.. to_doc 18.09 =============================== .. announce_start Enhancements ------------------------------- .. feature * Allow selecting subset of collection by group tag (thanks to `@mvdbeek `__). `Pull Request 5457`_ * Copy data from a cloud-based storage to a Galaxy history `Pull Request 5835`_ * Upload data to a cloud-based storage `Pull Request 6078`_ * New datatype: SBML (thanks to `@cmonjeau `__). `Pull Request 6201`_ * Enable automatic reload of dynamic job rules on change `Pull Request 6215`_ * Added daa (diamond alignment) datatype (thanks to `@bernt-matthias `__). `Pull Request 6313`_ * Allows DatasetMatcher to use multiple filters (thanks to `@ebolyen `__). `Pull Request 6443`_ * Adding 4 new GROMACS datatypes: cpt, xtc, top, and gro (thanks to `@simonbray `__). `Pull Request 6655`_ * Implement runtime parameters for subworkflows. `Pull Request 6664`_ * Expose workflow versions (thanks to `@mvdbeek `__). `Pull Request 6683`_ * Add Loom datatype and remove rdata.seurat `Pull Request 6723`_ .. enhancement * Add a ``FilterEmptyDatasetsTool`` and allow filtering tools to apply to arbitrary collection structures (thanks to `@Mataivic `__). `Pull Request 5640`_ * Minor enhancements for cgroup metrics `Pull Request 5993`_ * Optimize ``safe_walk`` to call ``realpath`` a lot less for typical calls `Pull Request 5995`_ * Documentation and typo fixes (thanks to `@nsoranzo `__). `Pull Request 6013`_ * Add hostname metric (thanks to `@hexylena `__). `Pull Request 6021`_ * Pause jobs with invalid inputs (thanks to `@mvdbeek `__). `Pull Request 6036`_ * Replace sharing mako with vue component `Pull Request 6048`_ * Rules - test case for apply rules tutorial. `Pull Request 6066`_ * Add resume job api (thanks to `@mvdbeek `__). `Pull Request 6072`_ * Add blib datatype for Mass Spectrometry spectral library (thanks to `@jj-umn `__). `Pull Request 6092`_ * Remove duplicate visualization list entries from masthead `Pull Request 6110`_ * Make cache_directory configurable in mulled Singularity resolvers. `Pull Request 6122`_ * Sharing.vue bootstrapping and a bugfix `Pull Request 6132`_ * Use ``from_work_dir`` in ``CONVERTER_fasta_to_fai`` (thanks to `@nsoranzo `__). `Pull Request 6135`_ * Make workflow editor ``toolTitle`` link include the tools description (thanks to `@scrathat `__). `Pull Request 6142`_ * Small fixes and small refactorings toward reuse in CWL branch (retry) `Pull Request 6148`_ * Add impersonate to main user grid when it's enabled `Pull Request 6176`_ * Common dataset selector `Pull Request 6195`_ * Permit numeric values of GRT instance ID in config (thanks to `@hexylena `__). `Pull Request 6200`_ * Add the newick extension for the Newick datatype, (thanks to `@gregvonkuster `__). `Pull Request 6206`_ * Some more upload/sniff tests. `Pull Request 6212`_ * Test ``element_identifier`` usage with single data parameters, in repeat/cond. `Pull Request 6213`_ * Charts filename download fix `Pull Request 6216`_ * Wrap inputs in labels (thanks to `@hexylena `__). `Pull Request 6221`_ * Workflow submit text links `Pull Request 6240`_ * Password encoding improvements (thanks to `@nsoranzo `__). `Pull Request 6242`_ * Align input element update mechanism `Pull Request 6248`_ * Fix collection mapping to allow subcollection mapping over multi-data inputs. `Pull Request 6255`_ * Use Mercurial CLI instead of API for ``archive_repository_revision()`` (thanks to `@nsoranzo `__). `Pull Request 6273`_ * Consolidate use of ``get_repo_for_repository()`` and ``clone_repository()`` (thanks to `@nsoranzo `__). `Pull Request 6277`_ * Index select2 field values `Pull Request 6286`_ * Job success message revision `Pull Request 6288`_ * To clear workflow tool search field press ESC or click the X button (thanks to `@scrathat `__). `Pull Request 6290`_ * Upload collections directly for tests. `Pull Request 6294`_ * Add specific datatype for CuffDiff SQLite database. `Pull Request 6302`_ * Fix default job script by moving env setup (thanks to `@rhpvorderman `__). `Pull Request 6305`_ * More use of Mercurial CLI instead of API (thanks to `@nsoranzo `__). `Pull Request 6307`_ * Lists-as-tuples collection operations `Pull Request 6312`_ * Replace unmaintained pycrypto dependency with pycryptodome (thanks to `@nsoranzo `__). `Pull Request 6324`_ * Add py34-first_startup to Travis and default tox tests (thanks to `@mvdbeek `__). `Pull Request 6325`_ * Visualization static staging `Pull Request 6344`_ * Add period to the list of allowed characters in user names (thanks to `@moskalenko `__). `Pull Request 6365`_ * Optimizations for dynamic output file collection. `Pull Request 6367`_ * More correct, more efficient collection operations. `Pull Request 6370`_ * Add gafa.sqlite datatype (thanks to `@nsoranzo `__). `Pull Request 6372`_ * Create client build hash on toplevel concurrent watch in addition to individual builds. `Pull Request 6381`_ * Change a file read to use ``with`` statement (thanks to `@qiagu `__). `Pull Request 6388`_ * Client library upgrades. `Pull Request 6400`_ * Allow resource selection for data managers (thanks to `@mvdbeek `__). `Pull Request 6402`_ * Update dev dependencies (thanks to `@nsoranzo `__). `Pull Request 6403`_ * Add py34-unit (allowed to fail) job to Travis (thanks to `@nsoranzo `__). `Pull Request 6406`_ * Allow supplying name of pasted data (thanks to `@FredericBGA `__). `Pull Request 6415`_ * Fixes for uploading empty files to Galaxy. `Pull Request 6418`_ * Remove installation of python-lzo system dependencies (thanks to `@nsoranzo `__). `Pull Request 6425`_ * Citation style work `Pull Request 6427`_ * Run workflows from published workflows menu (thanks to `@mvdbeek `__). `Pull Request 6428`_ * Fix a few tool_deps test errors (thanks to `@bgruening `__). `Pull Request 6436`_ * Replace the administration header in admin menu with version `Pull Request 6440`_ * Add zoom support to workflow editor. `Pull Request 6441`_ * Intermine Enhancements `Pull Request 6444`_ * Changing menu tabs without hard refresh (thanks to `@almahmoud `__). `Pull Request 6447`_ * Let data managers also use conda python. (thanks to `@rhpvorderman `__). `Pull Request 6466`_ * Make upload tool python3 compatible (thanks to `@mvdbeek `__). `Pull Request 6467`_ * Allow including paths in inputs json files. `Pull Request 6468`_ * Update cliff and other related dependencies (thanks to `@nsoranzo `__). `Pull Request 6469`_ * Fix bug noticed in sentry (thanks to `@hexylena `__). `Pull Request 6474`_ * Rulebuilder: Special case auto URL schema detection for SRA inputs. `Pull Request 6476`_ * GRT: fix the upload logging init `Pull Request 6478`_ * Add more information to the dataset template (thanks to `@hexylena `__). `Pull Request 6480`_ * Use bootstrap vue classes for workflow import form `Pull Request 6489`_ * Small improvement to the tool xsd docs regarding ``discovered_dataset`` (thanks to `@bernt-matthias `__). `Pull Request 6490`_ * Implement ``group:`` tags (toward multi-factor analysis with group tagging) `Pull Request 6491`_ * Allow setting tags on targets & contents in data fetch API. `Pull Request 6499`_ * Integrate tagging into the rule builder. `Pull Request 6500`_ * Cache ``chrom_info`` generation when mapping over collections. `Pull Request 6515`_ * More optimized HID generation - in one commit instead of two. `Pull Request 6516`_ * Improvements to Cloud Storage Manager `Pull Request 6519`_ * Handle pasted content in fetch API. `Pull Request 6523`_ * Use cached database identity to avoid many DB requests when creating jobs. `Pull Request 6524`_ * Removal of unreachable ``exit()`` `Pull Request 6529`_ * Optimizations for history copying. `Pull Request 6531`_ * Notify if newer tool version is available `Pull Request 6533`_ * Convert tool parameter XML attribute 'hidden' into the correct boolean Python type (thanks to `@andreyto `__). `Pull Request 6539`_ * Test case for nested collection input to flatten in a workflow. `Pull Request 6541`_ * Allow Consuming Tags in the Apply Rules Tool `Pull Request 6545`_ * Integration test for the interaction of nested object stores and jobs. `Pull Request 6546`_ * Configure object store for datasets in job handler instead of web thread. `Pull Request 6550`_ * Allow configuring object stores on a per-job-destination basis. `Pull Request 6552`_ * Unified dataset permission API. `Pull Request 6568`_ * Add tagging rule to history level rule builder, copy HDAs when building collection (thanks to `@mvdbeek `__). `Pull Request 6572`_ * Add API endpoint to fetch a history's workflow invocations. `Pull Request 6580`_ * Improve robustness of tour Selenium test. `Pull Request 6582`_ * Smarter Test Histories (Part I) `Pull Request 6586`_ * Add download option to workflow editor menu (thanks to `@bgruening `__). `Pull Request 6596`_ * Add trr datatype (thanks to `@bgruening `__). `Pull Request 6597`_ * Refresh an expired OIDC ID token `Pull Request 6606`_ * Handle driver shutdown, show all tests in pytest (thanks to `@mvdbeek `__). `Pull Request 6608`_ * Add dcd datatype for molecular dynamics (thanks to `@chrisbarnettster `__). `Pull Request 6613`_ * Py3 testing cleanups (thanks to `@nsoranzo `__). `Pull Request 6616`_ * Integration test for job recovery. `Pull Request 6620`_ * Update all dependencies (thanks to `@nsoranzo `__). `Pull Request 6628`_ * Update some run_tests.sh docs for recent changes. `Pull Request 6629`_ * Remove ``check_python_dependencies`` job from Travis (thanks to `@nsoranzo `__). `Pull Request 6630`_ * Testing framework improvements (thanks to `@mvdbeek `__). `Pull Request 6632`_ * Optimize tool execution permission checking `Pull Request 6635`_ * Document config for sniffing compressed files, enable by default `Pull Request 6641`_ * Small Optimizations to Adding Datasets to History `Pull Request 6644`_ * Add Seurat datatype: rdata.seurat (thanks to `@mblue9 `__). `Pull Request 6648`_ * Allow group tag selection also for multiple="true" inputs (thanks to `@mvdbeek `__). `Pull Request 6661`_ * Various link and documentation fixes (thanks to `@nsoranzo `__). `Pull Request 6662`_ * Upgraded genomespaceclient to newer version (thanks to `@gvlproject `__). `Pull Request 6668`_ * Workflow replacement parameters polish. `Pull Request 6678`_ * Keep newly broken tool in toolbox (thanks to `@mvdbeek `__). `Pull Request 6681`_ * Add self help to error reporting interface `Pull Request 6711`_ * Undo auto-propagation of group tags. `Pull Request 6750`_ * Client build startup changes `Pull Request 6753`_ * Add graph dot datatype and enable it in visualisations (thanks to `@bgruening `__). `Pull Request 6760`_ * Remove upgrade cruft related to datatypes. `Pull Request 6761`_ * Allow starting Galaxy under gunicorn when using galaxy.ini (thanks to `@mvdbeek `__). `Pull Request 6805`_ * Allow testing tags in input collections. `Pull Request 6823`_ .. small_enhancement * Remove duplicate metric sending (thanks to `@hexylena `__). `Pull Request 6011`_ * This strips the graphite-specific middleware `Pull Request 6018`_ * Make ``interactor._{get,post,put,...