September 2020 Galaxy Release (v 20.09)¶

Highlights¶

Plugin framework for uploading datasets: Galaxy administrators can now configure different sources from which users may upload files. These include global or user-specifc webdav servers, dropbox accounts as well as FTP and regular filesystem locations. Developers can add new types of sources by adding PyFileSystem2 compatible plugins. (Pull Request 9888)
Workflow import from GA4GH TRS servers: Galaxy can now search and import workflows from GA4GH TRS servers, such as Dockstore and WorkflowHub. We hope that sharing workflows on these platforms will facilitate re-use and collaboration. (Pull Request 9999, Pull Request 10158)
Simplified workflow submission form: Galaxy now presents a simpler and cleaner interface for submitting workflows that focuses on the parameters to set and datasets to choose. (Pull Request 9151).
Accelerate batch job creation and workflow step scheduling: Galaxy now batches database interactions for the creation of batch jobs. For large batches of jobs this can speed up job creation by 100 fold or more. (Pull Request 9926, Pull Request 9980, Pull Request 9985, Pull Request 10008, Pull Request 10019)

Also check out the 20.09 user release notes

Configuration Changes¶

The following configuration options have been changed

config/tool_shed.yml.sample:

uwsgi.static-safe has changed from client/galaxy/images to client/src/assets

config/galaxy.yml.sample:

uwsgi.static-safe has changed from client/galaxy/images to client/src/assets

config/reports.yml.sample:

uwsgi.static-safe has changed from client/galaxy/images to client/src/assets

New Configuration Files¶

The following configuration file is new:

config/trs_servers_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_20.09 https://github.com/galaxyproject/galaxy.git

To update an existing Galaxy repository run:

$ git fetch origin && git checkout release_20.09 && git pull --ff-only origin release_20.09

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

Release Testing Team¶

A special thanks to the release testing team for testing many of the new features and reporting many bugs:

