January 2022 Galaxy Release (v 22.01)¶

Highlights¶

Galaxy starts as FastAPI application by default: Starting Galaxy via run.sh will use the new gravity process manager. The new configuration uses gunicorn and FastAPI to drive Galaxy’s web process and starts job handler and Celery processes automatically. For more details and instructions please consult the Migrating to Gunicorn documentation. (Pull Request 13224).
User Preferences can be encrypted in Galaxy Vault: Galaxy can now be configured to store secrets in an external vault, which is useful for secure handling and centralization of secrets management. In particular, information fields in the “Manage information” section of the user profile, such as dropbox keys, can be configured to be encrypted at rest in a vault (Hashicorp, Custos or database) instead of being stored as plain text in the user preferences table. For detailed information on configuration, refer to the vault section of the admin documentation. (Pull Request 12940).
Resumable uploads via tus.io, improved upload provenance: Galaxy now supports chunked and resumable uploads via the tus protocol. This is more performant and easier to setup than the current nginx-based solutions. For detailed configuration instructions, see the documentation. Galaxy now displays all manipulations that were performed during an upload, such as newline conversions, converting spaces to tabs or dataset grooming. (Pull Request 12656, Pull Request 12861, Pull Request 13313, Pull Request 12912).

Also check out the 22.01 user release notes

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_22.01 https://github.com/galaxyproject/galaxy.git

To update an existing Galaxy repository run:

$ git fetch origin && git checkout release_22.01 && git pull --ff-only origin release_22.01

See the community hub for additional details on source code locations.

Deprecation Notices¶

PostgreSQL 9.x is now EOL and is no longer supported. Please upgrade to PostgreSQL 10 or higher. Python 3.6 is officially EOL and Galaxy no longer tests or maintains compatibility. This release will be the last Galaxy release that can run under Paste or uWSGI. Please consult the Migrating to Gunicorn documentation for . instructions on how to upgrade.

Configuration Changes¶

Added¶

The following configuration options are new

config/galaxy.yml.sample:galaxy¶

mapping.galaxy.mapping.enable_tool_source_display
mapping.galaxy.mapping.galaxy_url_prefix
mapping.galaxy.mapping.load_tool_shed_datatypes
mapping.galaxy.mapping.max_discovered_files
mapping.galaxy.mapping.maximum_upload_file_size
mapping.galaxy.mapping.tool_evaluation_strategy
mapping.galaxy.mapping.tus_upload_store
mapping.galaxy.mapping.vault_config_file

Changed¶

The following configuration options have been changed

config/galaxy.yml.sample:galaxy¶

mapping.reports.mapping.file_path.default has changed from
```
database/files
```
to
```
database/objects
```

Removed¶

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy¶

mapping.galaxy.mapping.check_migrate_tools
mapping.galaxy.mapping.enable_openid
mapping.galaxy.mapping.force_beta_workflow_scheduled_for_collections
mapping.galaxy.mapping.force_beta_workflow_scheduled_min_steps
mapping.galaxy.mapping.openid_consumer_cache_path

