @davelopez in #21169

• Enable drag-and-drop of collection elements in IGV by @guerler in #21173

• Save build date to GITHUB_OUTPUT by @ksuderman in #21181

• Don’t show the “view sheet” button for non-sample sheet collections. by @jmchilton in #21191

• Allow collection builder to be invoked consecutively by @ahmedhamidawan in #21193

• Add Hyphy Vision Result Viewer by @guerler in #21196

• Don’t create extra watchers when switching tabs by @natefoo in #21197

• Drop single ‘pair’ from standard upload UI, preferring lists, or lists of pairs as options for user by @dannon in #21200

• Assorted workbook upload fixes. by @jmchilton in #21203

• Wrap ontology card in tool discovery view below list view selector by @ahmedhamidawan in #21212

• Add missing more-itertools dependency by @nsoranzo in #21214

• Fix downloading subworkflows without stored workflow by @mvdbeek in #21223

• Fix href for tool links by @mvdbeek in #21232

• Apply tool test timeout only once by @bernt-matthias in #21246

• Fix workbook download link by @jmchilton in #21261

• Fixes download for restricted Zenodo records by @davelopez in #21274

• Update the mulled.py script to check json output by @nilchia in #21276

• Prevent duplicate current_history_json calls by @ahmedhamidawan in #21282

• Prevent duplicate fetches for full workflow in invocation view by @ahmedhamidawan in #21284

• Add a rate limiter to the API client factory by @ahmedhamidawan in #21286

• Fix keyed cache fetching over and over if fetched value is 0 by @ahmedhamidawan in #21293

• Fix invocations scroll list cards to show update time by @ahmedhamidawan in #21294

• Set create_time as the default time for sorting/display for invocations by @ahmedhamidawan in #21314

• Fix TERMINAL_STATES array has a duplicate state by @ahmedhamidawan in #21342

• Force correct client build by @mvdbeek in #21346

• Fix fastapi package conflict by @mvdbeek in #21349

• Backport smoke-test and pr jobs from dev branch by @ksuderman in #21350

• Use anaconda API to find package download URL by @nsoranzo in #21360

• Fix database revision tags by @jdavcs in #21377

• Use a new format tox environment in lint GitHub action by @nsoranzo in #21419

• Skip mako for rendering tool help by @mvdbeek in #21428

• Fix optional subworkflow input scheduling bug by @mvdbeek in #21435

• Maintain columns on sample sheet map over by @mvdbeek in #21436

Enhancements

• Don’t serialize view of item in delete/purge request by @mvdbeek in #18732

• Support credentials(secrets/variables) in tool requirements by @arash77 in #19084

• Allow several Galaxy Markdown directives to be embedded. by @jmchilton in #19086

• Add tags to output datasets from tool form by @PlushZ in #19225

• Implement Sample Sheets by @jmchilton in #19305

• Refactor and use ScrollList component in more places by @mvdbeek in #19318

• User preferences redesign by @itisAliRH in #19658

• Refactor Object Store Selection Modals UI by @itisAliRH in #19697

• Consider collections in on_strings for parameters accepting multiple datasets by @bernt-matthias in #19817

• Remove backbone-based charts modules by @guerler in #19892

• Add selectedItems composable by @ahmedhamidawan in #19973

• Update Python dependencies by @galaxybot in #20139

• Remove legacy visualizations by @guerler in #20173

• Add rerun.io web viewer by @guerler in #20202

• Selenium tests for various 24.2 features. by @jmchilton in #20215

• Update Javascript package licenses to MIT by @mr-c in #20264

• Split Login and Register, enable OIDC Registration. by @uwwint in #20287

• Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288

• Update GitHub workflows to use PostgreSQL 17 image by @nsoranzo in #20292

• Switch Default Visualization Endpoint to script, migrate to YAML by @guerler in #20303

• Add short term storage expiration indicator to history items by @davelopez in #20332

• Update Python dependencies by @galaxybot in #20347

• Install Visualization plugins as self-contained packages by @guerler in #20348

• Add LocusZoom Visualization by @elmedjadjirayane in #20354

• Refactor CollectionDescription component props to use HDCASummary by @davelopez in #20356

• Update create_time field to be required in history content items by @davelopez in #20357

• Prepare ToolBox.dynamic_tool_to_tool() for CWL formats by @nsoranzo in #20364

• Install visualizations directly to static path, avoid duplication by @guerler in #20372

• Update Python dependencies by @galaxybot in #20383

• Use full page width in reports and pages by @guerler in #20384

• Workflow Graph Search by @ElectronicBlueberry in #20390

• History CitationsList export improvements by @dannon in #20402

• Enhance citations page by @davelopez in #20408

• Base Implementation of GFormInput by @ElectronicBlueberry in #20418

• Type annotation fixes for mypy 1.16.0 by @nsoranzo in #20424

• Allow larger viz in pages by @guerler in #20427

• Implement dataset source requested transformations. by @jmchilton in #20435

• Add username_key setting to configure python-social-auth OIDC by @marius-mather in #20497

• Test case for using URL-based workflow inputs with implicit conversions. by @jmchilton in #20509

• Remove deprecated tool document cache by @nsoranzo in #20510

• Fixes for invocation import. by @jmchilton in #20528

• Update Python dependencies by @galaxybot in #20537

• Decode OIDC access token as part of authentication pipeline by @marius-mather in #20547

• Add Dataverse template by @davelopez in #20551

• Update Python dependencies by @galaxybot in #20577

• Display the Galaxy Citation within the Export Tool References List by @mschatz in #20584

• Add recent downloads page for STS requests by @davelopez in #20585

• Implement Data Landing Requests by @jmchilton in #20592

• Update Python dependencies by @galaxybot in #20601

• Improve BreadcrumbHeading and add unit tests by @itisAliRH in #20618

• Remove vue-tsc diff comparison from CI by @dannon in #20620

• Add a “Debug” (email report) tab to Workflow Invocations by @ahmedhamidawan in #20624

• Clean up code from pyupgrade by @nsoranzo in #20642

• Update location of latest tpv shared db by @nuwang in #20651

• Update Python dependencies by @galaxybot in #20653

• Add markdown hint to schema by @bgruening in #20654

• Update tiffviewer visualization to version 0.0.3 by @davelopez in #20658

• Improve GCard visibility handling and type definitions by @itisAliRH in #20663

• Removes entries from purged filter label in history grid by @guerler in #20664

• Unify History export UX using wizard by @davelopez in #20666

• Sort collection dialog by HID descending. by @jmchilton in #20674

• Update Python dependencies by @galaxybot in #20680

• Fix resource watcher composable race condition by @davelopez in #20690

• Add special case for BAM files in RStudio by @bgruening in #20692

• Add fsspec base implementation for File Source plugins by @davelopez in #20698

• Update Python dependencies by @galaxybot in #20699

• Add more info to inheritance chain by @arash77 in #20701

• History Components Navigation/Heading Improvements by @itisAliRH in #20702

• Improve cli and slurmcli runner traceability for job status and failure reasons by @selten in #20717

• Attempt to reuse previously materialized datasets by @mvdbeek in #20718

• Make workflow invocation tabs routable by @ahmedhamidawan in #20719

• Drop ucsc test server from sample build sites by @mvdbeek in #20723

• Refactor Files Sources Framework for stronger typing using pydantic models by @davelopez in #20728

• Hierarchical display collection dataset states by @mvdbeek in #20731

• Update Python dependencies by @galaxybot in #20732

• Fix Client Linting Run Error by @itisAliRH in #20734

• Add embed-compatible view for galaxy pages by @dannon in #20737

• Make invocations panel reactive using the invocation store by @ahmedhamidawan in #20738

• New History List Using GCard by @itisAliRH in #20744

• Change Advanced Tool Search to a Tool Discovery View by @ahmedhamidawan in #20747

