Warning
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 11188Replace 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 11905Update 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 11955Fix 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 11897Fix 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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