Release Notes¶

Enhancements¶

Swap to Webpack5 Pull Request 11710
Remote / Late evaluation of tools Pull Request 12459
File sources for gdrive, gcs, onedata, basespace (thanks to @nuwang). Pull Request 12500
Add support for caching the Singularity cached images directory Pull Request 12524
Various extensions and improvements for asserts (thanks to @bernt-matthias). Pull Request 12528
New interactive tool - iSEE (thanks to @neoformit). Pull Request 12650
Resumable file uploads with tus.io Pull Request 12656
Make directory path editable in remote files (thanks to @OlegZharkov). Pull Request 12759
Display tool source in tool form Pull Request 12811
Modify history contents/near endpoint to support new history scroller Pull Request 12892
Vault abstraction for Galaxy (thanks to @nuwang). Pull Request 12940
Sort icon on List Collection Creator (thanks to @assuntad23). Pull Request 12945
Provide more context for lint context (thanks to @bernt-matthias). Pull Request 12978
Add mulled-hash command to galaxy-tool-util (thanks to @simonbray). Pull Request 13061
Add parquet to csv datatype converter Pull Request 13078
XML macros: add named yields, tokenized macros, tokens for attributes, and fix replacement of toplevel yield (thanks to @bernt-matthias). Pull Request 13152
Enable setting SQLALCHEMY_WARN_20 Pull Request 13171
Add new datatype GRIB (thanks to @annefou). Pull Request 13175
Use Gravity to run Galaxy Pull Request 13224
Add datatype iml_dataset subclassing html (thanks to @knutwa-ext). Pull Request 12099
Mark sniffer for fastqillumina as not implemented (thanks to @bernt-matthias). Pull Request 12685
Create sniffer for GRO file type (thanks to @simonbray). Pull Request 12885
Agp datatype Pull Request 12891
Type updates from @mr-c - part 2 (thanks to @common-workflow-lab). Pull Request 12899
3rd round of type updates to support CWL import (thanks to @common-workflow-lab). Pull Request 12913
Tighten type ignores (thanks to @common-workflow-lab). Pull Request 12965
Remove is_multi_byte (thanks to @bernt-matthias). Pull Request 12996
Add ludwig model datatype (thanks to @qiagu). Pull Request 13073
Add ampvis2 datatype (thanks to @bernt-matthias). Pull Request 13083
Add Neper and Gmsh datatypes (thanks to @jj-umn). Pull Request 13087
Add description of inpcrd and prmtop (thanks to @thepineapplepirate). Pull Request 13126
Add compression converter (thanks to @gallardoalba). Pull Request 13223
Change display_in_upload to true for PHAR datatype (thanks to @simonbray). Pull Request 13238
Add gz as datatype (thanks to @astrovsky01). Pull Request 13271
Limit required element validation to safe elements Pull Request 13299
Add phyloseq datatype (thanks to @bernt-matthias). Pull Request 13462
Allow any format in export tool (thanks to @astrovsky01). Pull Request 13151
Add bioconductor as valid xref for tools (thanks to @bgruening). Pull Request 13268
Test cases to verify only admins can import workflows from paths. Pull Request 12513
Remove deprecated workflow run path through the API. Pull Request 12516
Type updates (thanks to @common-workflow-lab). Pull Request 12868
Allow workflows to automatically filter inputs by tag (thanks to @astrovsky01). Pull Request 12930
Enable macros for workflow scheduler config (thanks to @bernt-matthias). Pull Request 13167
Remove history service worker Pull Request 12510
Implement fastAPI prefix handling, run selenium tests against prefix Pull Request 13103
Hide form fields and button upon successful submission of bug report Pull Request 13237
Fix toolbox cache Pull Request 13333
Limit maximum number of discovered files per job Pull Request 13170
Fixes for HTML sanitization (thanks to @abretaud). Pull Request 13059
Make admin user list sortable by last login (thanks to @cat-bro). Pull Request 13209
Support “show all running” in admin job interface Pull Request 13215
Add config variable for setting tus upload directory Pull Request 13313
Document gunicorn and nginx Pull Request 13436
Update interactive tool docs for Gunicorn / dropping uWSGI Pull Request 13470
Add Migrating from uWSGI to Gunicorn and FastAPI document Pull Request 13480
Support --preload and worker_id for server processes Pull Request 13514
Separated data PVC (thanks to @almahmoud). Pull Request 12345