Release Notes¶

Enhancements¶

Simplified Workflow Run Form Pull Request 9151
Allow uploading directly from the tool form Pull Request 9809
Pluggable URI handling across upload components. Pull Request 9888
API + UI for importing workflows from a GA4GH TRS server. Pull Request 9999
GTN in Galaxy (thanks to @hexylena). Pull Request 10024
Revision of Workflow Reports Pull Request 10121
Markdown Editor Revision Pull Request 10134
GA4GH TRS Workflow Search Pull Request 10158
Vue rewrite of the data-library-folder (thanks to @OlegZharkov). Pull Request 9905
Improve workflow layout algorithm (thanks to @hexylena). Pull Request 10045
Added documentation for debugging Galaxy and unit/integration tests (thanks to @kxk302). Pull Request 9664
Feature/persist rule builder collection in web storage (thanks to @assuntad23). Pull Request 9718
Higlass InteractiveTool update (thanks to @astrovsky01). Pull Request 9805
Add allowed_cilogon list functionality (idphint short list) (thanks to @juleengraham). Pull Request 9862
Add lastdb datatype for last tool (thanks to @RomainDallet). Pull Request 9872
Adding user id to key so savedRules are specific for users (thanks to @assuntad23). Pull Request 9882
Add BLASTDBv5 datatype (for blast >=2.8.1) (thanks to @abretaud). Pull Request 9939
Add galaxyp MVP visualization plugin (thanks to @tmcgowan). Pull Request 10136
Connect/disconnect multiple custos (thanks to @juleengraham). Pull Request 10182
Add missing database indexes Pull Request 10385
Add build artifact destination for plugins Pull Request 9754
Plugin watchBuilding, and fixes for several older visualization builds Pull Request 10287
Add VCF_BGZIP to VCF converter (thanks to @almahmoud). Pull Request 7926
Add NcbiTaxonomySQlite class to describe NCBI Taxonomy SQLite databases (thanks to @pvanheus). Pull Request 9712
Add Anndata peek capability (thanks to @mtekman). Pull Request 10013
Add “tgz” datatype to config sample file for toolfactory and any other tools generating gzipped tar files (thanks to @fubar2). Pull Request 10080
Citations overhaul Pull Request 9757
Fix and simplify built-in trim tool (thanks to @wm75). Pull Request 10145
Allow unary plus and minus in filtering (thanks to @wm75). Pull Request 10154
Toolbox refactoring, styling, and a couple bugfixes Pull Request 10170
Support for BioCompute Object Export (thanks to @biocompute-objects). Pull Request 9077
Workflow reports: multiple argument & add single job parameter (thanks to @OlegZharkov). Pull Request 9686
Allow composite and extra file uploads via data fetch API. Pull Request 9860
Implement more Galaxy Markdown components. Pull Request 9938
Rework client datatype handling logic for reuse Pull Request 9955
Flush once for enqueue / workflow handler assignment Pull Request 10019
Workflow list: Add published column, add sort bookmarked (thanks to @OlegZharkov). Pull Request 10119
Add workflow invocation grabbing with db-skipped-lock Pull Request 10177
Add user-is-owner context for display of published workflows. Pull Request 10215
Allow execution of workflows for certain tool updates Pull Request 10569
Early 20.09 full client dependency update. Pull Request 9739
Improve mocha test output for rule DSL specification tests. Pull Request 9798
Change usage of whitelist/blacklist terms to allowlist/blocklist Pull Request 9864
Allow option to remember the previously used IDP for login (thanks to @juleengraham). Pull Request 10078
Infrastructure for writing to pluggable Galaxy file sources. Pull Request 10152
Add support for cleaning up kubernetes jobs after a specified number of seconds since finish (thanks to @nuwang). Pull Request 8122
Port and Vuefy AWS estimate from EU (thanks to @OlegZharkov). Pull Request 9621
View support for galaxy model, hdca.job_state_summary option Pull Request 9713
Allow tool submission with DatasetCollectionElements / make build_for_rerun consumable by API Pull Request 9802
Allow setting metadata_strategy per destination Pull Request 9956
Flush once per mapped over execution Pull Request 9985
Job cache improvements Pull Request 10020
Edit post-job email to add history link and format text (thanks to @astrovsky01). Pull Request 10133
Updated documentation to show how a job is de-queued and processed. (thanks to @kxk302). Pull Request 10185
Allow CLI runner modules to be loaded from sys.path Pull Request 10189
Make cached container resolver pick newest build (thanks to @torfinnnome). Pull Request 10242
