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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:

• Jayadev Joshi

• Luke Sargent

• Marius van den Beek

• John Davis

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

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