Revised download() so parallel get() is utilized. Small refactor. (thanks to @kxk302). Pull Request 12522
More linting for requirements (thanks to @bernt-matthias). Pull Request 12527
Preserve important dataset metadata when importing/exporting histories. Pull Request 12537
Modify description of the “database” label Pull Request 12540
Add Oleg Zharkov to committers group Pull Request 12544
Add David López to committers group Pull Request 12545
Update container_resolvers_conf.xml.sample (thanks to @gmauro). Pull Request 12560
Add test for dataset HTML sanitization interface Pull Request 12573
FastAPI: migrate history contents routes (thanks to @davelopez). Pull Request 12578
Update localization directive to trim whitepsace around text content. Pull Request 12580
Added more caching for github actions which use tox and venv (thanks to @nuwang). Pull Request 12632
More typing for API tests (especially test_workflows). Pull Request 12636
Better model store abstractions. Pull Request 12638
More Python unit test typing fixes. Pull Request 12647
Annotate more tests as requiring Github to be online. Pull Request 12649
Change logged-in-as to use username (thanks to @hexylena). Pull Request 12652
Add buttons to expand and collapse history dataset display in pages Pull Request 12660
Formalize dependency of galaxy-data package on galaxy.files module. Pull Request 12665
Check types of modules without type annotations in the their signatures on new modules. Pull Request 12691
Rev Python tooling to latest mypy release. Pull Request 12695
Assorted random typing fixes. Pull Request 12696
Add Tag validation in API requests (thanks to @davelopez). Pull Request 12697
Framework support for integration tests requiring celery. Pull Request 12700
Allow passing Pydantic models as arguments to Celery tasks. Pull Request 12701
Discourage the use of true/falsevalue for boolean test parameters (thanks to @bernt-matthias). Pull Request 12706
Extend debugging test instructions for GHA Pull Request 12707
Split integration tests more evenly Pull Request 12711
Tool linter: simple test for test params absent from inputs (thanks to @bernt-matthias). Pull Request 12723
Add test for invoking a workflow on a new autocreated history (thanks to @nsoranzo). Pull Request 12773
More Python type fixes from deferred data branch. Pull Request 12778
Type fixes for HDAs and LDDAs manager. Pull Request 12780
FastAPI: migrate Dataset Collections API (thanks to @davelopez). Pull Request 12781
Type fixes for various visualization backend Python files. Pull Request 12783
Add various include/exclude patterns for github workflows Pull Request 12787
Force strict channel priority when building images with mulled (thanks to @rhpvorderman). Pull Request 12788
More type fixes for various pieces of managers code. Pull Request 12801
Beta history menu reorg, display fixes. Pull Request 12802
More type fixes for managers code. Pull Request 12812
Fixes and test for PDF generation. Pull Request 12813
Upgrade FastAPI to v0.70.0 (thanks to @davelopez). Pull Request 12836
Stronger typing of upload code. Pull Request 12845
Sync Selenium GitHub workflows (thanks to @nsoranzo). Pull Request 12849
Update all Python dependencies (thanks to @nsoranzo). Pull Request 12858
Drop legacy uploadpost Pull Request 12861
Vuefy color input form element (thanks to @OlegZharkov). Pull Request 12867
Show error codes when running mypy (thanks to @nsoranzo). Pull Request 12894
Update cwltool pin to 3.1.20211107152837 (thanks to @nsoranzo). Pull Request 12895
Increase directory check specificity, of particular use with AnVIL (thanks to @luke-c-sargent). Pull Request 12902
Create codeql-analysis.yml (thanks to @common-workflow-lab). Pull Request 12908
Improved Upload Provenance and Correctness Pull Request 12912
Update Python dependencies (thanks to @galaxybot). Pull Request 12916
Lint for option without text or value (thanks to @bernt-matthias). Pull Request 12921
FastAPI: migrate datasets API (thanks to @davelopez). Pull Request 12924
Vuefy Number and Slider Form inputs (thanks to @OlegZharkov). Pull Request 12937
Allow labeling of subworkflow outputs in parent workflow Pull Request 12939
Linting: check for test expecting failure with outputs (thanks to @bernt-matthias). Pull Request 12960