Don’t run local runner job processes in an unnecessary shell (thanks to @nsoranzo). Pull Request 10257
Improve kubernetes job selection (thanks to @nuwang). Pull Request 10407
It docs additional info (thanks to @astrovsky01). Pull Request 9650
GitLab error reporting - further features (thanks to @selten). Pull Request 9775
Improve support for readonly tool caches Pull Request 10411
Dynamic options and metadata filter fixes (thanks to @bernt-matthias). Pull Request 8599
assign discovered extension, dbkey and designation for assign_primary=true (thanks to @bernt-matthias). Pull Request 9127
Add dataset deserializer for ‘datatype’ (thanks to @simonbray). Pull Request 9374
Add tests for admin interface jobs, dependencies, and containers sections Pull Request 9618
Remove DO_NOT_TEST from config unit tests Pull Request 9644
Framework for Browser Testing of Custom Configured Galaxy Instances Pull Request 9652
Clear error message for wrong authenticator type (thanks to @nsoranzo). Pull Request 9670
add doc for discover_datasets sort_by (thanks to @bernt-matthias). Pull Request 9674
Collection pagination api resource route Pull Request 9682
xsd, docs, and test for sort_by (discover_datasets) (thanks to @bernt-matthias). Pull Request 9684
Allow input element created by editable-text.js to change value on click/lose focus (thanks to @lawrence14701). Pull Request 9703
Allow oidc login icons to be specified through backend_config xml (thanks to @nuwang). Pull Request 9704
Display msg history no items (thanks to @lawrence14701). Pull Request 9706
Spinner in library folders (thanks to @OlegZharkov). Pull Request 9717
Implement HDCA update_time Pull Request 9722
Skip check for branch protection Pull Request 9723
Upgrade to the newer nodejs lts (v10 -> v12; 12.16.3) Pull Request 9725
Move containers test from selenium to selenium integration. Pull Request 9728
Update to IT comment (thanks to @astrovsky01). Pull Request 9735
Swap out node-sass for the new standard sass compiler Pull Request 9737
doc: dynamic destinations better set the id in JobDestination (thanks to @bernt-matthias). Pull Request 9742
Allow tool search on tool id and wildcard before search string (thanks to @juleengraham). Pull Request 9744
linkify Data Libraries description and bugfix (thanks to @OlegZharkov). Pull Request 9746
Improved dataset verification output (thanks to @bernt-matthias). Pull Request 9771
Added config parameter for irods connection pool size. (thanks to @kxk302). Pull Request 9774
Add selenium test for user toolbox filters. Pull Request 9782
Minor improvements to API errors Pull Request 9797
switch branch of IUC CI earlier in release process (thanks to @bernt-matthias). Pull Request 9806
Don’t use Backbone to define masthead elements. Pull Request 9811
Add selenium test for user API keys Pull Request 9820
More reactive, tested Masthead. Pull Request 9822
i18n for tool page about email notification (thanks to @shenweiyan). Pull Request 9830
Add option to text asserts to specify number of occurrences (thanks to @simonbray). Pull Request 9831
History DBkey and refactor dataset state (thanks to @OlegZharkov). Pull Request 9841
History Panel Tags&Annotation (thanks to @OlegZharkov). Pull Request 9846
Add support for relative paths in dependency resolver mappings (thanks to @rupertnash). Pull Request 9855
History structure (thanks to @OlegZharkov). Pull Request 9858
Improved UploadModal state handling during initialization. Pull Request 9869
Feature/9669 sort collection for paired collections (thanks to @assuntad23). Pull Request 9874
Full Python dependencies update (thanks to @nsoranzo). Pull Request 9912
Update AskOmics IT to askomics 4.0.0 (thanks to @xgaia). Pull Request 9915
Documentation on Galaxy startup (thanks to @kxk302). Pull Request 9918
Speed up output discovery Pull Request 9926
Modify email address domain extraction Pull Request 9949
Refactor toward real cohesion toward testing packages. (1/n) Pull Request 9951
Stub unit tests for galaxy-web-stack. Pull Request 9958
Progress toward proper packaging of galaxy-web-framework package. Pull Request 9959
Decouple API and Selenium tests from galaxy-test-driver (and the whole app!) Pull Request 9960
Added doc explaining what happens when you upload a file to Galaxy. (thanks to @kxk302). Pull Request 9963
More packaging touches. Pull Request 9964
Refactor more unit tests into the galaxy-data package. Pull Request 9966