}`` less repetitive (thanks to `@mvdbeek `__). `Pull Request 6070`_ * Workflow and remote-user related refactoring and a bug fix `Pull Request 6076`_ * Drop unused files (thanks to `@mvdbeek `__). `Pull Request 6150`_ * History import safari fix, overhaul `Pull Request 6153`_ * Strip legacy history structure view `Pull Request 6241`_ * Fix typo (UnitializedTree -> UninitializedTree) (thanks to `@mvdbeek `__). `Pull Request 6315`_ * Rewrite admin data types as vue component (thanks to `@scrathat `__). `Pull Request 6383`_ * Some style cleanup. `Pull Request 6386`_ * py3 compat (thanks to `@caleb-easterly `__). `Pull Request 6434`_ * Python3: Encode return values of JSON encoder (thanks to `@mvdbeek `__). `Pull Request 6439`_ * Python3: Drop ``json_fix``, doesn't seem to be necessary and fixes workflow unit tests (thanks to `@mvdbeek `__). `Pull Request 6446`_ * py3: fixes ``test_DatasetManager.py:DatasetManagerTestCase`` (thanks to `@caleb-easterly `__). `Pull Request 6452`_ * Fix test_toolbox for python 3 (thanks to `@mvdbeek `__). `Pull Request 6463`_ * Remove redundant/duplicate endpoint to edit user info `Pull Request 6501`_ * Remove the deprecated AOL openid backend. `Pull Request 6505`_ * Fix all py3 api tests (thanks to `@mvdbeek `__). `Pull Request 6561`_ * Setup py3 test job (thanks to `@mvdbeek `__). `Pull Request 6565`_ * Remove backbone version of thumbnail element `Pull Request 6587`_ * Migrate API tests in test_jobs.py to use test_history context. `Pull Request 6593`_ * Modernize data manager testing and strip twill (thanks to `@mvdbeek `__). `Pull Request 6595`_ * Enable and fix framework py3 tests (thanks to `@mvdbeek `__). `Pull Request 6605`_ * Order data parameters before unlinked multiplication (thanks to `@mvdbeek `__). `Pull Request 6609`_ * Fix remaining selenium py3 test failures (thanks to `@mvdbeek `__). `Pull Request 6610`_ * Raise an exception if a history with decoded id does not exist. `Pull Request 6611`_ * Test tools shipped with Galaxy (thanks to `@mvdbeek `__). `Pull Request 6627`_ * Tweak conda_* setting in test driver (thanks to `@mvdbeek `__). `Pull Request 6633`_ * Move tests to pytest setup (thanks to `@mvdbeek `__). `Pull Request 6638`_ * Upgrade CloudBridge to v1.0.1 `Pull Request 6660`_ * Increase robustness and accuracy of job search / cache use (thanks to `@mvdbeek `__). `Pull Request 6669`_ * Fix remaining selenium py3 errors (thanks to `@mvdbeek `__). `Pull Request 6803`_ * Drop gulp plugin staging task from default tasks `Pull Request 6808`_ Fixes ------------------------------- .. major_bug .. bug * Fix bowtie2 link (thanks to `@galaxyproject `__). `Pull Request 6009`_ * Fix some imports (thanks to `@nsoranzo `__). `Pull Request 6014`_ * Fix ``JobWrapper.get_destination_configuration()`` so that it actually checks the ``JobDestination`` params `Pull Request 6087`_ * Fixed small typo (thanks to `@bernt-matthias `__). `Pull Request 6094`_ * History click-to-rename bugfix `Pull Request 6159`_ * Remove defunct sharing column link `Pull Request 6177`_ * cutWrapper: fix wrong path in error message (thanks to `@abretaud `__). `Pull Request 6211`_ * Fix ``optional="True"`` inputs (thanks to `@mvdbeek `__). `Pull Request 6222`_ * Two minor aliases for (exterior) backwards compatibility, minor badge tweaks `Pull Request 6226`_ * Fix broken collection_type_source tool and test. `Pull Request 6227`_ * Add ``io_details`` and ``link_details`` in api tools doc (thanks to `@ValentinChCloud `__). `Pull Request 6228`_ * Fix file type error in RuleCollectionBuilder. `Pull Request 6231`_ * Fix non-strict tabular relabel operation (thanks to `@mvdbeek `__). `Pull Request 6234`_ * Hack paster args to not duplicate pid file stuff for RUN_ALL. (thanks to `@lparsons `__). `Pull Request 6239`_ * Backport of Workflow Execution Text Fixup `Pull Request 6243`_ * Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber `__). `Pull Request 6244`_ * Check context for textable mode of select fields `Pull Request 6251`_ * Mapping over ``from_param`` fixes (thanks to `@mvdbeek `__). `Pull Request 6253`_ * Fix history shared with me 'view' link `Pull Request 6257`_ * History view 'import' button display based on ownership. `Pull Request 6260`_ * Various fixes for the run scripts (thanks to `@nsoranzo `__). `Pull Request 6262`_ * Fix dataset sizes in GRT export script (thanks to `@atyryshkina `__). `Pull Request 6263`_ * Allow invalid optional param values for