Add CWL conformance API tests (thanks to @nsoranzo). Pull Request 12966
Allow unit testing tool init to specify paths. (thanks to @common-workflow-lab). Pull Request 12969
Lint for inputs with redundant name (thanks to @bernt-matthias). Pull Request 12974
Support running celery when cwd is not galaxy_root by setting $GALAXY_ROOT_DIR Pull Request 12977
Split run_tool_raw() out of BaseDatasetPopulator.run_tool() (thanks to @nsoranzo). Pull Request 12994
Move galaxy_tasks decorator to galaxy.celery Pull Request 13000
Show display applications together with visualizations in center panel Pull Request 13018
Update Python dependencies (thanks to @galaxybot). Pull Request 13029
Explicit singularity cache (thanks to @rhpvorderman). Pull Request 13032
Add “diff-format” Makefile target (thanks to @common-workflow-lab). Pull Request 13034
Drop support for Python 3.6, add Python 3.10 (thanks to @nsoranzo). Pull Request 13035
Allow param_value filter to refer to parameters with multiple values (thanks to @bernt-matthias). Pull Request 13039
Add support for CWL CommandLineTool and ExpressionTool to DynamicToolManager.create_tool() (thanks to @nsoranzo). Pull Request 13041
Update Python dependencies (thanks to @galaxybot). Pull Request 13051
Allow admin access to datasets API (thanks to @davelopez). Pull Request 13060
Drop non-actionable warnings from LibraryPermissionsWarning Pull Request 13063
Beta History: homogeneous collection indication (thanks to @davelopez). Pull Request 13068
Add documentation for test/param/metadata in xsd (thanks to @bernt-matthias). Pull Request 13082
Update Python dependencies (thanks to @galaxybot). Pull Request 13086
Add tox environment and GitHub workflow for reports startup test (thanks to @nsoranzo). Pull Request 13088
Allow duplicated static options (thanks to @bernt-matthias). Pull Request 13094
Beta History: additional small fixes at collection level (thanks to @davelopez). Pull Request 13097
Add Back button in file source navigation and ftp helper text (thanks to @itisAliRH). Pull Request 13104
Add job reports for node types and execution times (thanks to @gregvonkuster). Pull Request 13121
Initial typing for model discover module. Pull Request 13123
Remove Oleg from committers list Pull Request 13128
Remove Dave C. from committers list Pull Request 13129
Update Python dependencies (thanks to @galaxybot). Pull Request 13135
Fix MetadataValidator (thanks to @bernt-matthias). Pull Request 13139
Update DatasetError.vue Pull Request 13148
Assorted Data Libraries fixes (thanks to @davelopez). Pull Request 13159
Provide even more context to the lint context (thanks to @bernt-matthias). Pull Request 13186
Skip non-Selenium tests if only lib/galaxy_test/selenium is touched Pull Request 13227
Add documentation for output action attributes (thanks to @bernt-matthias). Pull Request 13236
Add openPBS cli support, rebuild CLI test images Pull Request 13251
Add missing collection types to xsd doc (thanks to @bernt-matthias). Pull Request 13267
Update dependencies Pull Request 13273
Only create HDAH entries for undeleted HDAs (thanks to @bernt-matthias). Pull Request 13309
Add version.json for exposing extra api information about docker container (thanks to @nuwang). Pull Request 13433
Document gunicorn and apache Pull Request 13439
Update jobs and cluster documentation Pull Request 13440
Update performance tracking for Gunicorn Pull Request 13441
Drop interactive environment build instructions from docs Pull Request 13442
Create config package, move app-related functionality to app Pull Request 13461
Fix pgcleanup.py for datasets stored by UUID Pull Request 13474
Pin gravity to 0.10.0 Pull Request 13483
Include gravity in sample config Pull Request 13531
FastAPI: Histories API migration (thanks to @davelopez). Pull Request 12386
Vue component dangling bracket style fix (prettier upgrade) Pull Request 12428
Remove unused relationships from model Pull Request 12468
Remove workflow API hooks for tool shed. Pull Request 12512
Vueify Form Recursion Pull Request 12518
FastAPI: Add request wrapper for SessionRequestContext (thanks to @davelopez). Pull Request 12531
Update SQLAlchemy to 1.4.25 Pull Request 12538