Revise workflow invocation status page Pull Request 9978
Simplify workflow invocations grid, remove drop down, add workflow execution option Pull Request 9986
Update Code of Conduct Pull Request 9989
Move unit tests to more appropriate packages. Pull Request 9993
Package rules DSL specification. Pull Request 9995
Optimize iRODS _exists() method (thanks to @kxk302). Pull Request 9998
Don’t flush after each dataset creation in DistributedObjectStore Pull Request 10008
Touch up of toolbox search adjustments and messages Pull Request 10036
Rework galaxy.tool_util.verify.wait for reuse in Planemo. Pull Request 10041
Add GALAXY_ALLOW_FUTURE_DATABASE option in migration check Pull Request 10044
Upload tests to clarify behavior around handling files without trailing newlines. Pull Request 10050
Fix Galaxy tool/workflow staging and refactor for reuse in Planemo. Pull Request 10052
Update docs on from_work_dir and delta (thanks to @pvanheus). Pull Request 10055
Update environment_modules_mapping.yml.sample Pull Request 10074
Add generic CORS preflight options response Pull Request 10077
Progressively render conditional as they are being displayed Pull Request 10083
Selenium: Library Dataset Download Zip (thanks to @OlegZharkov). Pull Request 10084
Selenium Delete Dataset from library folder (thanks to @OlegZharkov). Pull Request 10090
Test import dataset from path (thanks to @OlegZharkov). Pull Request 10102
Lib Folder pagination (backend) (thanks to @OlegZharkov). Pull Request 10104
User self-delete (thanks to @astrovsky01). Pull Request 10107
Add subworkflow_invocation_id to invocation step Pull Request 10109
Selenium Library Subfolder (thanks to @OlegZharkov). Pull Request 10110
expose dataset ‘in use state’ through api (thanks to @scholtalbers). Pull Request 10122
Jest-based client testing Pull Request 10123
Copy to clipboard, instead of pop-up (thanks to @OlegZharkov). Pull Request 10124
Open pages API a bit to allow anonymous users to view published pages Pull Request 10129
More structured errors for tool validation problems Pull Request 10146
Add hidden column, attach StoredWorkflow to subworkflows Pull Request 10160
Use tool_enable_ngram_search by default, whitespace search fix Pull Request 10175
Switch tool document cache to diskcache Pull Request 10191
Force pagination on Valid Galaxy Tools -> Tools page Pull Request 10195
Rebuild config for 20.09, including missing option in galaxy_options doc Pull Request 10527
Allow specyfying tool tests we expect to fail Pull Request 10548
Various fixes for conditional dependencies handling Pull Request 10575
Fixes/enhancements to use client tool test configs in Ephemeris Pull Request 10578
Mark test cases that use data tables or loc files Pull Request 10602
Fix saving rule builder rules when uploading in rule editing view (thanks to @assuntad23). Pull Request 10637
Porting Masthead to Vue.js (thanks to @inkuzmin). Pull Request 9071
Remove unused and deprecated parameters from kubernetes runner (thanks to @nuwang). Pull Request 9323
Add Vue components for Workflow Inputs and Outputs, reduce Workflow loading time Pull Request 9574
Refactor helper functions (thanks to @lawrence14701). Pull Request 9700
Modify loading of email white/blacklists Pull Request 9793
Cleanup and refactoring client code around upload/data dialog Pull Request 9827
Mount workflow nodes in v-for loop Pull Request 9883
Fix DeprecationWarning: Flags not at the start of the expression (thanks to @nsoranzo). Pull Request 9899
Trim the inflector Pull Request 9902
Fix name of container resolver method name. Pull Request 9914
Python3 cleanup Pull Request 9923
Small tweaks to packaging of unit test utilities. Pull Request 9953
Small refactoring for plugin_config. Pull Request 9982
Cleanup WorkflowRun.test.js with flush promises. Pull Request 9984
Fix copy/paste in workflow editor Pull Request 10056
Client error handling fixes, updates. Pull Request 10082
Client structure refactoring for packaging Pull Request 10086
Uniformly process config files Pull Request 10172
javascript es6 arrow functions (thanks to @juleengraham). Pull Request 10181
Abstraction for purging the dataset quota usage from a user. Pull Request 10208
Improve job error logging Pull Request 10226
Pass user to the ObjectStorePopulator Pull Request 10231
mvpapp visualization fixes and refinement Pull Request 10355
Move linting to GitHub action, fix linting Pull Request 10615

