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This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
May 2021 Galaxy Release (v 21.05)¶

Highlights¶
- New development stack
- Galaxy release 21.09 will ship with a new web framework (fastAPI),
Celery task queue and process management using Circus. You can preview new stack now by running
APP_WEBSERVER=dev ./run.sh
. - Celery for background tasks
- Galaxy can now run certain tasks in the background. The Celery workers are currently not required, but if activated can perform certain long-running tasks, such as creating history export archives. Celery tasks will bridge the gap between rapid requests that can be handled during a web request and jobs that require extensive and relatively slow setup. (Pull Request 11789, Pull Request 11772, Pull Request 11720)
- More robust selection of job handlers
- Job throughput can be increased by starting Galaxy with multiple external job handler processes. Jobs were traditionally assigned to a job handler process by the web handler or workflow handler process that created the job. Since Release 19.01 Galaxy has supported additional mechanisms that use database serialization techniques to let job handlers assign processes to themselves. This mechanism is more robust and doesn’t require that all job handler processes be alive and known by the web handler process. Galaxy now determines the best method for assigning jobs based on the database in use, if the assignment method is not set explicitly. Older job assignment methods will be removed in Galaxy release 21.09. For more details see the Job Handler Assignment Methods section of the Galaxy documentation. ( Pull Request 11792)
Also check out the 21.05 user release notes
Deprecation Notices¶
- Deprecation of support for PostgreSQL < 9.5
- When using PostgreSQL as database server, Galaxy now requires PostgreSQL 9.5 or newer. Instructions for updating PostgreSQL can be found in the official documentation.
Upcoming Deprecation Notices¶
- Deprecation of support for Python 3.6 in Galaxy release 21.09
- This Galaxy release (21.05) will be the last release that supports Python 3.6 or newer. We encourage updating to a newer Python if possible.
- Deprecation of uwsgi and paste
- This Galaxy release (21.05) will be the last release that supports the WSGI standard, and with it uwsgi and paste. From release 21.09 Galaxy will be an ASGI application. We will update documentation and playbooks during the upcoming development cycle to enable a smooth transition.
Configuration Changes¶
Added¶
The following configuration options are new
config/user_preferences_extra_conf.yml.sample¶
- preferences.dropbox
- preferences.owncloud
config/galaxy.yml.sample:galaxy¶
- mapping.galaxy.mapping.cache_dir
- mapping.galaxy.mapping.enable_celery_tasks
- mapping.galaxy.mapping.flush_per_n_datasets
- mapping.galaxy.mapping.matomo_server
- mapping.galaxy.mapping.matomo_site_id
- mapping.galaxy.mapping.plausible_domain
- mapping.galaxy.mapping.plausible_server
- mapping.galaxy.mapping.statsd_mock_calls
Changed¶
The following configuration options have been changed
config/user_preferences_extra_conf.yml.sample¶
preferences.localization.inputs has changed from
[{'label': 'Prefered language', 'name': 'locale', 'options': [['Navigator default', 'auto'], ['Chinese', 'zh'], ['English', 'en'], ['French', 'fr'], ['Japanese', 'ja']], 'required': False, 'type': 'select'}]
to
[{'label': 'Prefered language', 'name': 'locale', 'options': [['Navigator default', 'auto'], ['中文', 'zh'], ['English', 'en'], ['Español', 'es'], ['Français', 'fr'], ['日本語', 'ja']], 'required': False, 'type': 'select'}]
Removed¶
The following configuration options have been completely removed
config/galaxy.yml.sample:galaxy¶
- mapping.galaxy.mapping.transfer_manager_port
New Configuration Files¶
The following files are new, or recently converted to yaml
config/file_sources_conf.yml.sample
Get Galaxy¶
The code lives at GitHub and you should have Git to obtain it.
- To get a new Galaxy repository run:
$ git clone -b release_21.05 https://github.com/galaxyproject/galaxy.git
- To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_21.05 && git pull --ff-only origin release_21.05
See the community hub for additional details on source code locations.