tools profile versions < 18.09 (thanks to `@mvdbeek `__). `Pull Request 6264`_ * Python3 fixes (thanks to `@nsoranzo `__). `Pull Request 6265`_ * Fixes for phenotype association tools (thanks to `@nsoranzo `__). `Pull Request 6269`_ * Fix link to workflow list (thanks to `@galaxyproject `__). `Pull Request 6270`_ * Fix help text for renaming operation in workflows `Pull Request 6274`_ * Various fixes for mapping over collections (thanks to `@mvdbeek `__). `Pull Request 6278`_ * Fix tool search overlay selector (thanks to `@scrathat `__). `Pull Request 6279`_ * Fix delete "Collection Only" option in history menu. `Pull Request 6281`_ * telescope export: change to a more defensive approach `Pull Request 6285`_ * Only update options if provided in parameter definition `Pull Request 6289`_ * Update tabular.py (thanks to `@hrhotz `__). `Pull Request 6292`_ * Strip a spurious Slurm warning from job stderr (thanks to `@nsoranzo `__). `Pull Request 6293`_ * Fix ``GALAXY_RUN_ALL=1 ./run.sh --daemon`` (thanks to `@nsoranzo `__). `Pull Request 6295`_ * Add the canonical URL to grt config `Pull Request 6301`_ * Stop listening to history changes after job submission `Pull Request 6303`_ * Increase sleep if encountering (DB locking) exception (thanks to `@mvdbeek `__). `Pull Request 6304`_ * Fix undefined ``success_message`` (thanks to `@mvdbeek `__). `Pull Request 6316`_ * Allow ``#if $datasets #end if`` pattern for file lists (thanks to `@mvdbeek `__). `Pull Request 6317`_ * Fix target update for rule collection builder after input selection (thanks to `@scrathat `__). `Pull Request 6326`_ * Added missing level ``fatal_oom`` to galaxy.xsd (thanks to `@bernt-matthias `__). `Pull Request 6341`_ * Update description for installing pbs-python (thanks to `@mvdbeek `__). `Pull Request 6345`_ * Prevent throwing an exception if a dataset doesn't exist (and never will) due to a job error (thanks to `@dpryan79 `__). `Pull Request 6349`_ * Fix the ``--log-file`` option in the job handlers (thanks to `@dpryan79 `__). `Pull Request 6351`_ * grt - wrap every write in try-except `Pull Request 6354`_ * Fix 'share with another user' `Pull Request 6358`_ * Add fasta datatype to msa viewer `Pull Request 6361`_ * Fix small bug in logging output name in job finish. `Pull Request 6366`_ * Fix for rendering multiple dependent dynamic select lists (thanks to `@gregvonkuster `__). `Pull Request 6374`_ * Specify standard HTTPTransport for Sentry `Pull Request 6375`_ * Comma-separate tool names in missing tools error message `Pull Request 6378`_ * Revert "Remove bam to bai converter" `Pull Request 6385`_ * Fix ``data_column`` cast error when multiple is false (thanks to `@qiagu `__). `Pull Request 6389`_ * Optimize setting large numbers of HIDs for collection outputs. `Pull Request 6394`_ * Fixing ```` XML example (thanks to `@almahmoud `__). `Pull Request 6399`_ * Fix positioning for tool search box. `Pull Request 6416`_ * Removing binary as input for python compatibility (thanks to `@eslerm `__). `Pull Request 6417`_ * GCC2018 python3 unit-test fixes (thanks to `@ycgong `__). `Pull Request 6419`_ * Python 3 porting (thanks to `@caleb-easterly `__). `Pull Request 6420`_ * Fix panel drag resize. `Pull Request 6421`_ * Fix message fadeout by relying on hiding the message instead `Pull Request 6424`_ * Python 3 fixes from GCC-BOSC-2018 (thanks to `@johnbradley `__). `Pull Request 6429`_ * Unit testing with Python 3 (thanks to `@NicHerndon `__). `Pull Request 6430`_ * Do not encode a rendered Mako template (thanks to `@nsoranzo `__). `Pull Request 6431`_ * Decode potential encoded id `Pull Request 6433`_ * Fixes test/unit/jobs/test_job_output_checker.py; strange default? (thanks to `@caleb-easterly `__). `Pull Request 6438`_ * py3 compat: fixes test_vcf, test_sniff_compressed* (thanks to `@caleb-easterly `__). `Pull Request 6442`_ * Fix TS: resolve missing closing div and three extra closing divs `Pull Request 6445`_ * Fix all remaining unit tests under Python 3 (thanks to `@mvdbeek `__). `Pull Request 6450`_ * Fix droptarget:drop trigger (drag/drop in the multiview) `Pull Request 6451`_ * py3: Fix the dynamic tool destination unit test (thanks to `@mvdbeek `__). `Pull Request 6453`_ * py3: replace e.message with str(e) (thanks to `@caleb-easterly `__). `Pull Request 6454`_ * Various Python 3 fixes (thanks to `@nsoranzo `__). `Pull Request 6455`_ * GIE static url (thanks to `@thobalose `__). `Pull Request 6460`_ * Update common_startup_functions.sh (thanks to `@nagoue `__). `Pull Request 6481`_ * Fix for show params server error `Pull Request 6486`_ * Fix ``ftp_upload_purge`` in galaxy.yml (thanks to `@phac-nml `__). `Pull Request 6494`_ * Fix resume from history panel (thanks to `@mvdbeek `__). `Pull Request 6498`_ * Fix bam to bigwig error detection. (thanks to `@pvanheus `__). `Pull Request 6502`_ * Fix and docs for advanced container options in job_conf.xml. `Pull Request 6503`_ * Return a json blob containing redirect URI in OIDC login controller `Pull Request 6517`_ * Fix warning in ``CONVERTER_bam_to_bigwig_0`` and ``CONVERTER_sam_to_bigwig_0`` (thanks to `@nsoranzo `__). `Pull Request 6528`_ * Fix dataset copy tags `Pull Request 6532`_ * Fix ``to_dict`` with ``io_details=True`` for tools with collection outputs. `Pull Request 6538`_ * Fix "filter empty" rule in Python rule handling framework. `Pull Request 6542`_ * Fixes for API installation bugs. `Pull Request 6544`_ * Redirect unidentified routes in admin panel `Pull Request 6551`_ * Remove the sharing of toolbox in GRT (thanks to `@hexylena `__). `Pull Request 6553`_ * Restore ``log_destination = stdout`` configuration option. `Pull Request 6555`_ * Many Selenium tests fixes for recent dev changes. `Pull Request 6557`_ * More Selenium test fixes. `Pull Request 6562`_ * Misc Admin TS Panel Fixes `Pull Request 6564`_ * Use subworkflow index when setting auto-label (thanks to `@mvdbeek `__). `Pull Request 6570`_ * Fix workflow run link for extracted workflows `Pull Request 6571`_ * Typo and wording fixes for dependency resolvers docs `Pull Request 6575`_ * Use object store to check for existence of extra_files_path (thanks to `@mvdbeek `__). `Pull Request 6588`_ * Update UCSC genome-test server URLs `Pull Request 6591`_ * Resolve overlap of workflow parameter container with gear-icon in editor header `Pull Request 6592`_ * Respect unavailable display peek (thanks to `@mvdbeek `__). `Pull Request 6594`_ * Fix Location of Plugin Static Content In Documentation for 18.05 (thanks to `@phac-nml `__). `Pull Request 6602`_ * Fix cron/build_chrom_db.py and update UCSC builds (thanks to `@nsoranzo `__). `Pull Request 6623`_ * Fix for workflow extraction cleanup routine. `Pull Request 6636`_ * Row ids that are all numeric become ints... (thanks to `@bwlang `__). `Pull Request 6639`_ * Allow running ``scripts/galaxy-main`` without Galaxy on ``sys.path`` `Pull Request 6642`_ * Fix color of workflow panel background `Pull Request 6643`_ * Pages - fixes for encoded ids in the database `Pull Request 6647`_ * Strip API keys option from admin panel left side `Pull Request 6651`_ * Fix ``get_fileobj()`` call in ``Eland.set_meta()`` (thanks to `@nsoranzo `__). `Pull Request 6659`_ * Update bx-python to 0.8.2 (thanks to `@nsoranzo `__). `Pull Request 6670`_ * Serialize select field options, fixes beta install (thanks to `@mvdbeek `__). `Pull Request 6677`_ * Fix wf-editor when loading subworkflow with parenthesis in label (thanks to `@mvdbeek `__). `Pull Request 6680`_ * Add missing route for API endpoint. `Pull Request 6703`_ * Catch additional permutations of Slurm cgroup creation warnings `Pull Request 6705`_ * Unquote the ``tool_version`` in the tools API `Pull Request 6707`_ * Fix active highlight `Pull Request 6725`_ * Badge default fix `Pull Request 6726`_ * Remove html tags and newlines from the help text `Pull Request 6728`_ * Fix missing tests for data source sniffing. `Pull Request 6733`_ * Decode tool id and version in the client, not in the API (thanks to `@nsoranzo `__). `Pull Request 6737`_ * Fix and test anonymous error reports (thanks to `@mvdbeek `__). `Pull Request 6742`_ * Fix favicon.ico for uWSGI deployments `Pull Request 6743`_ * Dispose of dataset tooltip when the delete is being called `Pull Request 6744`_ * Generic tooltip hide for onclick faIconButtons `Pull Request 6745`_ * Fix page editor height for flex panels. `Pull Request 6747`_ * Use mapped-over ``collectionType`` when inferring ``collectionType`` through ``format_source`` (thanks to `@mvdbeek `__). `Pull Request 6749`_ * Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok `Pull Request 6755`_ * Don't attempt ``len(None)``, ensure stdout/stderr are strings in ``Job(Like).set_streams()``. `Pull Request 6765`_ * Increase the maximum number of stderr lines that will be scanned for slurm warnings `Pull Request 6766`_ * Backport of: Resilience of success message handling `Pull Request 6768`_ * Use ``UserRoleAssociation`` to get private roles (thanks to `@mvdbeek `__). `Pull Request 6771`_ * Update name of ``Workflow`` when updating ``StoredWorkflow`` name (thanks to `@mvdbeek `__). `Pull Request 6774`_ * All extracted datasets should be visible (thanks to `@mvdbeek `__). `Pull Request 6780`_ * Fix ``__encode_invocation`` signature `Pull Request 6782`_ * Strip all control characters from rules (thanks to `@mvdbeek `__). `Pull Request 6785`_ * Fix bam upload resulting in 'auto' datatype (thanks to `@mvdbeek `__). `Pull Request 6789`_ * Flex-related style fixes `Pull Request 6791`_ * Allow making all datasets within history public, when sharing `Pull Request 6793`_ * Drop unused peek method `Pull Request 6796`_ * Fix element identifier for non multiple true mapover in conditionals (thanks to `@mvdbeek `__). `Pull Request 6798`_ * Provide a useful exception message for object store exceptions `Pull Request 6799`_ * Cast rule.length to int when parsing rules (thanks to `@mvdbeek `__). `Pull Request 6802`_ * Don't delete referenced Datasets when purging users `Pull Request 6809`_ * Do not rule out numbers that are accessed with shift modifier `Pull Request 6810`_ * Upgrade concurrently for 'null' return fix `Pull Request 6828`_ * Update conda channel priority: conda-forge > bioconda (thanks to `@nsoranzo `__). `Pull Request 6830`_ * Register job monitor thread as postfork function (thanks