Establish unittest utils for galaxy-{data,objectstore} packages. Pull Request 12546
Move API services to their own package (thanks to @davelopez). Pull Request 12548
Establish galaxy-app unit tests. Pull Request 12549
Establish galaxy-job-execution unit test directory. Pull Request 12550
Establish galaxy-job-metrics unit test directory. Pull Request 12551
Fix up small issues around packaging of galaxy-tool-util code. Pull Request 12552
Move more webapps unit tests in test/unit/webapps. Pull Request 12554
Share a tool_util unittest method via packing to fix up unit test dependencies. Pull Request 12555
Better path handling in app unit tests for packaging. Pull Request 12556
Selenium abstractions for dataset information. Pull Request 12569
TS model: declarative mapping + prep for SQLAlchemy 2.0 Pull Request 12666
Remove unused script and history_delete controller endpoint Pull Request 12668
Remove ui-table backbone component Pull Request 12671
Libraries (legacy) backbone entrypoint and component removal Pull Request 12674
Ignore type in unused function Pull Request 12694
Misc. fixes for SQLAlchemy 2.0 Pull Request 12698
Upgrade to lagom 1.4.1 (thanks to @meadsteve). Pull Request 12703
Remove galaxy.util.getfullargspec (thanks to @bernt-matthias). Pull Request 12755
Convert install_model to declarative mapping Pull Request 12756
Mapping tests: restructure, refactor, decouple session and engine, improve Pull Request 12765
New pyupgrade cleanups (thanks to @nsoranzo). Pull Request 12774
Refactor workflow bookmark (thanks to @OlegZharkov). Pull Request 12810
Replace boolean input parameter with Vue component in forms Pull Request 12820
Replace hidden field input element with Vue Pull Request 12841
Refactor datasets API (thanks to @davelopez). Pull Request 12847
Vuefy library folder details modal (thanks to @OlegZharkov). Pull Request 12886
Remove chart utilities and artifacts from code base Pull Request 12890
Vuefy DirectoryUri form input field (thanks to @OlegZharkov). Pull Request 12898
Simplify Augustus datatype sniffer (thanks to @nsoranzo). Pull Request 12905
Modify logic in history_contents/near to accommodate scroller Pull Request 12914
FastAPI: Add response wrapper for SessionRequestContext (thanks to @davelopez). Pull Request 12929
Eliminate a lot of while: True loops in datatype code Pull Request 12942
Small tweaks to facilitate deferred dataset implementation. Pull Request 12944
Modifications to next hid_counter generation Pull Request 12948
Don’t bind model’s MetaData to engine Pull Request 12949
Vuefy library dataset (thanks to @OlegZharkov). Pull Request 12950
Assorted mapping cleanup Pull Request 12951
Move wait_for_invocation_and_jobs() method to BaseWorkflowPopulator (thanks to @nsoranzo). Pull Request 12954
Avoid setting response headers through trans in datatypes (thanks to @davelopez). Pull Request 12956
Use lazy="joined" instead of lazy=False Pull Request 12962
Minor type fixes Pull Request 12963
Add type hints to JobHandlerQueue Pull Request 12976
Fix flaky legacy API tests (hopefully) (thanks to @davelopez). Pull Request 12980
Create select() construct explicitly Pull Request 12983
Remove unused dataset conversion code Pull Request 12991
Remove unnecessary list creations (thanks to @nsoranzo). Pull Request 13002
Don’t use triple-quoted strings as comments (thanks to @nsoranzo). Pull Request 13007
Misc fixes - round 4 (thanks to @nsoranzo). Pull Request 13026
Refactor uploadbox / partially remove jQuery Pull Request 13047
Initial refactoring to separate History rendering and provider components Pull Request 13049
Log missing version file as warning. Pull Request 13062
Importing math.inf no longer needs try/except Pull Request 13065
Avoid imports of history provider internals Pull Request 13098
Drop tool migration scripts and related code Pull Request 13099
Remove duplicated pydantic models (thanks to @davelopez). Pull Request 13125
Remove migrate tools-related code Pull Request 13163
Replace backref with back_populates Pull Request 13165
Prevent a future regression Pull Request 13218
Remove jquery.complexify from everywhere (thanks to @itisAliRH). Pull Request 13228
Replace custom tour ids in forms with regular DOM identifiers Pull Request 13252
Drop pkg_resources Pull Request 13454