Release Notes¶
Enhancements¶
- Beta History scrolling behavior and polling efficiency tuning Pull Request 11693
- Add FastAPI routes for tours Pull Request 11089
- Add FastAPI routes for datatypes (thanks to @davelopez). Pull Request 11098
- Add cache_dir to schema Pull Request 11202
- Allow requesting extra scopes (thanks to @hexylena). Pull Request 11561
- Github workflow for updating dependencies Pull Request 11570
- Allow line break html tag in markdown pages Pull Request 11592
- Allow workflow imports in pages Pull Request 11607
- Add option to download collections in markdown pages Pull Request 11676
- Add the SimText shiny app as Interactive Tool (thanks to @dlal-group). Pull Request 11680
- Replace sqlalchemy-utilities with local implementation Pull Request 11696
- Circus + Celery - MVP Pull Request 11720
- Support role and group permissions in file sources plugins (thanks to @davelopez). Pull Request 11769
- Add circus + gunicorn option when using run.sh Pull Request 11772
- Run history export setup via celery, if configured Pull Request 11789
- Allow importing histories through pages / reports Pull Request 11863
- Migrate api/genomes to fastapi Pull Request 11241
- Add FlowCytometry and MetaCyto datatypes (thanks to @pcm32). Pull Request 9807
- Add mrc datatype (and Python dependency) (thanks to @gregvonkuster). Pull Request 11220
- Add HHR datatype (thanks to @bgruening). Pull Request 11661
- add meryldb datatype (thanks to @bgruening). Pull Request 11694
- Add datatype for PretextMap output Pull Request 11747
- add new datatype class for meryldb (thanks to @bgruening). Pull Request 11758
- Add Avivator GEDA and sniffer for ome.tiff datatype (thanks to @qiagu). Pull Request 11801
- jellyfish db datatype (thanks to @astrovsky01). Pull Request 11802
- Add new datatype JPEG 2000 in Galaxy (thanks to @annefou). Pull Request 11812
- Adding h5_model datatype for machine leaning models (thanks to @qiagu). Pull Request 11825
- Add support for the Relion STAR data format (thanks to @gregvonkuster). Pull Request 11831
- Add minerva display app for covid (thanks to @hexylena). Pull Request 11880
- Add toml datatype (thanks to @jj-umn). Pull Request 11909
- grep, tail, head: add option to keep header (thanks to @bernt-matthias). Pull Request 11859
- add a bit of docs to the add tags tool (thanks to @bernt-matthias). Pull Request 11874
- Add failed-to-submit error handling for simplified workflow run form Pull Request 12124
- Selenium test case for invocation grid + display. Pull Request 11160
- be more verbose on output filter errors (thanks to @bernt-matthias). Pull Request 11197
- Add UpgradeAllSteps workflow refactor action (thanks to @simonbray). Pull Request 11429
- Guess tool name when extracting workflows with imported datasets (thanks to @davelopez). Pull Request 11483
- Avoid appending imported source on workflow name multiple times. (thanks to @davelopez). Pull Request 11671
- Switch default handler assignment to skip locked or transaction isolation if possible Pull Request 11792
- Client testing/linting updates and followup Pull Request 11121
- replaced global vue with test vue in unit tests Pull Request 11138
- Manage folder rewrite in Vue & VueRouter (thanks to @OlegZharkov). Pull Request 11259
- Copy to Clipboard button next to the tool id in job information (thanks to @OlegZharkov). Pull Request 11478
- Better webpack-dev-server handling. Pull Request 11566
- Speed up get history list Pull Request 11883
- Implement switch to history modal for beta history panel Pull Request 11895
- Store job_id on Dataset table. Pull Request 10222
- Handle unschedulable jobs in k8s runner (thanks to @almahmoud). Pull Request 10496
- Establish a best practice for trans dependency management. Pull Request 11113
- Adding GALAXY_MEMORY_MB_PER_SLOT to k8s runner (thanks to @almahmoud). Pull Request 11227
- add reworked chronos job runner (thanks to @mtangaro). Pull Request 11228
- Generalise rule helper to detect whether tools can use any container (thanks to @pcm32). Pull Request 11274
- Only return a subset of jobs ready to run per user when querying for jobs ready to run Pull Request 11358
- ITs on Kubernetes (thanks to @almahmoud). Pull Request 11383
- Read cgroups from cgroup filesystem mount rather than cgget, which is not always installed Pull Request 11393