• Update Python dependencies by @galaxybot in #20753

• Consolidate visualization mako, avoid user agent styles by @guerler in #20760

• Add configfiles support and various enhancements for user defined tools by @mvdbeek in #20761

• Fix WorkflowComment tests warnings by @davelopez in #20762

• A production data types checklist to aid creating/reviewing new data types by @jmchilton in #20768

• Fail Jest tests on warn/error console logging. by @jmchilton in #20770

• Modernize and Refactor Tour components by @ahmedhamidawan in #20771

• Increase wait time (retry) in UCSC data source test by @davelopez in #20772

• Drop old load_workflow controller method, use API by @mvdbeek in #20774

• Apply eslint fixes by @mvdbeek in #20775

• Allow fine-grained selection of included files in Invocation Export Wizard by @davelopez in #20776

• Stabilize client build after client-dev-server by @davelopez in #20777

• Update Python dependencies by @galaxybot in #20779

• Remove Backbone from UI bootstrap initialization by @guerler in #20786

• Adapt S3 file source to fsspec by @davelopez in #20794

• Remove Backbone dependency from webhook wrappers by @guerler in #20797

• Fix fsspec fs path handling by @davelopez in #20799

• Add Hugging Face 🤗 file source and user-defined template by @davelopez in #20805

• Refactor MESSAGES constant in FileSourceTypeSpan.vue by @davelopez in #20806

• Fix new linting errors in unit test mounts by @davelopez in #20807

• Update Python dependencies by @galaxybot in #20812

• Enable data label column selection in basic Plotly plots and add heatmap by @guerler in #20813

• Upgrade Prettier 3 by @dannon in #20815

• Update 2 docs pages by @nsoranzo in #20824

• Add small improvements for running CWL tools by @nsoranzo in #20826

• Bump jspdf from 2.5.1 to 3.0.2 in /client by @dependabot[bot] in #20828

• Migrate icon defs in CollectionOperations.vue to best practices. by @jmchilton in #20829

• Update pytest to v8 by @nsoranzo in #20838

• Modernize tools in the filters/ dir by @natefoo in #20840

• Update Python dependencies by @galaxybot in #20841

• Update Integration tests by @nsoranzo in #20844

• Allow adding extra steps to the default pipeline of the OIDC authentication by @marius-mather in #20845

• Use a streaming based parser (ijson) when setting metadata for biom1 files. by @ksuderman in #20851

• Support remote file source hashes by @davelopez in #20853

• Various Container Execution Enhancements (including GCP Batch support) by @jmchilton in #20862

• Update maf tools with profiles, required_files, and requirements. by @natefoo in #20865

• Add support for hierarchical module systems in lmod + module dependency resolvers by @t1mk1k in #20866

• Replace tour_generator webhook with internal API and frontend by @ahmedhamidawan in #20868

• Update Python dependencies by @galaxybot in #20869

• Improve type annotation for job runners and InteractiveToolManager by @nsoranzo in #20871

• Add axt and maf to auto_compressed_types by @richard-burhans in #20875

• Drop Python helper script from sort1 tool by @nsoranzo in #20876

• Update JupyterLite version to 0.6.4 by @guerler in #20877

• Add visualization navigation guard by @dannon in #20881

• Add main tool CI tests by @nsoranzo in #20884

• Bump vite from 6.3.5 to 6.3.6 in /client-api by @dependabot[bot] in #20885

• Set default option to make datasets accessible only to individual users when sharing histories with particular users by @davelopez in #20886

• Refactor sharing logic for unified type handling by @davelopez in #20888

• Replace deprecated codecs.open() by @nsoranzo in #20891

• Small cleanup of tool execution code. by @jmchilton in #20899

• Update Python dependencies by @galaxybot in #20905

• Add Multiple Sequence Alignment Viewer 2.0 by @guerler in #20907

• Improve Invocation View step display by @ahmedhamidawan in #20912

• Allow creation of visualizations without dataset by @guerler in #20914

• Enable dependabot version updates for GitHub actions by @nsoranzo in #20915

• Add support for picking from_work_dir directory by @mvdbeek in #20916

• Include format in internal json model by @mvdbeek in #20917

• Bump docker/login-action from 2 to 3 by @dependabot[bot] in #20918

• Bump docker/build-push-action from 4 to 6 by @dependabot[bot] in #20919

• Bump actions/setup-node from 4 to 5 by @dependabot[bot] in #20921

• Bump docker/setup-buildx-action from 2 to 3 by @dependabot[bot] in #20922

• Add tool to add nesting level to collection by @bernt-matthias in #20926

• Update Python dependencies by @galaxybot in #20930

• Make jupyterlite default visualization for ipynb by @guerler in #20931

• Allow addressing user defined tools in job config by @mvdbeek in #20932

• Wire up and test resource requirement via tpv by @mvdbeek in #20936

• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #20937

• Bump peter-evans/create-pull-request from 6 to 7 by @dependabot[bot] in #20938

• Bump docker/metadata-action from 4 to 5 by @dependabot[bot] in #20939

• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #20940

• Bump actions/github-script from 7 to 8 by @dependabot[bot] in #20941

• Adds IGV.js Visualization by @guerler in #20943

• Add a dedicated ToolFormTags component for tool form output tags by @ahmedhamidawan in #20945

• Limit admin requirement of selected tool data api endpoints by @guerler in #20949

• Add resource docs and tweak tool source schema title generation by @mvdbeek in #20951

• Allow specifying a command for determining a docker host port by @natefoo in #20953

• Allow sending and tracking landing request origin by @mvdbeek in #20957

• Track landing request with invocation by @mvdbeek in #20960

• Use nodejs-wheel to install node by @mvdbeek in #20963

• Move tours schema to schema directory (to fix package structure) by @ahmedhamidawan in #20965

• Update Python dependencies by @galaxybot in #20968

• Log task execution errors with log.exception by @mvdbeek in #20970

• Bump actions/labeler from 5 to 6 by @dependabot[bot] in #20976

• Simplify plugin staging with explicit clean step by @dannon in #20983

• Bump vitessce to 3.8.2 by @guerler in #21003

• Update Python dependencies by @galaxybot in #21005

• Fix and migrate HIV-TRACE to Charts Visualization Framework by @guerler in #21006

• Add README and update the minimal visualization example by @guerler in #21007

• Add freq.json datatype subclass by @guerler in #21012

• Bump up total-perspective-vortex dependency by @mvdbeek in #21014

• Fix GCard Layout and White Spaces by @itisAliRH in #21026

• Add Keyboard Navigation to History Lists by @itisAliRH in #21035

• Add 2 net utilities to the min image by @afgane in #21085

• Use workflow-style payload in data landing request by @mvdbeek in #21107

• Release notes by @ahmedhamidawan in #21162

• Add Release Drafter GitHub Action integration by @dannon in #21195

• Tighter API for tool run tagging. by @jmchilton in #21210

• Makes “set as current” the primary action in history list by @davelopez in #21233

• Optimize /api/invocations/steps/{step_id} by @mvdbeek in #21249

• [igv] Allow selection of genomes from history fasta/2bit by @guerler in #21269

• Update tool profile version for credentials by @davelopez in #21273

• New datatype addition: HAL by @SaimMomin12 in #21379

• Add PNTS datatype for 3D Tiles Point Cloud by @kgerb in #21414

• A better way to designate config_watcher by @jdavcs in #21426

• Optionally include column headers in sample sheet file by @mvdbeek in #21439

Other changes

• Small tweaks and cleanup from sample sheets branch by @jmchilton in #20229

• Version 25.1.dev by @ahmedhamidawan in #20268

• Merge release_25.0 into dev by @davelopez in #20484

• Merge release_25.0 into dev by @davelopez in #20490

• Bump pillow from 11.2.1 to 11.3.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20591

• Bump linkifyjs from 4.1.1 to 4.3.2 in /client by @dependabot[bot] in #20707

• Sample Sheet Bug Fixes around Preserving Collection Metadata by @jmchilton in #20749