to `@mvdbeek `__). `Pull Request 6836`_ * Unified panel style bottom padding fix `Pull Request 6839`_ * Fix slurm cli on secure shell (thanks to `@mvdbeek `__). `Pull Request 6845`_ * update paramiko dep `Pull Request 6859`_ * Fix ``LocalShell`` doctest (thanks to `@nsoranzo `__). `Pull Request 6863`_ * Keep xlsx files compressed (thanks to `@mvdbeek `__). `Pull Request 6867`_ * Do not traceback when uploading a TS repo with no changes (thanks to `@nsoranzo `__). `Pull Request 6875`_ * Create composite file archives in new_file_path instead of TMP (thanks to `@mvdbeek `__). `Pull Request 6885`_ * Fix pretty printing of shed_tool_conf.xml file (thanks to `@mvdbeek `__). `Pull Request 6904`_ * Fix ``make config-validate`` (thanks to `@nsoranzo `__). `Pull Request 6908`_ * Fix stopping DRMAA jobs `Pull Request 6912`_ * Fix toolshed error in display_tool if tool is invalid (thanks to `@mvdbeek `__). `Pull Request 6932`_ .. github_links .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457 .. _Pull Request 5640: https://github.com/galaxyproject/galaxy/pull/5640 .. _Pull Request 5835: https://github.com/galaxyproject/galaxy/pull/5835 .. _Pull Request 5982: https://github.com/galaxyproject/galaxy/pull/5982 .. _Pull Request 5993: https://github.com/galaxyproject/galaxy/pull/5993 .. _Pull Request 5995: https://github.com/galaxyproject/galaxy/pull/5995 .. _Pull Request 6004: https://github.com/galaxyproject/galaxy/pull/6004 .. _Pull Request 6009: https://github.com/galaxyproject/galaxy/pull/6009 .. _Pull Request 6011: https://github.com/galaxyproject/galaxy/pull/6011 .. _Pull Request 6013: https://github.com/galaxyproject/galaxy/pull/6013 .. _Pull Request 6014: https://github.com/galaxyproject/galaxy/pull/6014 .. _Pull Request 6018: https://github.com/galaxyproject/galaxy/pull/6018 .. _Pull Request 6021: https://github.com/galaxyproject/galaxy/pull/6021 .. _Pull Request 6036: https://github.com/galaxyproject/galaxy/pull/6036 .. _Pull Request 6048: https://github.com/galaxyproject/galaxy/pull/6048 .. _Pull Request 6066: https://github.com/galaxyproject/galaxy/pull/6066 .. _Pull Request 6070: https://github.com/galaxyproject/galaxy/pull/6070 .. _Pull Request 6072: https://github.com/galaxyproject/galaxy/pull/6072 .. _Pull Request 6076: https://github.com/galaxyproject/galaxy/pull/6076 .. _Pull Request 6078: https://github.com/galaxyproject/galaxy/pull/6078 .. _Pull Request 6087: https://github.com/galaxyproject/galaxy/pull/6087 .. _Pull Request 6092: https://github.com/galaxyproject/galaxy/pull/6092 .. _Pull Request 6094: https://github.com/galaxyproject/galaxy/pull/6094 .. _Pull Request 6110: https://github.com/galaxyproject/galaxy/pull/6110 .. _Pull Request 6122: https://github.com/galaxyproject/galaxy/pull/6122 .. _Pull Request 6132: https://github.com/galaxyproject/galaxy/pull/6132 .. _Pull Request 6135: https://github.com/galaxyproject/galaxy/pull/6135 .. _Pull Request 6142: https://github.com/galaxyproject/galaxy/pull/6142 .. _Pull Request 6148: https://github.com/galaxyproject/galaxy/pull/6148 .. _Pull Request 6150: https://github.com/galaxyproject/galaxy/pull/6150 .. _Pull Request 6153: https://github.com/galaxyproject/galaxy/pull/6153 .. _Pull Request 6159: https://github.com/galaxyproject/galaxy/pull/6159 .. _Pull Request 6171: https://github.com/galaxyproject/galaxy/pull/6171 .. _Pull Request 6176: https://github.com/galaxyproject/galaxy/pull/6176 .. _Pull Request 6177: https://github.com/galaxyproject/galaxy/pull/6177 .. _Pull Request 6195: https://github.com/galaxyproject/galaxy/pull/6195 .. _Pull Request 6200: https://github.com/galaxyproject/galaxy/pull/6200 .. _Pull Request 6201: https://github.com/galaxyproject/galaxy/pull/6201 .. _Pull Request 6206: https://github.com/galaxyproject/galaxy/pull/6206 .. _Pull Request 6211: https://github.com/galaxyproject/galaxy/pull/6211 .. _Pull Request 6212: https://github.com/galaxyproject/galaxy/pull/6212 .. _Pull Request 6213: https://github.com/galaxyproject/galaxy/pull/6213 .. _Pull Request 6215: https://github.com/galaxyproject/galaxy/pull/6215 .. _Pull Request 6216: https://github.com/galaxyproject/galaxy/pull/6216 .. _Pull Request 6221: https://github.com/galaxyproject/galaxy/pull/6221 .. _Pull Request 6222: https://github.com/galaxyproject/galaxy/pull/6222 .. _Pull Request 6226: https://github.com/galaxyproject/galaxy/pull/6226 .. _Pull Request 6227: https://github.com/galaxyproject/galaxy/pull/6227 .. _Pull Request 6228: https://github.com/galaxyproject/galaxy/pull/6228 .. _Pull Request 6231: https://github.com/galaxyproject/galaxy/pull/6231 .. _Pull Request 6234: https://github.com/galaxyproject/galaxy/pull/6234 .. _Pull Request 6237: https://github.com/galaxyproject/galaxy/pull/6237 .. _Pull Request 6239: https://github.com/galaxyproject/galaxy/pull/6239 .. _Pull Request 6240: https://github.com/galaxyproject/galaxy/pull/6240 .. _Pull Request 6241: https://github.com/galaxyproject/galaxy/pull/6241 .. _Pull Request 6242: https://github.com/galaxyproject/galaxy/pull/6242 .. _Pull Request 6243: https://github.com/galaxyproject/galaxy/pull/6243 .. _Pull Request 6244: https://github.com/galaxyproject/galaxy/pull/6244 .. _Pull