Fixes¶

Hyphyvision visualization dependency fix Pull Request 10011
Bugfix: include an index link in visualization base Pull Request 10391
Use compression_utils to safely peek in compressed datasets (thanks to @pvanheus). Pull Request 9990
fix OSError in fastq_to_fqtoc converter (thanks to @bgruening). Pull Request 10042
Don’t display download link for optional, non-existant metadata files Pull Request 10068
Fix determining ‘int’, ‘float’ column type in Tabular and BaseCSV (thanks to @selten). Pull Request 10155
Decrease pysam verbosity Pull Request 10225
Remove references to missing types from sample config file Pull Request 10269
Fix Wav datatype to inherit from Audio (thanks to @nsoranzo). Pull Request 10312
Fix wiggle estimated_display_viewport Pull Request 10333
AnnData Peek Fix (thanks to @mtekman). Pull Request 10555
Fix Anndata index access, use numpy-safe JSON encoder (thanks to @mtekman). Pull Request 10640
Allow submission of tools with unset hidden parameters (thanks to @bernt-matthias). Pull Request 9656
Fix error in get_open_tempfile() Pull Request 10060
Backport bugfix in #10060 to 20.05 Pull Request 10138
Fix filtering.py failing all expressions (thanks to @almahmoud). Pull Request 10266
Rev gxformat2 for a bunch of bug fixes. Pull Request 10028
Fix running workflows with parameters restricted on connections Pull Request 10048
Count all terminal jobs when rendering job complete string Pull Request 10089
Remove duplicates from tool recommendations (thanks to @anuprulez). Pull Request 10094
Tensorflow update to support python 3.8 Pull Request 10096
Fix tool recommendation node injection Pull Request 10097
Fix Workflow node insertion via recommendations (thanks to @anuprulez). Pull Request 10103
Fix change datatype PJA not applied when loaded from server Pull Request 10237
Fix db-skip-locked invocation grabbing for pool members Pull Request 10371
Fix TRS search when Galaxy deployed behind a proxy. Pull Request 10406
Fix wf step annotations dropped after rename. Pull Request 10464
Fix workflow extraction if nested collection in input step Pull Request 10560
Mark workflow as changed if tools were upgraded Pull Request 10570
Fix workflow editor version switching Pull Request 10597
Fix trs_id and trs_server query strings (thanks to @OlegZharkov). Pull Request 10616
Fix Workflow node input terminal not updating Pull Request 10626
Rework pollUntil* to avoid building up queries Pull Request 10710
Speed up invocation serialization Pull Request 10711
Tool recommendation node bug (thanks to @juleengraham). Pull Request 9836
Fix history sharing link (ref. #10040) Pull Request 10112
fix history import and export for real user setups (thanks to @bernt-matthias). Pull Request 9001
Rev pulsar-galaxy-lib for latest fixes. Pull Request 9910
Fix MetadataFile handing with metadata_strategy: extended Pull Request 9974
Fix metadata_source handling when dataset does not exist in object store Pull Request 10059
Fix change_datatype PJA when dataset is not yet in object store Pull Request 10087
Fix outputs_to_working_directory with extended metadata Pull Request 10100
Don’t fail to complete the job fail method if job outputs cannot be updated Pull Request 10111
Fix for the hour value depicted as a float value in CPU and Job Runtime (thanks to @npinter). Pull Request 10159
Restore the use of set_job_destination() in the Pulsar runner’s queue_job() method Pull Request 10255
Fix webless handler –attach-to-pool Pull Request 10294
Ensure that kubernetes job ids are unique (thanks to @nuwang). Pull Request 10307
Prevent endless cleanup loops when duplicate job or kubernetes job not found (thanks to @nuwang). Pull Request 10308
enable validation of ITs Pull Request 10341
Defer metadata strategy resolution in job wrapper Pull Request 10367
Restrict kubernetes max job name length to 63 and shorten prefix (thanks to @nuwang). Pull Request 10416
Fixing bug in kubernetes runner’s k8s_pod_retrials (thanks to @almahmoud). Pull Request 10444
Move more non-dns compliant labels to annotations (thanks to @nuwang). Pull Request 10470
Fix maximum_workflow_jobs_per_scheduling_iteration and set 1000 as default value Pull Request 10490
Fix get_output_path when HDA identity changes Pull Request 10552
Don’t pass resources as job params when reading job config as a dict Pull Request 10561
Stop monitoring terminal Pulsar Kubernetes jobs Pull Request 10572
Fix IntegrityError when flushing DC/DCE relationship Pull Request 10606
Fix admin data_types_list bug (thanks to @cat-bro). Pull Request 10148