- SLURM: stop editing job stderr file (thanks to @bernt-matthias). Pull Request 11575
- Fixes for extended metadata working with Pulsar. Pull Request 11788
- Fix collection state updates by setting collection update time Pull Request 11849
- Test a better Pulsar configuration for extended metadata. Pull Request 11852
- Add handler column in admin jobs, remove webcontroller Pull Request 11868
- improve three debug messages (thanks to @bernt-matthias). Pull Request 11908
- Add documentation on how to setup Pulsar’s two-container job runner Pull Request 11557
- sortable columns in Admin->Users (thanks to @OlegZharkov). Pull Request 11665
- Create install database with create_db.sh Pull Request 11753
- Include more info on test input staging exception Pull Request 11953
- Add indexes on update_time columns used in ORDER BY clauses Pull Request 11988
- Don’t assert output_metadata state Pull Request 12100
- Fix and enhance subworkflow step upgrade messages Pull Request 12120
- Performance testing infrastructure. Pull Request 10117
- Stub MQ docs (thanks to @brinkmanlab). Pull Request 10347
- Implement read-only conda resolver. Pull Request 10810
- really test variables in conditionals (thanks to @bernt-matthias). Pull Request 11111
- Updated API Design Guidelines Pull Request 11115
- uvicorn-compatible factory function for fastapi. Pull Request 11116
- Dynamic discovery of FastAPI routers. Pull Request 11124
- FastAPI routes for configuration Pull Request 11126
- Start type signature for UniverseApplication. Pull Request 11142
- Various testing framework cleanups. Pull Request 11156
- FastAPI routes for tool data tables (thanks to @davelopez). Pull Request 11167
- Recommend 2FA and commit signing (thanks to @nsoranzo). Pull Request 11173
- Warns that build_mulled_singularity requires docker (thanks to @pcm32). Pull Request 11176
- Documentation and helpers for using galaxy-selenium package within Jupyter Pull Request 11177
- History beta poll decay time reset Pull Request 11178
- Holistic approach to dependency injection. Pull Request 11180
- Selenium test for
library_import_dir
(thanks to @OlegZharkov). Pull Request 11188 - Replace pipenv with poetry. Update all dependencies (thanks to @nsoranzo). Pull Request 11192
- Add missing xml:lang attribute to documentation annotations (thanks to @davelopez). Pull Request 11198
- Selenium tests for user library import dir (thanks to @OlegZharkov). Pull Request 11203
- FastAPI route for remote files (thanks to @davelopez). Pull Request 11211
- More debug info for failed integration selenium tests during CI. Pull Request 11217
- Implement abstraction around InferringApiRouter tailored to typical Galaxy usage. Pull Request 11219
- FastAPI route for tags (Disabled) (thanks to @davelopez). Pull Request 11224
- Remove folder_up button from data folder (thanks to @OlegZharkov). Pull Request 11230
- add ActionChains example in documentation of galaxy-selenium package within Jupyter (thanks to @OlegZharkov). Pull Request 11232
- Sync x-frame-options handling across frameworks and test. Pull Request 11235
- FastAPI/ASGI CORS handling. Pull Request 11240
- FastAPI routes for Pages (Disabled) (thanks to @davelopez). Pull Request 11262
- Don’t fail silently in User.system_user_pwent() (thanks to @nsoranzo). Pull Request 11272
- Move docstring linting to GitHub workflows (thanks to @nsoranzo). Pull Request 11300
- Add Nuwan Goonasekera to the committers group Pull Request 11304
- ignore subdirectories if recurse is false (thanks to @bernt-matthias). Pull Request 11307
- Fix transiently failing roles API test. Pull Request 11319
- Allow GET /api/dataset_collections/{hdca_id} without specifying instance_type (thanks to @nsoranzo). Pull Request 11346
- Add support for Plausible analytics and Matomo analytics (thanks to @selten). Pull Request 11351
- Lint for optional or multiple selects with radio display (thanks to @bernt-matthias). Pull Request 11385
- Test library dataset permissions (thanks to @OlegZharkov). Pull Request 11402
- Use request id middleware to scope session Pull Request 11411
- Move unit tests to GitHub workflows, test also under Python 3.9 (thanks to @nsoranzo). Pull Request 11452
- Allow anonymous access to S3 buckets via file sources plugins. Pull Request 11458
- add copy tooldID btn (thanks to @OlegZharkov). Pull Request 11477
- Libraries rewrite (thanks to @OlegZharkov). Pull Request 11485