• Add tool_id and tool_version column to tool_landing_request table by @mvdbeek in #20795

• Implement bare-bones view of sample sheet collections as sheet. by @jmchilton in #20798

• Fix webpack dev server detection by @mvdbeek in #20822

• Fix optional numeric column definitions for sample sheets. by @jmchilton in #20830

• Validate sample sheet column definitions in workflow definitions on backend. by @jmchilton in #20880

• Bump axios from 1.8.2 to 1.12.0 in /client by @dependabot[bot] in #20906

• Merge 25.0 into dev by @ahmedhamidawan in #20911

• Bump default milestone to 26.0 by @ahmedhamidawan in #20946

• Add 25.1 migration tags by @ahmedhamidawan in #21017

• Update version to 25.1.rc1 by @ahmedhamidawan in #21019

• Restore .get_metadata function by @mvdbeek in #21045

• Fix TOOL_WITH_SHELL_COMMAND import source by @mvdbeek in #21070

• Drop fastapi extra dep from sentry-sdk by @mvdbeek in #21156

• Resolve possible symlink before establishing tool file location by @mvdbeek in #21175

• Fix forward merge by @mvdbeek in #21307

• Fix db revision tags by @mvdbeek in #21442

25.0.4 (2025-11-18)

Bug fixes

• Add safetensors datatype by @nilchia in #20754

• Skip sam metadata if we have too many references by @mvdbeek in #20820

• Fix select field cut off in dataset view by @ahmedhamidawan in #20947

• Check for expiration in refresh token dictionary by @jdavcs in #20954

• Deactivate user file source on unknown error by @mvdbeek in #20962

• Don’t create workflow outputs to recover input parameter outputs by @mvdbeek in #20980

• Fix test_multiple_decorators unit test for FastAPI 0.118.0 by @nsoranzo in #20982

• Fix PUT /api/workflows for user defined tools by @mvdbeek in #20987

• Backport of #20984 by @davelopez in #20994

• Improves zip file type detection for uploads under windows by @caroott in #20999

• Store pulsar job prep error messages by @mvdbeek in #21013

• Require OK datasets for filtering empty datasets by @bernt-matthias in #21023

• Fix InvalidRequestError when saving workflow step with dynamic tool by @mvdbeek in #21056

• Fix has_size assertion by @bernt-matthias in #21081

• Run landing request state through validator by @mvdbeek in #21087

• Fix workflow run form input restrictions by @mvdbeek in #21095

• Backport fix anndata datatype update by @nilchia in #21111

• Prefix download link by @martenson in #21112

• Create new datasets when creating skipped database operation tool outputs by @mvdbeek in #21142

• Fix workflow landing rendering if public query param not provided by @mvdbeek in #21165

• Fix optional param unset in RO-Crate export by @davelopez in #21192

• Fix MIME type for LAZ datatype by @kysrpex in #21202

• Fix refresh token expiration retrieval logic by @nuwang in #21213

• Fix direct tool execution not using the latest version by @jmchilton in #21240

• Fix proxy url validation for non-printable characters by @davelopez in #21280

• Swap to NPM trusted publishing for prebuilt client by @dannon in #21290

Enhancements

• Add Auspice JSON datatype by @pvanheus in #20466

• Add SpatialData datatype by @nilchia in #21000

• Use job cache also for implicit conversions by @mvdbeek in #21021

• Add LAS and LAZ file format by @bgruening in #21049

• New datatype addition: gam for vg toolkit by @SaimMomin12 in #21096

• Harden proxy redirect validation by @davelopez in #21185

• support ZARR v3 for Spatialdata dt by @nilchia in #21265

Other changes

• New datatype addition: beast.trees datatype by @SaimMomin12 in #21055

• Add display_in_upload to LAZ and LAS by @bgruening in #21060

• Backport Fix proxy endpoint encoding by @davelopez in #21184

25.0.3 (2025-09-23)

Bug fixes

• Cascade newly created windows in window manager by @guerler in #20780

• Remove packages/meta/requirements.txt by @nsoranzo in #20782

• Ensure that workflow invocations are persisted with state by @mvdbeek in #20784

• Fix password reset functionality for lowercase emails by @jdavcs in #20801

• Fix token refresh bug (cilogon) by @jdavcs in #20821

• Disable Run Tool button when there are errors by @ahmedhamidawan in #20839

• Update Celery section in admin docs by @jdavcs in #20856

• Drop eager argument from invocation related methods by @mvdbeek in #20863

• Improve dataset collection fetch performance in the invocation view by @ahmedhamidawan in #20870

• Use populated_optimized when serializing collection by @mvdbeek in #20872

• Fix role.description bug by @jdavcs in #20883

• Speed up ImplicitCollectionJobs.job_list by @mvdbeek in #20887

• Bump up integration test k8s version by @mvdbeek in #20889

• Make check for existing user in custos_authnz.py case insensitive by @cat-bro in #20893

• Add LDDA purged property by @mvdbeek in #20895

• Avoid potential race condition in replacement_for_connection by @mvdbeek in #20909

• Fix sessionless tag creation by @mvdbeek in #20925

• Fix collection element sorting in extended_metadata by @mvdbeek in #20928

Enhancements

• Render Tool Descriptions in Markdown in TRS imports by @itisAliRH in #20814

• Fix DOCX detection and add PPTX support by @arash77 in #20827

• Include galaxy user agent in data source tools by @mvdbeek in #20836

• Add HiC datatype by @abretaud in #20874

Other changes

• Undo accidental push by @bernt-matthias in #20854

• Merge 25.0 into dev by @ahmedhamidawan in #20911

25.0.2 (2025-08-13)

Bug fixes

• Remove num_unique_values tiff metadata element by @mvdbeek in #20464

• Bump up python for for pulsar package tests by @mvdbeek in #20521

• Update Gravity to 1.0.8 by @natefoo in #20523

• Prevent DCE collections from being renamed by @ahmedhamidawan in #20534

• Use venv instead of virtualenv in package make setup-venv by @natefoo in #20536

• Move definition of DatasetCollectionDescriptionT before its use by @nsoranzo in #20539

• Fix docs versioning by @nsoranzo in #20542

• Fix restricting user defined tool input datasets extensions by @mvdbeek in #20545

• Fix description and metadata of some packages by @nsoranzo in #20546

• Fix activity bar reordering persistence by @dannon in #20550

• Fix PDF preview functionality in dataset view by @dannon in #20552

• Propagate cached job output replacement to copies of outputs by @mvdbeek in #20553

• Fix workflow invocation report pdf generate by @itisAliRH in #20558

• Fix Storage Dashboard Link to Dataset Details by @itisAliRH in #20565

• Upgrade requests-unixsocket for requests compatibility by @natefoo in #20566

• Don’t assume cwd = job directory when running prepare dirs by @natefoo in #20571

• Fix planemo serve, need user list by @mvdbeek in #20575

• Fix apply rules ownership check by @mvdbeek in #20582

• Don’t fail volume mount construction for tools without tool directory by @mvdbeek in #20593

• Prevent importing workflows with invalid step UUID by @davelopez in #20596

• Fix workflow loading error handling by @davelopez in #20597

• Do not set attribute on a namedtuple by @jdavcs in #20599

• Constraint conditional redis version to allow only minor updates by @davelopez in #20603

• fix Admin job limit query by @martenson in #20626

• Correct visualization response schema by @guerler in #20627

• Ignore webob http exceptions for logging purposes by @mvdbeek in #20630

• Fix HistoryDatasetAsTable by @mvdbeek in #20636

• Fix bug: tool output file may be overwritten by Runner’s multi work t… by @jianzuoyi in #20639

• Fix IntersectionObserver updates when replacing items by @davelopez in #20646

• Fix optional unspecified input to conditional step by @mvdbeek in #20647

• Avoid postgres truncation of aliases and labels by @mvdbeek in #20649

• Fix deferred datasets in multiple dataset parameters. by @jmchilton in #20650

• Fix empty default Optionals for tool_shed_repositories API. by @jmchilton in #20656