Fixes¶

Large peptide IDs (thanks to @reid-wagner). Pull Request 13261
Try to unit test more of DictParser in Viz component. Pull Request 13385
Fix jqplot_bar import, adjust plugin hash saving Pull Request 13493
Allow trailing semicolon in last column of gff3 (thanks to @bernt-matthias). Pull Request 12673
Fix gff-version header sniffing (thanks to @nsoranzo). Pull Request 12676
Fix gff and scidx parsing (thanks to @bernt-matthias). Pull Request 12687
Version bump galaxy tool util and converter dependency fix Pull Request 12844
Downgrade bowtie requirement for CONVERTER_fasta_to_bowtie_color_index (thanks to @nsoranzo). Pull Request 12851
Fix constructive_solid_geometry.py for non_utf8_error (thanks to @jj-umn). Pull Request 13057
Show yaml files in preview Pull Request 13176
Enable display of BAM data without sequence info (thanks to @wm75). Pull Request 13219
Fix containerized NCBI Datasets Genomes data source tool Pull Request 12915
Update interactivetool_pyiron.xml (thanks to @gmauro). Pull Request 12990
Add dynamic step to FormNumber range slider (thanks to @davelopez). Pull Request 13233
FormNumber: notify value change on slider change (thanks to @davelopez). Pull Request 13260
Always display digest in name for refgenie assets. Pull Request 13403
Fix UnboundLocalError in sort collection tool (thanks to @davelopez). Pull Request 13429
Misc fixes - round 2 (thanks to @nsoranzo). Pull Request 12982
Fix workflow connections for outputs that are not displayed in uploads Pull Request 13174
Sync tool identifier string with tool version in workflow editor Pull Request 13185
Allow mapping of collection outputs to parameter inputs Pull Request 13189
Fix tool id update when updating tool shed tools in editor Pull Request 13196
Ensure tool_id/content_id is updated when refactoring workflows (thanks to @simonbray). Pull Request 13231
Fix construction of SelectToolParameter default value Pull Request 13293
Return actual tool id instead of specified tool id in workflow step Pull Request 13536
RxJS major version upgrade, client unit testing enhancements. Pull Request 12686
Polyfill overhaul, fixes. Pull Request 12889
Fix publicPath and asset handling when using webpack-dev-server for HMR Pull Request 13155
Bump markdown-it from 12.2.0 to 12.3.2 in /client Pull Request 13205
Bump engine.io from 4.1.1 to 4.1.2 in /client Pull Request 13206
Bump follow-redirects from 1.14.4 to 1.14.7 in /client Pull Request 13207
Bump log4js from 6.3.0 to 6.4.0 in /client Pull Request 13225
Bump nanoid from 3.1.29 to 3.2.0 in /client Pull Request 13226
Guard against instance of GenomeIndexToolData Pull Request 12523
Fix job runner shutdown Pull Request 12744
Fix parsing of yml job conf file in galaxy.dependencies (thanks to @cat-bro). Pull Request 12893
Rev pulsar-galaxy-lib. Pull Request 12896
Don’t pass all Galaxy environment variables to jobs (thanks to @nsoranzo). Pull Request 13011
Unit test fixes (thanks to @nsoranzo). Pull Request 13033
Fix re-run with rerun_remap_job_id hiding collection Pull Request 13157
Fix univa job runner setup without nativeSpecification (thanks to @Smithsonian). Pull Request 13301
Make __link_file_check more robust Pull Request 13316
Don’t record version command as part of command line Pull Request 13317
Fix resuming job when job has optional data parameters Pull Request 13325
Allow UNIVA destinations without runtime and memory max given in the nativespec (thanks to @bernt-matthias). Pull Request 13343
Fix header content-length, add test for send_file Pull Request 13120
Add option for disabling tool shed datatypes Pull Request 13250
Drop OpenID post authentication protocols Pull Request 13281
Restore Metadata size limit Pull Request 13315
Drop uWSGI from scaling documentation Pull Request 13381
Reimplement collection order test, add wrong order, add expect_test_failure attribute (thanks to @bernt-matthias). Pull Request 10304
Fix test_sharing_valid_by_id selenium test (thanks to @OlegZharkov). Pull Request 12547
Update and correct sample object store config file Pull Request 12571
Fix user_library_import_symlink_allowlist option (thanks to @scholtalbers). Pull Request 12608