- adding nameSuggestion to PairCollectionCreator (thanks to @assuntad23). Pull Request 11489
- xsd: use validator as child of param (thanks to @bernt-matthias). Pull Request 11497
- add sshfs plugin to the new file infrastructure (thanks to @bgruening). Pull Request 11507
- add ftp files.plugin (thanks to @bgruening). Pull Request 11508
- Add ready-to-go gitpod config Pull Request 11509
- Create pull_request_template.md (thanks to @assuntad23). Pull Request 11530
- Add more filtering options to api/jobs endpoint (thanks to @rikeshi). Pull Request 11560
- Migrate metrics API to FastAPI (thanks to @davelopez). Pull Request 11568
- Sample conf for dropbox and owncloud file sources (thanks to @abretaud). Pull Request 11580
- An attempt to improve dependency management Pull Request 11619
- Overhaul make-based release process Pull Request 11641
- Pin fs.webdavfs requirement to latest version (thanks to @abretaud). Pull Request 11648
- Update all Python dependencies (thanks to @nsoranzo). Pull Request 11649
- update to cope with impending changes to cwltool internals (thanks to @rupertnash). Pull Request 11655
- Lint for duplicated options (thanks to @bernt-matthias). Pull Request 11662
- Single User Mode - Disable irrelevant and broken options Pull Request 11669
- Swap ‘Analyze Data’ to home icon Pull Request 11674
- Bugfix/11476/disabled upload button explanation (thanks to @assuntad23). Pull Request 11682
- Break up dynamic dataset collection into chunks Pull Request 11697
- enable the S3 plugin to use non-AWS resrouces (thanks to @bgruening). Pull Request 11703
- Implement selenium tests for exporting library datasets to history collections. (thanks to @OlegZharkov). Pull Request 11716
- lint for checkboxes select (thanks to @bernt-matthias). Pull Request 11727
- Refactor stdout/stderr in Job Information (thanks to @OlegZharkov). Pull Request 11731
- Copy collections dbkey (thanks to @assuntad23). Pull Request 11732
- Fix CI docs build for feature branches (thanks to @nsoranzo). Pull Request 11740
- Updated Code of Conduct to point to the exact copy of this CoC on the hub. Pull Request 11750
- Allow AWS s3 access for ec2 instances without hardcoding credentials (thanks to @crashGoBoom). Pull Request 11757
- Add an explicit statement of assent to licensing to the pull request template Pull Request 11777
- Fixes for installed Galaxy Pull Request 11779
- Update Python dependencies Pull Request 11782
- Handle deprecated postgresql db urls; update postgres version in ci Pull Request 11790
- Update localisation options to include Español (thanks to @hexylena). Pull Request 11791
- Open update deps PRs from galaxybot’s fork (thanks to @nsoranzo). Pull Request 11795
- Make k8s container 39 MB smaller by using vim-tiny (thanks to @rhpvorderman). Pull Request 11826
- Make tool parameter options capable of referring to metadata file (thanks to @qiagu). Pull Request 11832
- Restore triggers dropped in #10821 (thanks to @nsoranzo). Pull Request 11843
- Do not invoke workflow if not all tools are available (thanks to @simonbray). Pull Request 11844
- Improve error handling when creating a new History with the master API key (thanks to @davelopez). Pull Request 11846
- Expose StoredWorkflowId in invocation API (thanks to @simonbray). Pull Request 11871
- Create FastAPI entry points for Tool Shed and Reports (thanks to @davelopez). Pull Request 11872
- Rev mypy. Pull Request 11877
- Backport #11871 (thanks to @scholtalbers). Pull Request 11881
- Allow to filter /api/invocations by job_id (thanks to @scholtalbers). Pull Request 11882
- Complete Spanish language version (thanks to @nomadscientist). Pull Request 11891
- Add subpathing to k8s_persistent_volume_claims (thanks to @anvilproject). Pull Request 11899
- Make _metadata regular JSONType field Pull Request 11902
- Abstraction for fetching qualified app URL across webapp types Pull Request 11904
- Add
delete account
selenium test (thanks to @OlegZharkov). Pull Request 11905 - Update framework dependencies Pull Request 11907
- expose copied_from_ldda_id on dataset api endpoint (thanks to @scholtalbers). Pull Request 11922
- Fix remaining issues reported by bugbear; add it to flake8 reqs (thanks to @nsoranzo). Pull Request 11153
- Fix all E203, E741 and W504 flake8 errors (thanks to @nsoranzo). Pull Request 11155