• Remove content from packages/meta/requirements.txt by @nsoranzo in #20662

• Add num_unique_values tiff metadata element, fixed by @kostrykin in #20669

• Bump up pulsar dependency to 0.15.9 by @mvdbeek in #20672

• Fix invocation header by @qchiujunhao in #20676

• Fix scratchbook display by @dannon in #20684

• Fix Invenio file downloads for published records with draft by @davelopez in #20685

• Input linter: add missing attribute to sort_by by @bernt-matthias in #20693

• Fix dataset serializers and response models by @arash77 in #20694

• Add username filter to published pages grid by @ahmedhamidawan in #20703

• Fix parameter models for optional color params. by @jmchilton in #20705

• Prevent negative offset in historyStore handleTotalCountChange by @davelopez in #20708

• Fix click to edit link by @mvdbeek in #20710

• Fix test_base_image_for_targets mulled test to use mzmine by @nsoranzo in #20713

• DatasetView Header - fixes text wrapping issues on small screens by @dannon in #20721

• Update galaxy-release-util by @mvdbeek in #20727

• Fix maximum workflow invocation duration test by @mvdbeek in #20729

• Remove base_dir from zip in make_fast_zipfile by @davelopez in #20739

• fix config for nginx in docs by @martenson in #20757

Enhancements

• add fasta.bz2 as auto_compressed type by @bernt-matthias in #20496

• Add redis conditional dependency by @davelopez in #20502

• Improve workflow monitor loop times by @mvdbeek in #20522

• Add datatype for LexicMap index by @Smeds in #20586

• Clarify how to separate job and workflow scheduling by @mvdbeek in #20625

• Add mzMLb and MBI datatypes by @chambm in #20632

• Pairtool updated format and sniffers by @Smeds in #20634

• Add support for M4A audio files by @arash77 in #20667

Other changes

• Require user for visualizations create endpoint by @mvdbeek in #20629

• Merge 24.2 into 25.0 by @ahmedhamidawan in #20681

25.0.1 (2025-06-20)

Bug fixes

• Fix single data element identifier to be a regular string by @mvdbeek in #20438

• Relax validation of XML test assertion parsing by @mvdbeek in #20511

• Add id-token: write for npm publishing by @mvdbeek in #20519

• Do not expose user info to non authenticated users by @bernt-matthias in #20524

• names of package extras cannot contain underscores by @mr-c in #20525

• Pin isa-rwval 0.10.11, drop conditional import handling by @natefoo in #20527

• Fix import of galaxy.tool_util.cwl module by @nsoranzo in #20529

• Fix galaxy-config script, move install to galaxy-dependencies in app package by @natefoo in #20531

Enhancements

• Bump gravity dependency to 1.1.0 by @mvdbeek in #20520

• Update the dev package build and install script by @natefoo in #20526

Other changes

• Merge Release 25.0 into the master branch by @ahmedhamidawan in #20514

• Fixes for static handling and the web_client package by @natefoo in #20516

• Fix link in user release notes by @bgruening in #20518

• Bump Gravity to 1.1.1 by @natefoo in #20533

25.0.0 (2025-06-18)

Bug fixes

• Stabilize HistoryView.test.js by @jmchilton in #19165

• Cleanup Jest Test Output (part 2) by @jmchilton in #19178

• Fix Pesky warning with PersistentTaskProgressMonitorAlert.test.ts by @ElectronicBlueberry in #19180

• Cleanup Jest Test Output (part 3) by @jmchilton in #19185

• Cleanup Jest Test Output (part 4) by @jmchilton in #19186

• Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by @dependabot[bot] in #19189

• Don’t calculate dataset hash for datasets in non-OK state by @nsoranzo in #19191

• Cleanup test output console for tool panel tests. by @jmchilton in #19210

• Update Vizarr package version to 0.1.6 by @davelopez in #19228

• Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by @dependabot[bot] in #19233

• Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331

• Require importlib-resources also for Python 3.9-3.11 by @nsoranzo in #19358

• Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot[bot] in #19369

• Node 22 unreachable fixes by @mvdbeek in #19378

• Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394

• Alternative format_source fix by @mvdbeek in #19395

• Use id entity attribute when setting exampleOfWork property by @nsoranzo in #19396

• Display email activation help only if user activation is enabled by @jdavcs in #19402

• Prevent negative offset by @jdavcs in #19409

• Avoid using custos refresh tokens which are expired by @martenson in #19411

• Fix wrong id in test_combined_mapping_and_subcollection_mapping by @mvdbeek in #19481

• Fix preferred object store id reactivity by @ElectronicBlueberry in #19491

• Fix wrong URI written to ExportObjectResultMetadata when exporting histories to eLabFTW by @kysrpex in #19541

• Fix test_mulled_build.py::test_mulled_build_files_cli with use_mamba=True by @kysrpex in #19545

• Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5 by @jdavcs in #19620

• Update eLabFTW file source template docs by @kysrpex in #19632

• Fix more vue tsc indicated type issues by @jmchilton in #19650

• Yet More Vue Typing Error Fixes by @jmchilton in #19680

• Fix incorrect type in tool_util.deps and fix package structure. by @jmchilton in #19702

• Add linter argument to linter report function calls by @bernt-matthias in #19708

• Refactor tool panel handling, resolve transiently failing jest test by @guerler in #19733

• Jest Cleanup (Part 5) by @jmchilton in #19743

• Use fissix also when python3-lib2to3 is not installed by @nsoranzo in #19749

• Fix setting env and tags on resubmission by @bernt-matthias in #19753

• Revise consistently failing edam tool panel view test. by @jmchilton in #19762

• Add missing tool test file by @jmchilton in #19763

• Bump axios from 1.7.4 to 1.8.2 in /client by @dependabot[bot] in #19773

• Fix wording of API doc string by @bernt-matthias in #19776

• Add better WorkflowSummary type by @ahmedhamidawan in #19779

• Fix workflow run graph non input steps not appearing bug by @ahmedhamidawan in #19781

• Update webdav user file source template help text by @sanjaysrikakulam in #19784

• HelpText improvements (content, sizing) and WorkflowInvocationHeader tweaks. by @dannon in #19792

• Remove unused (define* - compiler macro) imports from TextEditor.vue by @dannon in #19793

• Fix Selenium workflow tests not updating param type properly. by @jmchilton in #19810

• Fix Galaxy ignoring job object_store_id for quota check by @bernt-matthias in #19854

• Cleanup circular dependencies around utils.ts. by @jmchilton in #19857

• Remove circular dependency around user store. by @jmchilton in #19859

• Move some store types out into own file to reduce circular dependencies. by @jmchilton in #19860

• Fix most new vue typescript errors discovered in #19851 by @jmchilton in #19862

• Create rucio.cfg from inside Rucio objectstore by @SergeyYakubov in #19863

• Fix broken optimisation introduced in #19852 by @nsoranzo in #19871

• Fix various mypy issues around mapped attributes by @mvdbeek in #19883

• More fixes to FormData drag and drop and typing by @ahmedhamidawan in #19900

• Use FA Component (w/svg) instead of span+font in RunWorkflow header by @dannon in #19901

• Change wording in the google drive user file source template by @sanjaysrikakulam in #19927

• Move FormBoolean back to FormElement field in workflow run form by @ahmedhamidawan in #19938

• Fix test_in_directory on osx by @mvdbeek in #19943

• Fix adding tags popup closing logic on focus out by @itisAliRH in #19950

• Use lower case extension for setting datatype in data discovery by @bernt-matthias in #19954