Restore welcome html link for non-uwsgi setups Pull Request 10623
Python37 lock fix Pull Request 9642
Fix history panel collapse (thanks to @juleengraham). Pull Request 9688
Improve tool recommendations (thanks to @anuprulez). Pull Request 9708
Various spelling and log message error fixes. Pull Request 9721
Minor fixes to docs on how to build a job runner (thanks to @nuwang). Pull Request 9749
Client watch fix – force everything to use modern chokidar Pull Request 9755
Handled unexpected exceptions in iRods objectstore (thanks to @kxk302). Pull Request 9765
Remove unused code and other fixes (thanks to @nsoranzo). Pull Request 9766
Added the missing return value. Added try/catch for another irods call. (thanks to @kxk302). Pull Request 9768
Hide masthead dropdown on iframe click (thanks to @OlegZharkov). Pull Request 9789
Fix refactoring in linkifing libraries description (thanks to @OlegZharkov). Pull Request 9790
Babel peer dependency fix, Pull Request 9795
InteractiveTool unit test fix Pull Request 9800
Make AuthN attribute optional for Azure and GCP. Pull Request 9801
Fix bug: add self arg to method Pull Request 9808
Fix conditional conda activate syntax in job script (thanks to @brinkmanlab). Pull Request 9832
Fix line-height property for upload button in tool panel Pull Request 9845
hide expression tools (thanks to @OlegZharkov). Pull Request 9859
Added missing dev flag to hot module reload script, sourcemaps work now Pull Request 9891
Typo in the uWSGI default umask description (thanks to @gmauro). Pull Request 9909
Do not automatically overwrite the output labels for subworkflows Pull Request 9917
Fix issues reported by flake8-bugbear and W504 errors 1/N (thanks to @nsoranzo). Pull Request 9943
Using context manager for irods session object (thanks to @kxk302). Pull Request 9944
Strip leading whitespace before calling urlparse Pull Request 9947
Fixes to package dependency declarations. Pull Request 9950
Various small fixes for galaxy packages. Pull Request 9952
actually set -e for non-legacy tools (thanks to @bernt-matthias). Pull Request 9962
Fix workflow run default icon Pull Request 9971
Remove unnecessary log statements for number of connections (thanks to @kxk302). Pull Request 9975
Use optimized path of setting dataset size during output discovery Pull Request 9980
Cookie names to work with PR #9921 and py3 Exception printing (thanks to @almahmoud). Pull Request 9991
Tweak requirements for recent changes to package structure. Pull Request 9992
Properly update active version in workflow attribute form Pull Request 10009
Fix pip error around markdown tables. Pull Request 10014
Pass stdin to hg clone to fix planemo tests Pull Request 10018
Mulled packaging dependency fixes Pull Request 10025
Fix reports webapp template resolution Pull Request 10037
Encoding issue fix for hmac_new Pull Request 10047
add missing $ in docs (thanks to @bernt-matthias). Pull Request 10057
Fix non-unique entries in tool search index Pull Request 10061
Restore preview rendering of bam files Pull Request 10067
Allow numbers as filenames while adding datasets to library folder (thanks to @OlegZharkov). Pull Request 10070
Fix library zip download Pull Request 10072
fix masthead dropdown (thanks to @OlegZharkov). Pull Request 10098
Handle python2-related syntax errors in Cheetah code Pull Request 10099
Filter pages of deleted users from the published list. Pull Request 10106
Update toolshed/ie js dist locations Pull Request 10143
Pin latex-to-unicode js module Pull Request 10157
Make visualization unit tests independent Pull Request 10162
Keycloak/custos tweaks and cleanup Pull Request 10168
Don’t include hidden tools in tool search index Pull Request 10173
Send activation email upon custos account creation (thanks to @juleengraham). Pull Request 10174
Fix ToolValidator get_list_of_copied_sample_files Pull Request 10183
Bump http-proxy from 1.17.0 to 1.18.1 in /lib/galaxy/web/proxy/js (thanks to @galaxyproject). Pull Request 10190
Unicodify binary strings in Tool Shed alert emails (thanks to @nsoranzo). Pull Request 10196
use GalaxyTagHandlerSession for data library uploads (thanks to @scholtalbers). Pull Request 10197
Display proper clientside error (thanks to @juleengraham). Pull Request 10199
Add pwd when overriding tool_config_file in run.sh Pull Request 10200
If a config file is not found, try resolving w.r.t. root Pull Request 10201
Use pagination on most tool shed pages Pull Request 10207
Remove exec permissions from tools/__init__.py Pull Request 10213