- Remove unused TS methods. Pull Request 11179
- Remove some seemingly unused cruft in GalaxyWebTransaction Pull Request 11234
- Drop unused transfer_manager.py Pull Request 11238
- Get rid of legacy decorator in api/tours Pull Request 11253
- Update vscode dev instructions, drop helper script Pull Request 11258
- Replace $.isArray with Array prototype check Pull Request 11264
- Drop docker testing image Pull Request 11329
- Renamed virtualscroller since it is no longer virtual Pull Request 11331
- Dataset lib permissions Vue rewrite (thanks to @OlegZharkov). Pull Request 11347
- Refactor libraries API logic into LibrariesManager (thanks to @davelopez). Pull Request 11359
- Refactor display_applications API logic into DisplayApplicationsManager (thanks to @davelopez). Pull Request 11386
- Repair styleguide Pull Request 11404
- Refactor groups API logic into GroupsManager (thanks to @davelopez). Pull Request 11412
- Refactor group_roles API logic into GroupRolesManager (thanks to @davelopez). Pull Request 11417
- Refactor group_users API logic into GroupUsersManager (thanks to @davelopez). Pull Request 11418
- Pin mypy to 0.790 to prevent linting errors when running v 0.8 Pull Request 11422
- Use galaxy Router instead of InferringRouter (thanks to @davelopez). Pull Request 11591
- Front-end Library Routing refactor (thanks to @OlegZharkov). Pull Request 11614
- Remove unused TraceLogger class (thanks to @nsoranzo). Pull Request 11616
- Refactor library folder API logic into FoldersService (thanks to @davelopez). Pull Request 11631
- Rewrite Library Permissions (thanks to @OlegZharkov). Pull Request 11637
- Fix prop mutation in FolderTopBar (thanks to @OlegZharkov). Pull Request 11638
- Refactor library folder contents api (thanks to @davelopez). Pull Request 11686
- Update Python dependencies Pull Request 11702
- Partial refactor ShareableMixin into ShareableService (thanks to @davelopez). Pull Request 11712
- Incorporate changes from Pulsar’s copy of galaxy.jobs.runners.util Pull Request 11810
- Separate tests for “remote” and “remote + extended” metadata. Pull Request 11840
- Unify security decode id exceptions (thanks to @davelopez). Pull Request 11856
- Optimized beta history polling by leveraging history.update_time + loading behavior bug fixes Pull Request 11884
- Eslint tweaks Pull Request 11925
Fixes¶
- Shared visualization display fix Pull Request 11906
- remove duplicated qcml from datatypes_conf sample (thanks to @bernt-matthias). Pull Request 11378
- Limit max column in tabular dataset preview Pull Request 11901
- Use keep_original in pysam.tabix_index to not remove original data Pull Request 11913
- Open input file in read mode in liftover wrapper Pull Request 12001
- Resolve session problems, enabled pages and tags fastAPI routes Pull Request 11342
- Make filter work with file containing header (thanks to @bernt-matthias). Pull Request 11365
- Fix copying text in workflow editor Pull Request 12118
- Make failure to save workflow dismissible Pull Request 12122
- Allow trs_version to refer to name or id field Pull Request 12021
- Workflow editor null/zero fixes Pull Request 11265
- Fix reconnecting terminals Pull Request 11660
- Fix tags not included when importing shared workflow (thanks to @davelopez). Pull Request 11663
- Fix workflow rename dropping metadata. Pull Request 11670
- Use Modal to show wrong RuntimeValue Pull Request 11678
- Ensure new outputs have correct mapOver state Pull Request 11683
- Redraw connections when adding or removing inputs Pull Request 11684
- Fix displaying data column parameters in workflow editor Pull Request 11692
- Fix workflow refactor schema parsing for pydantic 1.8. Pull Request 11778
- fix undefined error in ui-file-source (thanks to @OlegZharkov). Pull Request 11586
- Remove filter from list:paired element names when filter is not _1 Pull Request 11486
- Beta history current history mismatch with legacy code. Pull Request 11850
- Reposition history scroller during new updates Pull Request 11879
- ITs on K8S tweaks and SSL (thanks to @almahmoud). Pull Request 11947
- Fix anonymous user job walltime query Pull Request 11951
- Fix container port parsing if IPv6 hostname is
::
Pull Request 11955 - Fix isolated job home dir on pulsar Pull Request 12037
- Don’t start workflow scheduler for handler in job pool Pull Request 12075
