Galaxy server metapackage
Project description
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
25.0.1 (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
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
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
Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394
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
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 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
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
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
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
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
Fix NFDI auth by @bgruening in #20217
Fix next milestone by @martenson in #20219
Replace Bootstrap Popover with Popper wrapper by @guerler in #20246
Fix tool-provided metadata for CONVERTER_tar_to_directory by @mr-c in #20260
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
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 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
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
Prevent waiting for history item state to be ok in uploader by @ahmedhamidawan in #20397
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
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
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
Drop thumbs up reaction as pull request approval method by @nsoranzo in #19202
Update visualizations to latest charts package by @guerler in #19213
Explicitly add cwl-utils to dependencies by @nsoranzo in #19257
Refactor for better reuse of workflow parameter type constants by @nsoranzo in #19260
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
eLabFTW integration via Galaxy file source by @kysrpex in #19319
Add workflow selection and bulk actions by @itisAliRH in #19336
Use popper wrapper for help text popover by @guerler in #19340
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
Clarify that extra_scopes is sometimes non-optional by @martenson in #19385
Documentation around highlighting PRs for release notes. by @jmchilton in #19390
Change galaxy system user uid for K8s image by @afgane in #19403
Set safe default extraction filter for tar archives by @nsoranzo in #19406
Prevent users from reusing a banned email after account is purged by @jdavcs in #19413
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
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
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
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
Add Zenodo file source template by @davelopez in #19638
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
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
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
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
Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852
Migrate from Prism to Monaco for ToolSource display. by @dannon in #19861
Update Python dependencies by @galaxybot in #19874
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
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
Migrate Page editing controller endpoint to API by @guerler in #19923
Update Python dependencies by @galaxybot in #19929
Show pre-populated landing data values in workflow run form by @ahmedhamidawan in #19935
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
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
Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008
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
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 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
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
Migrate Transition Systems Visualization by @guerler in #20125
Add logo, description and help for aequatus by @guerler in #20128
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
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
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
Enable visualizations for anonymous user by @guerler in #20210
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
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
Release notes by @ahmedhamidawan in #20386
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
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
Fix import and update_page type signature by @mvdbeek in #19932
Merge 24.2 into dev by @ahmedhamidawan in #19933
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 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
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
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
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
Lazy-load invocation step jobs as needed by @mvdbeek in #19877
Fix tabular metadata setting on pulsar with remote metadata by @mvdbeek in #19891
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
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
Fix attempt restriction on multiple connections by @mvdbeek in #19948
Fix various parameter validation issues. by @jmchilton in #19949
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
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
Fix mulled-search –destination quay, add index reuse by @natefoo in #20107
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
Skip validation of expression.json input in workflow parameter validator by @mvdbeek in #20412
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
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
19.9.0 (2019-11-21)
Initial import from dev branch of Galaxy during 19.09 development cycle.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file galaxy-25.0.1.tar.gz
.
File metadata
- Download URL: galaxy-25.0.1.tar.gz
- Upload date:
- Size: 64.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/6.1.0 CPython/3.13.3
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 |
589f9604528f780c2eb49c258307e4acf5a0557bbce47210b03cb009328aad1d
|
|
MD5 |
84e447188169a9cdb0cc4cb0b43166e5
|
|
BLAKE2b-256 |
274b5935eac9ad8eb389409ea7d18b8e8206cf19f4836a06b04595f361285e76
|
File details
Details for the file galaxy-25.0.1-py3-none-any.whl
.
File metadata
- Download URL: galaxy-25.0.1-py3-none-any.whl
- Upload date:
- Size: 25.7 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/6.1.0 CPython/3.13.3
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 |
f8438802c097163e47a9138a4ca1f0d4b8f1bbc507e431fd359df9010c0356c1
|
|
MD5 |
a5e6c83dce298f771928f44ce8a6ce2f
|
|
BLAKE2b-256 |
70084741fd2c1083f31c13b04ee7ea0c34fd1e8e92b885ee5a239b724da56b43
|