• Fix ownership check in history contents update route by @mvdbeek in #19969

• Remove hgv_sift from tool_conf.xml.sample by @natefoo in #19972

• Unwind more client dependencies at top of stack. by @jmchilton in #19983

• Fix keyedCache never allowing multiple fetches by @ahmedhamidawan in #20020

• Pass host url to visualizations by @guerler in #20022

• Also chown R lib in RStudio BioC tool by @natefoo in #20025

• Add new line to vtpascii test file by @guerler in #20051

• Fix linting with markdown in tool help by @bgruening in #20058

• Update breadcrumb item ‘to’ type for better routing support by @itisAliRH in #20065

• Always render Outputs tab in invocation view by @ahmedhamidawan in #20073

• Remove collapse invocations panel on mouseleave feature by @ahmedhamidawan in #20074

• Bump http-proxy-middleware from 2.0.7 to 2.0.9 in /client by @dependabot[bot] in #20086

• Fix test_workflow_run export selenium by @ahmedhamidawan in #20089

• Fix and migrate Drawrna by @guerler in #20102

• Add hid to selection field in visualization creation form by @guerler in #20108

• Remove only the Docker images specific for the test by @nsoranzo in #20109

• Fixes for GButtons with disabled state by @ahmedhamidawan in #20121

• Sort visualization datasets by hid by @guerler in #20123

• Wait for Gbutton to become enabled by @mvdbeek in #20131

• Allow deferred and ok state datasets for vis by @guerler in #20143

• Fix certain cases of collection parameter handling during workflow execution. by @jmchilton in #20152

• Yaml parser fixes part2 by @mvdbeek in #20162

• Fix tapis module typing errors by @jdavcs in #20175

• Use backports.zoneinfo in job_metrics package under Python <3.9 by @nsoranzo in #20178

• Update tabular_csv.py to use less memory in tsv->csv conversion by @cat-bro in #20187

• Corrects header levels in Visualization Help Markdown by @guerler in #20199

• Move UnprivilegedToolResponse into api by @mvdbeek in #20207

• Package fixes by @nsoranzo in #20208

• Fix NFDI auth by @bgruening in #20217

• Fix next milestone by @martenson in #20219

• Group Tool Versions in IT Panel by @dannon in #20244

• Fix vue-tsc issue in ParameterStep by @dannon in #20245

• Replace Bootstrap Popover with Popper wrapper by @guerler in #20246

• Fix tool-provided metadata for CONVERTER_tar_to_directory by @mr-c in #20260

• Fix theme selector by @guerler in #20275

• Fix interactive activity highlighting by @guerler in #20276

• Fix inconsistent header sizes by @guerler in #20277

• Add non-dev httpx dependency by @mvdbeek in #20281

• Remove duplicated job id in job success view by @ahmedhamidawan in #20289

• Skip multiple pasted URLs when checking for remote Zip by @davelopez in #20300

• Fix masthead logo height by @guerler in #20302

• Increase proxy API robustness by validating URL before use by @davelopez in #20311

• Rerun workflows for the correct version/instance by @ahmedhamidawan in #20313

• Avoid displaying dataset tab view in window manager by @guerler in #20317

• Fix display urls by @dannon in #20318

• Fix workflow bookmark filtering by @davelopez in #20325

• Add test for workflow instance download fix by @ahmedhamidawan in #20326

• Add basic validation to workflow creator attribute by @jdavcs in #20328

• Fix broken admin navigation option and add missing menu items by @dannon in #20333

• Error on duplicate labels by @ElectronicBlueberry in #20335

• Small UI fixes for ag-grid based rule grid. by @jmchilton in #20358

• Fix selection issue when adding tags to workflows in bulk by @davelopez in #20362

• Log invalid vault paths by @mvdbeek in #20363

• Remove redundant badge when creating collection from upload by @ahmedhamidawan in #20367

• Make invocation errors more compact by @ahmedhamidawan in #20369

• Generate a tenant-unique UID for tapis. by @dannon in #20370

• Use router to route to creating a new file source by @ahmedhamidawan in #20374

• Fix radio button options in CopyModal by @davelopez in #20378

• Fix conda_link to use platform.machine() for architecture detection by @chrisagrams in #20381

• Fix create file source button, show only at root by @davelopez in #20385

• Force Monaco into a separate bundle by @dannon in #20396

• Prevent waiting for history item state to be ok in uploader by @ahmedhamidawan in #20397

• Fix toolshed-installed tool icons by @dannon in #20399

• Add job config variable for singularity –contain by @bernt-matthias in #20400

• Fix form select input sorting by @davelopez in #20401

• Bug fix: allow any collection type in FormCollectionType. by @jmchilton in #20403

• Fixes for the admin jobs interface by @martenson in #20405

• Fix $app attribute access in cheetah templates by @mvdbeek in #20414

• Fix job rerun with tool version change by @mvdbeek in #20417

• Update pulsar-galaxy-lib to 0.15.8 by @mvdbeek in #20419

• Update triggers by @jdavcs in #20425

• Fix workflow logo URL not being persisted. by @jmchilton in #20428

• Fix css alignment styling of login page by @ahmedhamidawan in #20429

• Add user-facing explanation for legacy workflow run form usage by @ahmedhamidawan in #20431

• Upgrade tensorflow conditional dependency version to 2.15.1 by @cat-bro in #20434

• Fix copying of job metrics for cached jobs by @mvdbeek in #20436

• Dataset Display and Preferred Viz fixes by @dannon in #20439

• Wrap Tool and Workflow run headers properly by @ahmedhamidawan in #20440

• Fix inconsistent styling in List Collection Builder selector by @ahmedhamidawan in #20442

• Fix add button is enabled when empty tag list by @davelopez in #20443

• Set GALAXY_CONFIG_FILE env var if starting handler with -c by @mvdbeek in #20449

• Fix pagination state in FilesDialog by @davelopez in #20452

• Data Libraries - persist number of entries displayed in folders by @dannon in #20455

• Fix multiple remote file upload to collection creator by @ahmedhamidawan in #20456

• Bug fix: paired_or_unpaired also endswith paired. by @jmchilton in #20458

• Fix bug with handling compressed file names while auto-pairing. by @jmchilton in #20459

• Fix dataset error button not using router by @ahmedhamidawan in #20472

• Don’t fit workflow if it doesn’t have steps by @mvdbeek in #20480

• Remove rename modal from List Collection Creator by @ahmedhamidawan in #20487

• Use DatasetAsImage component for DatasetView image display by @dannon in #20488

• Recreate triggers by @jdavcs in #20491

• Allow workflow description to show full text by @davelopez in #20500

Enhancements

• Dynamic options: add data table filter by @bernt-matthias in #12941

• Run the tool working dir backup/restore on Pulsar by @natefoo in #16696

• Strip galaxy filename annotation on upload by @GomeChas in #18561

• Isolate singularity containers more thoroughly for better reproducibility. by @rhpvorderman in #18628

• Upgrade bundled/requested node version to 22.15.0 by @dannon in #18710

• Workflow Editor Activity Bar by @ElectronicBlueberry in #18729

• Add author and tools details in RO-Crate by @Marie59 in #18820

• Extend image metadata by @kostrykin in #18951

• Implement tool markdown reports. by @jmchilton in #19054

• Avoid persisting credentials on checkout step of the Github actions by @arash77 in #19089

• Let file sources choose a path for uploaded files by @kysrpex in #19154

• Move heatmap visualization to new script endpoint by @guerler in #19176

• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181

• Update Python dependencies by @galaxybot in #19190

• Move phylocanvas to script entry point by @guerler in #19193

• Fix UP031 errors - Part 1 by @nsoranzo in #19194

• Drop thumbs up reaction as pull request approval method by @nsoranzo in #19202

• Fix UP031 errors - Part 2 by @nsoranzo in #19204

• Add plotly.js by @guerler in #19206

• Switch h5web to script endpoint by @guerler in #19211

• Update visualizations to latest charts package by @guerler in #19213

• Fix UP031 errors - Part 3 by @nsoranzo in #19218

• Add Vitessce Viewer by @guerler in #19227

• Fix UP031 errors - Part 4 by @nsoranzo in #19235

• Explicitly add cwl-utils to dependencies by @nsoranzo in #19257

• Refactor for better reuse of workflow parameter type constants by @nsoranzo in #19260