Fix selenium populators to respect the json parameter. Pull Request 12626
Fix how beta history panel decides when downloads are available. Pull Request 12642
Typing fixes for various unit tests. Pull Request 12644
Fix database display for beta history panel. Pull Request 12646
Fix deprecation warnings from the threading module (thanks to @nsoranzo). Pull Request 12659
Join thread that hosts asyncio loop for embedded uvicorn Pull Request 12710
Removing unusable Name field from Collections upload (thanks to @assuntad23). Pull Request 12736
Removing last character of pair name for Paired List Collections if it’s a . or _ (thanks to @assuntad23). Pull Request 12739
Avoid double ‘/’ when generating fully qualified API URLs in API tests (thanks to @davelopez). Pull Request 12791
Create new history for anonymous API users via history/current_histor… Pull Request 12829
Avoid console error when cloning newly created nodes Pull Request 12831
GxITs: don’t always add trailing slash to entry point url (thanks to @abretaud). Pull Request 12833
fix typo in bookmarking (thanks to @OlegZharkov). Pull Request 12838
Fix bookmarking workflow twice (thanks to @OlegZharkov). Pull Request 12840
Temporary downgrade FastAPI to v0.68.2 (thanks to @davelopez). Pull Request 12856
Fix startup with edam (thanks to @abretaud). Pull Request 12860
Fixes for packages (thanks to @nsoranzo). Pull Request 12883
Fix parse_input_sources() method to return a list (thanks to @nsoranzo). Pull Request 12888
Consider a history not new once there are any items in it Pull Request 12897
Bump tensorflow from 2.5.1 to 2.5.2 in /lib/galaxy/dependencies Pull Request 12900
Sync package deps with pyproject.toml (thanks to @nsoranzo). Pull Request 12904
Fix menu overflow in right panel Pull Request 12906
Tweak docs for container_resolver_* options Pull Request 12910
Fix installation of tools with biotools id Pull Request 12919
Fix linter for select inputs (thanks to @bernt-matthias). Pull Request 12920
Fix OpenAPI docs not rendering (thanks to @davelopez). Pull Request 12923
Fix default value of runners in job_conf_dict (thanks to @nsoranzo). Pull Request 12926
Provide 2 types of scoped_session in DI (initially “type of session parameter should be scoped_session”) Pull Request 12931
Move the titleonly option to input element component Pull Request 12932
fix value_in_data_table validator for multiple selects (thanks to @bernt-matthias). Pull Request 12936
Update link to “Python for Biologists” page. (thanks to @neoformit). Pull Request 12946
Try cimg/node:14 to fix circleci js builds Pull Request 12947
Misc fixes (thanks to @nsoranzo). Pull Request 12972
BugFix: Update social-auth-core library version to fix OIDC problem (thanks to @IslamHeggy). Pull Request 12973
Fix Rerun in the new form (thanks to @OlegZharkov). Pull Request 12984
Show error message when history id is invalid (thanks to @OlegZharkov). Pull Request 12985
Reconstruct separate scoped session for ToolShedRepositoryCache Pull Request 12989
Misc fixes - round 3 (thanks to @nsoranzo). Pull Request 12993
Bump python-ldap from 3.2.0 to 3.4.0 in /lib/galaxy/dependencies Pull Request 13003
Fix known marcos typo Pull Request 13009
Refactor Sentry middleware/client changes for Tool Shed Pull Request 13010
Drop stream_template_mako function, replace with fill_template_mako Pull Request 13017
Copy HDCA member items to new history when copying history Pull Request 13021
Make dataset display route sessionless as well as anonymous Pull Request 13024
Trigger visualization update on chart initialization Pull Request 13025
Fix running test/integration/test_remote_files.py directly. Pull Request 13038
Misc fixes - round 5 (thanks to @nsoranzo). Pull Request 13044
Fix dynamic optional + multiple select parameters: allow to select no option (thanks to @bernt-matthias). Pull Request 13048
Add tools to IMPLICITLY_REQUIRED_TOOL_FILES in tools/__init__.py (thanks to @cat-bro). Pull Request 13050
Only check profile version in Galaxy Pull Request 13055
Fix private history publishing (thanks to @davelopez). Pull Request 13056
Improve dataset search help (thanks to @wm75). Pull Request 13058
Change default file_path variable for galaxy reports (thanks to @quacksawbones). Pull Request 13067