Request 6248: https://github.com/galaxyproject/galaxy/pull/6248 .. _Pull Request 6251: https://github.com/galaxyproject/galaxy/pull/6251 .. _Pull Request 6252: https://github.com/galaxyproject/galaxy/pull/6252 .. _Pull Request 6253: https://github.com/galaxyproject/galaxy/pull/6253 .. _Pull Request 6255: https://github.com/galaxyproject/galaxy/pull/6255 .. _Pull Request 6257: https://github.com/galaxyproject/galaxy/pull/6257 .. _Pull Request 6260: https://github.com/galaxyproject/galaxy/pull/6260 .. _Pull Request 6262: https://github.com/galaxyproject/galaxy/pull/6262 .. _Pull Request 6263: https://github.com/galaxyproject/galaxy/pull/6263 .. _Pull Request 6264: https://github.com/galaxyproject/galaxy/pull/6264 .. _Pull Request 6265: https://github.com/galaxyproject/galaxy/pull/6265 .. _Pull Request 6269: https://github.com/galaxyproject/galaxy/pull/6269 .. _Pull Request 6270: https://github.com/galaxyproject/galaxy/pull/6270 .. _Pull Request 6273: https://github.com/galaxyproject/galaxy/pull/6273 .. _Pull Request 6274: https://github.com/galaxyproject/galaxy/pull/6274 .. _Pull Request 6277: https://github.com/galaxyproject/galaxy/pull/6277 .. _Pull Request 6278: https://github.com/galaxyproject/galaxy/pull/6278 .. _Pull Request 6279: https://github.com/galaxyproject/galaxy/pull/6279 .. _Pull Request 6281: https://github.com/galaxyproject/galaxy/pull/6281 .. _Pull Request 6285: https://github.com/galaxyproject/galaxy/pull/6285 .. _Pull Request 6286: https://github.com/galaxyproject/galaxy/pull/6286 .. _Pull Request 6288: https://github.com/galaxyproject/galaxy/pull/6288 .. _Pull Request 6289: https://github.com/galaxyproject/galaxy/pull/6289 .. _Pull Request 6290: https://github.com/galaxyproject/galaxy/pull/6290 .. _Pull Request 6292: https://github.com/galaxyproject/galaxy/pull/6292 .. _Pull Request 6293: https://github.com/galaxyproject/galaxy/pull/6293 .. _Pull Request 6294: https://github.com/galaxyproject/galaxy/pull/6294 .. _Pull Request 6295: https://github.com/galaxyproject/galaxy/pull/6295 .. _Pull Request 6300: https://github.com/galaxyproject/galaxy/pull/6300 .. _Pull Request 6301: https://github.com/galaxyproject/galaxy/pull/6301 .. _Pull Request 6302: https://github.com/galaxyproject/galaxy/pull/6302 .. _Pull Request 6303: https://github.com/galaxyproject/galaxy/pull/6303 .. _Pull Request 6304: https://github.com/galaxyproject/galaxy/pull/6304 .. _Pull Request 6305: https://github.com/galaxyproject/galaxy/pull/6305 .. _Pull Request 6307: https://github.com/galaxyproject/galaxy/pull/6307 .. _Pull Request 6312: https://github.com/galaxyproject/galaxy/pull/6312 .. _Pull Request 6313: https://github.com/galaxyproject/galaxy/pull/6313 .. _Pull Request 6315: https://github.com/galaxyproject/galaxy/pull/6315 .. _Pull Request 6316: https://github.com/galaxyproject/galaxy/pull/6316 .. _Pull Request 6317: https://github.com/galaxyproject/galaxy/pull/6317 .. _Pull Request 6324: https://github.com/galaxyproject/galaxy/pull/6324 .. _Pull Request 6325: https://github.com/galaxyproject/galaxy/pull/6325 .. _Pull Request 6326: https://github.com/galaxyproject/galaxy/pull/6326 .. _Pull Request 6341: https://github.com/galaxyproject/galaxy/pull/6341 .. _Pull Request 6344: https://github.com/galaxyproject/galaxy/pull/6344 .. _Pull Request 6345: https://github.com/galaxyproject/galaxy/pull/6345 .. _Pull Request 6349: https://github.com/galaxyproject/galaxy/pull/6349 .. _Pull Request 6351: https://github.com/galaxyproject/galaxy/pull/6351 .. _Pull Request 6354: https://github.com/galaxyproject/galaxy/pull/6354 .. _Pull Request 6358: https://github.com/galaxyproject/galaxy/pull/6358 .. _Pull Request 6361: https://github.com/galaxyproject/galaxy/pull/6361 .. _Pull Request 6365: https://github.com/galaxyproject/galaxy/pull/6365 .. _Pull Request 6366: https://github.com/galaxyproject/galaxy/pull/6366 .. _Pull Request 6367: https://github.com/galaxyproject/galaxy/pull/6367 .. _Pull Request 6370: https://github.com/galaxyproject/galaxy/pull/6370 .. _Pull Request 6371: https://github.com/galaxyproject/galaxy/pull/6371 .. _Pull Request 6372: https://github.com/galaxyproject/galaxy/pull/6372 .. _Pull Request 6374: https://github.com/galaxyproject/galaxy/pull/6374 .. _Pull Request 6375: https://github.com/galaxyproject/galaxy/pull/6375 .. _Pull Request 6377: https://github.com/galaxyproject/galaxy/pull/6377 .. _Pull Request 6378: https://github.com/galaxyproject/galaxy/pull/6378 .. _Pull Request 6381: https://github.com/galaxyproject/galaxy/pull/6381 .. _Pull Request 6383: https://github.com/galaxyproject/galaxy/pull/6383 .. _Pull Request 6385: https://github.com/galaxyproject/galaxy/pull/6385 .. _Pull Request 6386: https://github.com/galaxyproject/galaxy/pull/6386 .. _Pull Request 6388: https://github.com/galaxyproject/galaxy/pull/6388 .. _Pull Request 6389: https://github.com/galaxyproject/galaxy/pull/6389 .. _Pull Request 6394: https://github.com/galaxyproject/galaxy/pull/6394 .. _Pull Request 6399: https://github.com/galaxyproject/galaxy/pull/6399 .. _Pull Request 6400: https://github.com/galaxyproject/galaxy/pull/6400 .. _Pull Request 6402: https://github.com/galaxyproject/galaxy/pull/6402 .. _Pull