- Fix set metadata for primary discovered outputs Pull Request 12088
- Fix mule job messaging Pull Request 11148
- Deal with empty claim names in k8s runner (thanks to @nuwang). Pull Request 11223
- Fix SLURM runner for real user setups and avoid uneccesary chowns (thanks to @bernt-matthias). Pull Request 11403
- Prevent endless fail_job cycles Pull Request 11673
- Fix value of ‘unknown_error’ resubmit condition variable (thanks to @brinkmanlab). Pull Request 11749
- Pulsar: mark cancelled jobs as finished (thanks to @abretaud). Pull Request 11763
- Lower tool id case while populating resource params (thanks to @eancelet). Pull Request 11793
- Don’t overwrite $GALAXY_MEMORY_MB if it’s already set Pull Request 11808
- Transfer fewer unneeded files back to Galaxy when using remote extended metadata with Pulsar. Pull Request 11814
- Don’t write job and job-related attributes when creating export model Pull Request 11815
- Handle resubmission before changing job state in CLI runner (thanks to @pcm32). Pull Request 11886
- fix broken docs links Pull Request 11384
- Add missing ssl keyword in nginx example [docs] (thanks to @rhpvorderman). Pull Request 11633
- Create history_audit table to avoid write deadlocks during history.update_time updates Pull Request 11914
- Fix GET /api/datasets/ docs (thanks to @nsoranzo). Pull Request 11933
- Don’t move the update_time goalpost (thanks to @nsoranzo). Pull Request 11934
- Force galaxy_id to string in galactic_job_json (thanks to @simonbray). Pull Request 11965
- Update default base images, make DEFAULT_CHANNELS configurable via env var Pull Request 11966
- Fix mulled singularity building Pull Request 11979
- restrict invalid input in library pagination (thanks to @OlegZharkov). Pull Request 11996
- Fix breadcrumb in dataset details in libraries (thanks to @OlegZharkov). Pull Request 11998
- Fix deleted libs for user (thanks to @OlegZharkov). Pull Request 12011
- fix library dataset permissions (thanks to @OlegZharkov). Pull Request 12015
- Disable import button during “Import to History” (thanks to @OlegZharkov). Pull Request 12016
- Hide edit libraries for users (thanks to @OlegZharkov). Pull Request 12023
- Fix downloading (sub)folders from data-libraries (thanks to @OlegZharkov). Pull Request 12028
- Fix subworkflow / update all steps upgrade action Pull Request 12029
- Fix uploading multiple files in ftp upload / choose remote files Pull Request 12030
- add GALAXY_MEMORY_MB* to passt hrough (thanks to @bgruening). Pull Request 12039
- invocation_time report fix Pull Request 12070
- Fix edit field reactivity in libraries (thanks to @OlegZharkov). Pull Request 12080
- Fix select all in import from history backbone modal (thanks to @OlegZharkov). Pull Request 12082
- Fix export select_all in collections (thanks to @OlegZharkov). Pull Request 12086
- fix library search filter (thanks to @OlegZharkov). Pull Request 12087
- Fix name of datasets with invalid contents Pull Request 12107
- Beta History: implement missing advanced search filters Pull Request 10972
- Fix mypy error with Union in response_model (thanks to @davelopez). Pull Request 11132
- Minor spelling error fix (thanks to @selten). Pull Request 11135
- Fix permission in user dir library import (thanks to @OlegZharkov). Pull Request 11137
- fix error message (thanks to @bernt-matthias). Pull Request 11157
- changing tooltip to match functionality (thanks to @assuntad23). Pull Request 11204
- Copy only dataset tags in Extract Dataset tool (thanks to @pvanheus). Pull Request 11206
- Fix regression of ‘disabled’ masthead items. Pull Request 11215
- fix test_user_library_import_dir_warning (thanks to @OlegZharkov). Pull Request 11226
- Make OIDC email matching case-insensitive (thanks to @selten). Pull Request 11251
- Tool XML container requirements: fix example (thanks to @selten). Pull Request 11271
- Bugfix/8488/rule builder fails for one bad url (thanks to @assuntad23). Pull Request 11276
- Fix printing non-dict output in api/display script Pull Request 11278
- Fix images in workflow PDF report (thanks to @OlegZharkov). Pull Request 11296
- consider collections in all tests (thanks to @bernt-matthias). Pull Request 11313
- Replace Query with Path Pull Request 11320
- Custos aud handling fix Pull Request 11322
- Get latest pull request labels in maintenance bot (thanks to @nsoranzo). Pull Request 11326