Drop old sqlalchemy patterns that break reports app Pull Request 13069
Add iRODS resource name in calls to irods (thanks to @kxk302). Pull Request 13072
Fix Cloud object store (thanks to @bioflowy). Pull Request 13074
Use yield_per option to limit amount of ORM objects loaded into memory Pull Request 13076
Fix issue with uploading cached file to irods (thanks to @kxk302). Pull Request 13080
Fix tag attribute parsing on input element (thanks to @astrovsky01). Pull Request 13081
Fix dataset details button when using prefix Pull Request 13092
Fix center panel reload when clicking help button Pull Request 13093
Limit possible size of info field, read only 100 MB of stdio Pull Request 13096
Disable cleanup thread for cloud object store in set metadata (thanks to @bioflowy). Pull Request 13102
Prevent select all in FilesDialog when no entries and select empty resource (thanks to @itisAliRH). Pull Request 13107
Fix selenium test via dropping redundant test case Pull Request 13112
Delay iframe creation for news until clicked Pull Request 13116
Webhooks robustification for news and gtn Pull Request 13118
Fix routing for tool execution from gtn webhook Pull Request 13130
Fix history import for datasets with tags Pull Request 13134
Add more required dependencies for installed Galaxy Pull Request 13143
Path resolution fixes for installed Galaxy Pull Request 13147
Limit lifetime of repository cache Pull Request 13154
converting forward and reverse filters to reactive Vue array (thanks to @assuntad23). Pull Request 13166
Fix stdio parsing (thanks to @bernt-matthias). Pull Request 13178
Catch exceptions when job.user is None (thanks to @rhpvorderman). Pull Request 13179
Fix redirect to login page when login is required to perform operations Pull Request 13188
Fix workflow invocation name overflow (thanks to @davelopez). Pull Request 13193
Fix metadata source access in tool shed Pull Request 13202
Fix error getting toolshed repo metadata when no repo found (thanks to @simonbray). Pull Request 13203
Bugfix for allowing +’s in tool urls Pull Request 13204
Fix test_deserialize_* unit tests (thanks to @nsoranzo). Pull Request 13208
Fix hide collections in batch (thanks to @davelopez). Pull Request 13214
Handle unique tag name constraints Pull Request 13216
Ensure that jQuery updates drop target locations during dragging Pull Request 13217
Fix adding new files via tarball upload Pull Request 13230
Initialize error attribute in input model for workflows Pull Request 13246
Fix imported sub-workflows cannot be edited (thanks to @davelopez). Pull Request 13254
Fix expect_test_failure for expect_num_outputs (thanks to @bernt-matthias). Pull Request 13265
Fix gravity requirement for Poetry (thanks to @nsoranzo). Pull Request 13278
Fix dataset details and drag and drop Pull Request 13290
Fix stopping ITs on slurm Pull Request 13304
Ensure Notification API is available prior to trying to use it Pull Request 13322
Fix toolbox handling of spaces in old tools Pull Request 13347
Fix macro parsing (thanks to @bernt-matthias). Pull Request 13373
Clarify that history exports are not kept forever Pull Request 13389
Fix history search help popover not closing on click outside (thanks to @davelopez). Pull Request 13390
Ensure $GRAVITY_STATE_DIR is present in venv activate script any time run.sh/common_startup.sh is called normally Pull Request 13392
Use a2wsgi to serve WSGI app Pull Request 13396
Dataset annotations are optional and should not be required Pull Request 13420
Fix repository uploads with remove_repo_files_not_in_tar Pull Request 13425
Wrap reports app in static, fix tool shed entry point Pull Request 13430
enabling Reset button for Rule Builder tab (thanks to @assuntad23). Pull Request 13443
Initial fix for quay.io repo query issue Pull Request 13468
Add profile version to ethercalc Pull Request 13469
Backport and fix webapps tests Pull Request 13478
Use timeout instead of interval when polling, optionally terminate polling Pull Request 13485
Pin corresponding playbook repo to sync with Galaxy release (thanks to @nuwang). Pull Request 13497

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