• Fix UP031 errors - Part 5 by @nsoranzo in #19282

• Workflow Run Form Enhancements by @ahmedhamidawan in #19294

• Minor drag style adjustment for activities by @guerler in #19299

• Extract and typescript-ify datatype selection in wfeditor. by @jmchilton in #19304

• Migrate WF Collection Input Form Definition to Client Side by @jmchilton in #19313

• Fix UP031 errors - Part 6 by @nsoranzo in #19314

• eLabFTW integration via Galaxy file source by @kysrpex in #19319

• Update pydantic to 2.10.3 by @nsoranzo in #19326

• Add workflow selection and bulk actions by @itisAliRH in #19336

• Refactor and add tests for Popovers by @guerler in #19337

• Use popper wrapper for help text popover by @guerler in #19340

• Misc fixes 202412 by @nsoranzo in #19341

• Rework some form components for reuse. by @jmchilton in #19347

• Hide outdated visualizations from visualizations activity panel by @guerler in #19353

• Update Python dependencies by @galaxybot in #19366

• Add Dataverse RDM repository integration by @KaiOnGitHub in #19367

• Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372

• Make conditional discriminators literals instead of generic string/bool by @mvdbeek in #19374

• Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in #19377

• Remove apptainer-version pin by @nsoranzo in #19380

• Clarify that extra_scopes is sometimes non-optional by @martenson in #19385

• SQLAlchemy 2.0 follow-up by @jdavcs in #19388

• Documentation around highlighting PRs for release notes. by @jmchilton in #19390

• Change galaxy system user uid for K8s image by @afgane in #19403

• Gulp build improvements, update. by @dannon in #19405

• Set safe default extraction filter for tar archives by @nsoranzo in #19406

• Remove transaction helper by @jdavcs in #19407

• Prevent users from reusing a banned email after account is purged by @jdavcs in #19413

• Irods objectstore templates by @pauldg in #19415

• Update Python dependencies by @galaxybot in #19418

• Enable cloning subworkflows by @ElectronicBlueberry in #19420

• Allow controlling strict channel priority in mulled-build by @bernt-matthias in #19425

• Add IGB display support for CRAM files by @paige-kulzer in #19428

• Document $__user_name__ by @bernt-matthias in #19433

• Add User-Defined Tools by @mvdbeek in #19434

• Type annotations improvements by @nsoranzo in #19442

• Handles S3 listing errors by @itisAliRH in #19446

• Improve asynchronous tasks error handling and reporting by @davelopez in #19448

• Reset invocation export wizard after completion by @davelopez in #19449

• Workflow Editor Auto Zoom by @ElectronicBlueberry in #19451

• Update main citation to 2024 community paper by @nsoranzo in #19453

• Add test that verifies workflow source_metadata is preserved on landing claim by @mvdbeek in #19454

• Update Python dependencies by @galaxybot in #19464

• Type annotation improvements by @nsoranzo in #19485

• Add eLabFTW file source from file source templates by @kysrpex in #19493

• Update Python dependencies by @galaxybot in #19510

• Remote File Sources and Storage Locations redesign by @itisAliRH in #19521

• Support setting and displaying timezone with the core metrics plugin by @natefoo in #19527

• Allow to send notifications when Admins cancel jobs by @davelopez in #19547

• Add config options for tool dependency installs by @afgane in #19565

• Update Python dependencies by @galaxybot in #19567

• Remove tags used by @ElectronicBlueberry in #19576

• Support setting masthead height in a theme by @ksuderman in #19581

• Expand workflow metadata for readme. by @jmchilton in #19591

• Add vue-tsc baseline comparison to client-lint workflow by @dannon in #19593

• Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in #19594

• Enhance OpenAI Chat Integration by @uwwint in #19612

• Add InvenioRDM file source template by @davelopez in #19619

• Use discriminated unions in object stores and file source template configs by @davelopez in #19621

• Use correct plugin_kind in user file sources by @davelopez in #19622

• Update Python dependencies by @galaxybot in #19623

• Format code with black 25.1.0 by @nsoranzo in #19625

• Add Zenodo file source template by @davelopez in #19638

• Type annotation improvements by @nsoranzo in #19642

• Workflow landing request - collapse activity bar by default. by @dannon in #19652

• Enhance ListHeader Component for Reusability by @itisAliRH in #19655

• Add Breadcrumb Heading Component by @itisAliRH in #19656

• Mention default values for truevalue and falsevalue by @pvanheus in #19657

• Update test_create_dataset_in_subfolder to check for the dataset presence by @davelopez in #19660

• Relax job status check in test_delete_user_cancel_all_jobs by @davelopez in #19661

• Refactor dependencies for tool output actions. by @jmchilton in #19662

• More Vue Typescript Fixes by @jmchilton in #19663

• Click to edit history name in HistoryPanel by @ahmedhamidawan in #19665

• Generate correct types for Dataset source transformations on backend. by @jmchilton in #19666

• Remove unused(?) data_dialog form element type. by @jmchilton in #19669

• Add webdavclient3 to conditional-requirements.txt by @bgruening in #19671

• Update Python dependencies by @galaxybot in #19682

• Drop support for Python 3.8 by @nsoranzo in #19685

• Define simple models for job messages. by @jmchilton in #19688

• Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. by @jaidevjoshi83 in #19689

• Add forgotten linter test by @bernt-matthias in #19690

• Fix MarkdownDialog types by @davelopez in #19703

• Move RequiredAppT back into galaxy packages. by @jmchilton in #19704

• Use model classes from galaxy.model instead of app.model object - Part 1 by @nsoranzo in #19706

• Improved simplicity and isolation in transiently failing test. by @jmchilton in #19709

• Update RStudio IT by @afgane in #19711

• Speedup mulled build test by @bernt-matthias in #19712

• Update TypeScript version to 5.7.3 by @davelopez in #19713

• Augments popper wrapper, add click and escape handler by @guerler in #19717

• Move vega wrapper to shared common directory and add error handler by @guerler in #19718

• Move Markdown components to subdirectory for modularity by @guerler in #19719

• Rucio templates by @SergeyYakubov in #19720

• Preserve workflow labels in final invocation reports by @guerler in #19721

• ToolShed 2.1 - Various bugfixes and enhancements. by @jmchilton in #19722

• Use model classes from galaxy.model instead of app.model object - Part 2 by @nsoranzo in #19726

• Update Python dependencies by @galaxybot in #19727

• Add a script to reorganize tool data based on the new layout for genomic Data Managers by @natefoo in #19728

• Move history watcher and minor fixes by @guerler in #19732

• Fix Tours and add tooltips to history items by @guerler in #19734

• Show workflow help (and readme?) in run form by @ahmedhamidawan in #19736

• Enhance breadcrumb navigation UX in small screen sizes by @itisAliRH in #19737

• ToolShed2 - Add more context when navigating between tools an repositories. by @jmchilton in #19738

• Improvements to package decomposition. by @jmchilton in #19759

• Add cell-based markdown editor for pages by @guerler in #19769

• Rename tool “Citations” to “References” by @nsoranzo in #19770

• Update Python dependencies by @galaxybot in #19772

• Add visualization framework interface to cell-based markdown editor by @guerler in #19775

• Allow overriding datatypes for planemo lint by @selten in #19780

• Introduce reusable GCard component for unified card layout by @itisAliRH in #19785

• Add history sharing and accessibility management view by @ahmedhamidawan in #19786

• Add bigbed to bed converter and tests by @d-callan in #19787

• xsd: use CollectionType for collections in tests by @bernt-matthias in #19802

• Update Python dependencies by @galaxybot in #19816

• Workflow Run Form Enhancements follow up by @ahmedhamidawan in #19825

• More user feedback in FormRulesEdit (for Apply Rules tool) by @jmchilton in #19827