Strip deprecated dir from all paths in comma-separated option values (thanks to @nsoranzo). Pull Request 10220
Fix flake8 issues in dev Pull Request 10234
Logout fix and refactoring Pull Request 10248
Catch all possible repo install errors Pull Request 10250
Include an upgrade warning for 20.05 regarding the drop of the blue symlink in static Pull Request 10256
Persist tool_cache_data_dir tag if specified Pull Request 10281
Bump tensorflow from 2.3.0 to 2.3.1 in /lib/galaxy/dependencies (thanks to @galaxyproject). Pull Request 10300
Fix container resolution when requirement version is not specified (thanks to @nsoranzo). Pull Request 10305
Fix tool search to not display ‘no results’ prior to result return Pull Request 10317
Respect use_shared_home="false" when running tools in container (thanks to @nsoranzo). Pull Request 10321
Fix double masthead in some spaces Pull Request 10329
Fix composite data download from collection Pull Request 10330
Handle resend_activation_email gracefully without session Pull Request 10331
Strip trailing / from tool_id for data source redirects Pull Request 10332
Allow ‘planemo run’ to stage in existing datasets without reuploading (thanks to @simonbray). Pull Request 10335
Pin pytest < 6.1 Pull Request 10337
Fix ‘Newer Version Available’ tag in admin tool management section (thanks to @cat-bro). Pull Request 10339
Use block elements for labels to handle wrapping indentation Pull Request 10342
Add missing index migrations Pull Request 10344
Bugfix: chrome forgets scroll offset upon show/hide cycle of GTN in Galaxy webhook (thanks to @hexylena). Pull Request 10362
Allow GEDAs to respond to Access-Control-Request-* Pull Request 10384
Fix regex replacement wrongly appearing in rule builder Pull Request 10390
add recurse attribute for discover_datasets (thanks to @bernt-matthias). Pull Request 10394
Try case-insensitive match on email also when it’s lowercase (thanks to @nsoranzo). Pull Request 10401
Python 3 fix and client build fix for the proxy (thanks to @bgruening). Pull Request 10403
Rework new collection order testing in 20.09. Pull Request 10434
backport #10365: add test for data_column parameter referring to non-tabular data (bed) and fix bug (thanks to @bernt-matthias). Pull Request 10438
Change response body from str to bytes (thanks to @qiagu). Pull Request 10441
Add *requirements.txt files to source packages (thanks to @nsoranzo). Pull Request 10447
Fix mulled-search to not assume conda APIs from vanilla environments Pull Request 10465
Fix trailing commas in history dataset search (thanks to @cat-bro). Pull Request 10518
Allow username or email for authenticate API identity Pull Request 10521
Improved error handling for data_fetch API. Pull Request 10543
Fix composite dataset listing in upload modal Pull Request 10551
allow adding dataset to library from history by default (thanks to @OlegZharkov). Pull Request 10556
Make package names lowercase for mulled dependency resolving (thanks to @nsoranzo). Pull Request 10559
Fix listing idps Pull Request 10567
Fix progress bar floating text Pull Request 10579
bugfix: external login component fetching idps when it should not Pull Request 10581
Resolve LDDA <-> Library Dataset circular dependency Pull Request 10582
Fix file_path bug; change default assignment of file_path and id/uuid Pull Request 10617
Fix masthead items disappearing on small screens Pull Request 10641
Fix hide history panel glitch Pull Request 10644
Fix cache key for lint CI workflow (thanks to @nsoranzo). Pull Request 10649
Fix creating hdas without history when creating collection from library Pull Request 10654
Backport: Fix saving rule builder rules when uploading in rule editing view Pull Request 10661
Fix border between list items Pull Request 10675
Fix UTC Date date change (thanks to @OlegZharkov). Pull Request 10678
Several fixes for multipanel interface Pull Request 10680
Fix element_is_set for MetadataWrapper (thanks to @bernt-matthias). Pull Request 10691
Bugfix for tool search filtering for tools outside sections. Pull Request 10693
Bump cryptography dependency to 3.2.1 Pull Request 10704
Add ‘Constant’ to allowed node types. (thanks to @brinkmanlab). Pull Request 10709
Pathbar race bugfix (thanks to @OlegZharkov). Pull Request 10724
Use newer setup-miniconda action Pull Request 10731

To stay up to date with Galaxy’s progress watch our screencasts, visit our community hub, and follow @galaxyproject on Twitter.

You can always reach us on Gitter or IRC.

Thanks for using Galaxy!

The Galaxy Team