- Update OIDC links (thanks to @selten). Pull Request 11362
- fix profile logic for configfile generation (thanks to @bernt-matthias). Pull Request 11380
- Standardise tool param attribute docs (thanks to @nsoranzo). Pull Request 11390
- Run maintainance bot on ready_for_review and edit Pull Request 11400
- Decrease verbosity of messages in poetry Pull Request 11405
- Rename fixtures to fix test database object name conflict Pull Request 11424
- Check for binary files at the middle of the file instead of at the beginning (thanks to @pcm32). Pull Request 11425
- Set default USE_UVICORN to true only on python >= 3.7 Pull Request 11454
- Fix galaxy.files.sources plugin unit tests being missed by CI. Pull Request 11469
- Fix exception handling in datasets display API. Pull Request 11482
- Mark some tool reload tests as expected to fail (thanks to @davelopez). Pull Request 11496
- Fix clearing of search inputs Pull Request 11526
- Fix bug with Pulsar and $__tool_directory__ (thanks to @abretaud). Pull Request 11599
- Allow any extra field in Pages API (thanks to @davelopez). Pull Request 11600
- Fix workflow labelling Pull Request 11604
- Pin refgenconf to <0.10.0 (thanks to @nsoranzo). Pull Request 11627
- Pin SQAlchemy to <1.4.0 Pull Request 11629
- Change Upload button tooltip position (thanks to @OlegZharkov). Pull Request 11634
- Set minimum requirements for starlette-context and fastapi Pull Request 11643
- Match environment variable set up by doc building workflow Pull Request 11646
- Don’t check for missing kind/ label for minor merged PRs (thanks to @nsoranzo). Pull Request 11647
- Library folder_contents API tests + small fixes (thanks to @davelopez). Pull Request 11650
- Refactor default mounting of $tmp_directory in containers (thanks to @brinkmanlab). Pull Request 11654
- Fix datatype defined column name display Pull Request 11664
- Expose command line if expose_dataset_path is set Pull Request 11687
- Hotfix/paired list builder from data library (thanks to @assuntad23). Pull Request 11700
- Make extra user preferences behave like defaultdict Pull Request 11708
- Fix importing collections to new history and import correct elements Pull Request 11718
- Removedreference to remove-extensions (thanks to @assuntad23). Pull Request 11724
- Refgenie table del (thanks to @abretaud). Pull Request 11728
- Fix job filtering by date_range_max / date_range_mix (thanks to @nsoranzo). Pull Request 11736
- Fix a bug when unzipping collections with nametags. Pull Request 11741
- Fix API job filtering by workflow or invocation (thanks to @nsoranzo). Pull Request 11751
- Assorted tool shed fixes Pull Request 11762
- Fix format=”input” with implicit conversions Pull Request 11764
- galaxy.webapps.tool_shed to webapp.tool_shed (thanks to @almahmoud). Pull Request 11765
- Fix auto-pair naming in list paired creator. Pull Request 11773
- Fix library scrolling Pull Request 11776
- Use assertRaisesRegex() to fix new B017 linting errors (thanks to @nsoranzo). Pull Request 11783
- Fix typo in upstream_mod_zip admin docs (thanks to @nsoranzo). Pull Request 11794
- Fix tool profile details in schema docs (thanks to @nsoranzo). Pull Request 11798
- Activate virtualenv in updateucsc.sh.sample (thanks to @nsoranzo). Pull Request 11800
- Backport #11815: Don’t write job and job-related attributes when creating export model Pull Request 11816
- do not chown pasted urls (thanks to @bernt-matthias). Pull Request 11818
- Fixed uploader link on tool list and legacy empty history message Pull Request 11830
- Join QueueWorker thread Pull Request 11835
- Patch to click the button which should be more stable (thanks to @hexylena). Pull Request 11838
- fix data stickiness on folder change (thanks to @OlegZharkov). Pull Request 11845
- BUGFIX: Also check for boolean True, not just string ‘True’ when evaluating conditional dependencies. (thanks to @rhpvorderman). Pull Request 11861
- Fix
Delete account
visibility Pull Request 11897 - Fix S3 backend support in iRODS object store (thanks to @kxk302). Pull Request 11910
- fix GalaxyInteractorApi get_tool_tests (thanks to @cat-bro). Pull Request 11911
- Stabilize test_history_options selenium test Pull Request 11918
- update legacy_framework.grids.StateColumn (bug fix) (thanks to @cat-bro). Pull Request 11923
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