• Use direct icon references in FormSelectMany.vue. by @jmchilton in #19829

• Populate image metadata without allocating memory for the entire image content by @kostrykin in #19830

• Syntactic sugar to ease TPV configuration. by @jmchilton in #19834

• Improve markdown editor modularity and structure by @guerler in #19835

• Add mandatory RO-Crate metadata when exporting by @elichad in #19846

• Enable lazy loading for ace-builds by @ElectronicBlueberry in #19847

• Add basic support for icons in tools by @davelopez in #19850

• Webpack build performance improvements by @dannon in #19851

• Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852

• Client circular dependency check by @dannon in #19858

• Migrate from Prism to Monaco for ToolSource display. by @dannon in #19861

• Drop old galaxy_session records by @jdavcs in #19872

• Update Python dependencies by @galaxybot in #19874

• Add Tapis auth support by @dannon in #19887

• Make preferences drop down available in single user deployments by @ksuderman in #19888

• Clarify is_active method usage for Python Social Auth in Galaxy by @dannon in #19899

• FITS Graph Viewer - script name tweak. by @dannon in #19902

• Improve docs for output filters by @bernt-matthias in #19904

• Various styling improvements to Workflow Run and Invocation views by @ahmedhamidawan in #19905

• Overhaul workflow runtime settings display. by @dannon in #19906

• Allow embedding vitessce visualizations by @mvdbeek in #19909

• Replace backend-based page creation controller endpoint by @guerler in #19914

• Remove unnecessary code duplications by @nsoranzo in #19921

• Migrate Page editing controller endpoint to API by @guerler in #19923

• RStudio IT updates to work on .org by @afgane in #19924

• Update Python dependencies by @galaxybot in #19929

• Show pre-populated landing data values in workflow run form by @ahmedhamidawan in #19935

• Drop old job metrics by @jdavcs in #19936

• Fix local import in __resolvers_dict by @mvdbeek in #19944

• First steps of bootstrap replacement by @ElectronicBlueberry in #19946

• Decrease sentry_sdk.errors log level to INFO by @natefoo in #19951

• Allow PathLike parameters in make_fast_zipfile() by @nsoranzo in #19955

• Add link to view history on dataset info page by @natefoo in #19956

• Allow resizing Visualizations in Markdown editor by @guerler in #19958

• Add share button for invocations by @ahmedhamidawan in #19959

• Add type hints around collection copying and job things by @mvdbeek in #19961

• Job cache allow different names when possible by @mvdbeek in #19962

• Button replacement batch 1 by @ElectronicBlueberry in #19963

• Update Python dependencies by @galaxybot in #19964

• Adds a trimInputs prop to FormGeneric to trim string values on submit. by @dannon in #19971

• Add Katex Equation rendering plugin to Markdown Editor by @guerler in #19988

• Allow different AI providers (as long as they are openai compatible) by @uwwint in #19989

• Button replacement batch 2 by @ElectronicBlueberry in #19990

• Improve type annotation of tool parameter wrapping by @nsoranzo in #19991

• Add Niivue viewer by @guerler in #19995

• IT Activity Panel by @dannon in #19996

• Selenium test cases for running workflow from form upload. by @jmchilton in #19997

• Update Python dependencies by @galaxybot in #19998

• Restore Visualization insertion options in Reports Editor by @guerler in #20000

• Implement dataset collection support in workflow landing requests by @mvdbeek in #20004

• Add kepler.gl visualization by @guerler in #20005

• Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008

• Update vitessce version by @mvdbeek in #20016

• Merge Inputs/Parameters and Outputs/Collections Tabs by @ahmedhamidawan in #20019

• Show workflow README in split view next to the form inputs by @ahmedhamidawan in #20026

• Add vitesscejson datatype by @guerler in #20027

• Add VTK Visualization Toolkit Plugin by @guerler in #20028

• Move README to center panel in workflow editor by @ahmedhamidawan in #20029

• Add help text popovers for workflow runtime settings by @ahmedhamidawan in #20031

• Add rerun option for workflows by @ahmedhamidawan in #20032

• Add DOI to workflow metadata by @jdavcs in #20033

• Add support for Markdown help text in visualizations by @guerler in #20043

• Add sample datasets for visualizations by @guerler in #20046

• Add ZIP explorer to import individual files from local or remote ZIP archives by @davelopez in #20054

• Add docx datatype by @bgruening in #20055

• Add markdown datatype by @bgruening in #20056

• Add flac audio format by @bgruening in #20057

• Client refactorings ahead of #19377. by @jmchilton in #20059

• Add rd datatype by @richard-burhans in #20060

• GLink implementation by @ElectronicBlueberry in #20063

• GCard Full Description by @itisAliRH in #20064

• Enhance Storage Dashboard Selected Item UI by @itisAliRH in #20070

• Add activity panel width to local storage by @ahmedhamidawan in #20072

• Hide non-functional and replaced visualizations (e.g. Nora, MSA) by @guerler in #20077

• Flexible mapping from collection parameter types to collection builder components. by @jmchilton in #20082

• Route to creating a new file source in remote file browser modal by @ahmedhamidawan in #20084

• Use visualization dropdown solely for examples by @guerler in #20094

• Set node version to 22.13.0 by @davelopez in #20095

• Update Python dependencies by @galaxybot in #20096

• Adds Example Datasets and Help Text for Visualizations by @guerler in #20097

• Enhance external login interface styling by @ahmedhamidawan in #20100

• Add Molstar by @guerler in #20101

• Improve type annotation of galaxy.util submodules by @nsoranzo in #20104

• Add alignment.js for multiple sequence alignment rendering by @guerler in #20110

• Add specific datatypes for Cytoscape and Kepler.gl by @guerler in #20117

• Run integration tests on latest Ubuntu by @nsoranzo in #20118

• Add role creation form by @guerler in #20119

• Migrate Transition Systems Visualization by @guerler in #20125

• Add logo, description and help for aequatus by @guerler in #20128

• Drop now unused controller method by @mvdbeek in #20129

• Add updated PCA plot by @guerler in #20140

• Browse multiple trees in phylocanvas by @guerler in #20141

• Add more metadata, esp infer_from to datatypes configuration by @bgruening in #20142

• Show job ids on job success by @ahmedhamidawan in #20145

• Additional type hints for toolbox.get_tool / toolbox.has_tool by @mvdbeek in #20150

• Create working dir output outside of tool evaluator by @mvdbeek in #20153

• Improved rule builder display for non-nested lists (most of them). by @jmchilton in #20156

• Revise transiently failing data source test. by @jmchilton in #20157

• Yaml parser fixes and improvements (part 1) by @mvdbeek in #20158

• Fix remaining vue-tsc errors by @dannon in #20163

• Add three AAI providers by @martenson in #20165

• Add replacement_dataset option to collection filter tools by @simonbray in #20166

• Implement file source to integrate Galaxy with RSpace by @kysrpex in #20167

• G modal implementation by @ElectronicBlueberry in #20168

• Add client package by @natefoo in #20171

• Add JupyterLite by @guerler in #20174

• Standalone Galaxy API Client Package by @dannon in #20181

• Add visualization test data by @nilchia in #20183

• Bump vega from 5.30.0 to 5.32.0 in /client by @mvdbeek in #20188

• Visualization-First Display functionality by @dannon in #20190

• Improve type annotation of galaxy.model.dataset_collections by @nsoranzo in #20194

• Have make dist in the web_client package build the client by @natefoo in #20195

• Add plotly 6.0.1 to JupyterLite by @guerler in #20201

• Enable visualizations for anonymous user by @guerler in #20210

• Migrate ChiraViz by @guerler in #20214

• Display invocation inputs and outputs in workflow report by @mvdbeek in #20222

• Use TUS streaming and remove redundant IndexDB temp store in Zip Explorer by @davelopez in #20226

• Add more descriptions to custom tool source schema by @mvdbeek in #20266

• Improve handling of very large files in Tabulator by @guerler in #20271

• Touch up Dataset View by @guerler in #20290

• Improve performance of job cache query by @mvdbeek in #20319

• Remove type import side-effects by @ElectronicBlueberry in #20321

• Enable retrieving contents from extra file paths when request contains leading / by @mvdbeek in #20336

• DatasetView and Card Polish by @dannon in #20342

• Release notes by @ahmedhamidawan in #20386

• Deprecate enable_tool_document_cache by @nsoranzo in #20433

• Update tiffviewer to latest version supporting more formats by @davelopez in #20457

• Add Aladin as standard FITS viewer by @bgruening in #20465

• Add molstar as default viewer for some molecule formats by @bgruening in #20467

• Add /api/datasets/{dataset_id}/extra_files/raw/{filename:path} by @mvdbeek in #20468

Other changes

• Merge 24.2 into dev. by @jmchilton in #19273

• Fix package versions by @jdavcs in #19566

• Merge 24.2 into dev by @jdavcs in #19590

• Bump @babel/runtime-corejs3 from 7.23.2 to 7.26.10 in /client by @dependabot[bot] in #19788

• Rebuild API schema for latest dev. by @jmchilton in #19789

• Make job cache generally available by @dannon in #19798

• Fix workflow license component typing by @guerler in #19878

• Fix import and update_page type signature by @mvdbeek in #19932

• Merge 24.2 into dev by @ahmedhamidawan in #19933

• Log controller exceptions by @natefoo in #19974

• Fix copying job output from discovered outputs by @mvdbeek in #19999

• Add env var to skip CircularDependencyPlugin in development mode by @dannon in #20038

• Bump h11 from 0.14.0 to 0.16.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20088

• Fix formatting in webapp and client/install.py by @dannon in #20185

• Bump default milestone to 25.1 by @mvdbeek in #20189

• Bump axios from 1.7.4 to 1.8.2 in /client by @dependabot[bot] in #20205

• Bug fixes around wizard usage. by @jmchilton in #20224

• Bug fix - allow file drops into PasteData widget. by @jmchilton in #20232

• Only show custom tool editor in activity bar settings when user has access by @mvdbeek in #20247

• Fix job rerun for dynamic tools by @mvdbeek in #20259

• Add 25.0 migration tags by @ahmedhamidawan in #20265

• Update version to 25.0.rc1 by @ahmedhamidawan in #20267

• Bug fix - auto-pairing step not connected to collection builder in wizard. by @jmchilton in #20345

• Fix minor IT panel/display issues by @dannon in #20404

• Rename vitessce_json file_ext to vitessce.json by @mvdbeek in #20473

24.2.4 (2025-06-17)

Bug fixes

• Fix #19515 - invalid citation handling changed with 24.2. by @jmchilton in #19716

• Fix collection builder input states by @mvdbeek in #19797

• Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819

• Backport #19810: Fix workflow param tests not updating param type. by @mvdbeek in #19820

• Fix various job concurrency limit issues by @mvdbeek in #19824

• Do not reorder options in FormSelect component when multiselect disabled by @jdavcs in #19837

• Decode/encode FormDirectory paths to allow spaces (and other characters) by @ahmedhamidawan in #19841

• Try to recover from recurring activation link error by @jdavcs in #19844

• Add spacing between workflow author and invocation count by @ahmedhamidawan in #19849

• Fix default ordering of items sorted by name by @jdavcs in #19853

• Handle directories with percents directories with export_remote.xml. by @jmchilton in #19865

• Fix drag and drop for dataset collection elements by @ahmedhamidawan in #19866

• Don’t collect unnamed outputs twice in extended metadata mode by @mvdbeek in #19868

• Check if index exists before creating by @jdavcs in #19873

• Lazy-load invocation step jobs as needed by @mvdbeek in #19877

• Fix tabular metadata setting on pulsar with remote metadata by @mvdbeek in #19891

• Skip data_meta filter in run form by @mvdbeek in #19895

• Drop unused alembic-utils from galaxy-data package requirements by @nsoranzo in #19896

• Fix duplicate extensions for data inputs by @ahmedhamidawan in #19903

• Skip implicit HDA conversions in DataToolParameter options by @davelopez in #19911

• Fix duplicate entries when using drag and drop in multiple mode by @davelopez in #19913

• Let pysam use extra threads available in job by @mvdbeek in #19917

• Handle special charater in raw SQL by @jdavcs in #19925

• Report TestCaseValidation as linter error for 24.2 and above by @bernt-matthias in #19928

• Better interactive tool entry point query by @mvdbeek in #19942

• Drop unnecessary job cache job subquery by @mvdbeek in #19945

• Use make_fast_zipfile directly by @mvdbeek in #19947

• Fix attempt restriction on multiple connections by @mvdbeek in #19948

• Fix various parameter validation issues. by @jmchilton in #19949

• Sort intersected options by @mvdbeek in #19953

• Do not print OIDC access tokens to the logs by @kysrpex in #19966

• Renew OIDC access tokens using valid refresh tokens by @kysrpex in #19967

• Fix bug in psa-authnz redirect handling by @dannon in #19968

• Add missing job state history entry for queued state by @mvdbeek in #19977

• Restrict job cache to terminal jobs (and other fixes) by @mvdbeek in #19978

• Do not display default labels obscuring selectable options in a vue-multiselect component by @jdavcs in #19981

• Fix dynamic filter option access when building command line by @mvdbeek in #19982

• Always set copy_elements to true by @mvdbeek in #19985

• ChatGXY Error Handling by @dannon in #19987

• Ensure job states are fetched in invocation view by @ahmedhamidawan in #20010

• Renew access tokens from PSA using valid refresh tokens by @kysrpex in #20040

• Fix edit permission for datasets delete button in storage dashboard overview by location by @itisAliRH in #20066

• Job cache backports by @mvdbeek in #20078

• Fix mulled-search –destination quay, add index reuse by @natefoo in #20107

• Fix edam selenium test by @mvdbeek in #20134

• Skip param_value filter if ref value is runtime value by @mvdbeek in #20144

• Fix DataCollectionParameterModel factory by @mvdbeek in #20164

• Fix invocation failure dataset reference by @mvdbeek in #20200

• Conditionally import from galaxy.config in galaxy.model.mapping if TYPE_CHECKING by @natefoo in #20209

• Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by @natefoo in #20239

• Fall back to name in job summary if no input label given by @mvdbeek in #20258

• Fix WF Run RO-Crate logo width in Firefox by @davelopez in #20305

• Fix searching roles in admin UI by @jdavcs in #20394

• Skip validation of expression.json input in workflow parameter validator by @mvdbeek in #20412

• Fix unit tests returning values by @nsoranzo in #20413

• Fix mull_targets() with mamba 2.x by @nsoranzo in #20416

• Make response header values strings by @mvdbeek in #20475

• Fix legacy get_metadata_file controller route by @mvdbeek in #20477

• Prevent running datatype autodetect on purged datasets by @mvdbeek in #20479

• Link workflow invocation outputs upon importing invocation by @mvdbeek in #20485

• Make optional edam-ontology in datatypes registry optional by @natefoo in #20492

Enhancements

• Bump up max_peek_size to 50MB by @mvdbeek in #19823

• Point install_requires at requirements.txt file by @mvdbeek in #19864

• Fix Invenio file source downloads not working with some Invenio instances by @davelopez in #19930

• Update selectable object stores after adding or editing them by @davelopez in #19992

Other changes

• Backport parts of #19659 by @bernt-matthias in #19805

• Remove unused client route for standalone wizard interface by @dannon in #19836

• Publish pre-built client with (point-)release by @mvdbeek in #19879

• Update dev package version in meta package by @natefoo in #20159

19.9.0 (2019-11-21)

• Initial import from dev branch of Galaxy during 19.09 development cycle.