Request 6403: https://github.com/galaxyproject/galaxy/pull/6403 .. _Pull Request 6406: https://github.com/galaxyproject/galaxy/pull/6406 .. _Pull Request 6415: https://github.com/galaxyproject/galaxy/pull/6415 .. _Pull Request 6416: https://github.com/galaxyproject/galaxy/pull/6416 .. _Pull Request 6417: https://github.com/galaxyproject/galaxy/pull/6417 .. _Pull Request 6418: https://github.com/galaxyproject/galaxy/pull/6418 .. _Pull Request 6419: https://github.com/galaxyproject/galaxy/pull/6419 .. _Pull Request 6420: https://github.com/galaxyproject/galaxy/pull/6420 .. _Pull Request 6421: https://github.com/galaxyproject/galaxy/pull/6421 .. _Pull Request 6424: https://github.com/galaxyproject/galaxy/pull/6424 .. _Pull Request 6425: https://github.com/galaxyproject/galaxy/pull/6425 .. _Pull Request 6427: https://github.com/galaxyproject/galaxy/pull/6427 .. _Pull Request 6428: https://github.com/galaxyproject/galaxy/pull/6428 .. _Pull Request 6429: https://github.com/galaxyproject/galaxy/pull/6429 .. _Pull Request 6430: https://github.com/galaxyproject/galaxy/pull/6430 .. _Pull Request 6431: https://github.com/galaxyproject/galaxy/pull/6431 .. _Pull Request 6433: https://github.com/galaxyproject/galaxy/pull/6433 .. _Pull Request 6434: https://github.com/galaxyproject/galaxy/pull/6434 .. _Pull Request 6436: https://github.com/galaxyproject/galaxy/pull/6436 .. _Pull Request 6438: https://github.com/galaxyproject/galaxy/pull/6438 .. _Pull Request 6439: https://github.com/galaxyproject/galaxy/pull/6439 .. _Pull Request 6440: https://github.com/galaxyproject/galaxy/pull/6440 .. _Pull Request 6441: https://github.com/galaxyproject/galaxy/pull/6441 .. _Pull Request 6442: https://github.com/galaxyproject/galaxy/pull/6442 .. _Pull Request 6443: https://github.com/galaxyproject/galaxy/pull/6443 .. _Pull Request 6444: https://github.com/galaxyproject/galaxy/pull/6444 .. _Pull Request 6445: https://github.com/galaxyproject/galaxy/pull/6445 .. _Pull Request 6446: https://github.com/galaxyproject/galaxy/pull/6446 .. _Pull Request 6447: https://github.com/galaxyproject/galaxy/pull/6447 .. _Pull Request 6449: https://github.com/galaxyproject/galaxy/pull/6449 .. _Pull Request 6450: https://github.com/galaxyproject/galaxy/pull/6450 .. _Pull Request 6451: https://github.com/galaxyproject/galaxy/pull/6451 .. _Pull Request 6452: https://github.com/galaxyproject/galaxy/pull/6452 .. _Pull Request 6453: https://github.com/galaxyproject/galaxy/pull/6453 .. _Pull Request 6454: https://github.com/galaxyproject/galaxy/pull/6454 .. _Pull Request 6455: https://github.com/galaxyproject/galaxy/pull/6455 .. _Pull Request 6460: https://github.com/galaxyproject/galaxy/pull/6460 .. _Pull Request 6463: https://github.com/galaxyproject/galaxy/pull/6463 .. _Pull Request 6466: https://github.com/galaxyproject/galaxy/pull/6466 .. _Pull Request 6467: https://github.com/galaxyproject/galaxy/pull/6467 .. _Pull Request 6468: https://github.com/galaxyproject/galaxy/pull/6468 .. _Pull Request 6469: https://github.com/galaxyproject/galaxy/pull/6469 .. _Pull Request 6474: https://github.com/galaxyproject/galaxy/pull/6474 .. _Pull Request 6476: https://github.com/galaxyproject/galaxy/pull/6476 .. _Pull Request 6478: https://github.com/galaxyproject/galaxy/pull/6478 .. _Pull Request 6480: https://github.com/galaxyproject/galaxy/pull/6480 .. _Pull Request 6481: https://github.com/galaxyproject/galaxy/pull/6481 .. _Pull Request 6486: https://github.com/galaxyproject/galaxy/pull/6486 .. _Pull Request 6489: https://github.com/galaxyproject/galaxy/pull/6489 .. _Pull Request 6490: https://github.com/galaxyproject/galaxy/pull/6490 .. _Pull Request 6491: https://github.com/galaxyproject/galaxy/pull/6491 .. _Pull Request 6494: https://github.com/galaxyproject/galaxy/pull/6494 .. _Pull Request 6496: https://github.com/galaxyproject/galaxy/pull/6496 .. _Pull Request 6498: https://github.com/galaxyproject/galaxy/pull/6498 .. _Pull Request 6499: https://github.com/galaxyproject/galaxy/pull/6499 .. _Pull Request 6500: https://github.com/galaxyproject/galaxy/pull/6500 .. _Pull Request 6501: https://github.com/galaxyproject/galaxy/pull/6501 .. _Pull Request 6502: https://github.com/galaxyproject/galaxy/pull/6502 .. _Pull Request 6503: https://github.com/galaxyproject/galaxy/pull/6503 .. _Pull Request 6505: https://github.com/galaxyproject/galaxy/pull/6505 .. _Pull Request 6515: https://github.com/galaxyproject/galaxy/pull/6515 .. _Pull Request 6516: https://github.com/galaxyproject/galaxy/pull/6516 .. _Pull Request 6517: https://github.com/galaxyproject/galaxy/pull/6517 .. _Pull Request 6519: https://github.com/galaxyproject/galaxy/pull/6519 .. _Pull Request 6520: https://github.com/galaxyproject/galaxy/pull/6520 .. _Pull Request 6521: https://github.com/galaxyproject/galaxy/pull/6521 .. _Pull Request 6523: https://github.com/galaxyproject/galaxy/pull/6523 .. _Pull Request 6524: https://github.com/galaxyproject/galaxy/pull/6524 .. _Pull Request 6528: https://github.com/galaxyproject/galaxy/pull/6528 .. _Pull Request 6529: https://github.com/galaxyproject/galaxy/pull/6529 .. _Pull Request 6531: https://github.com/galaxyproject/galaxy/pull/6531 .. _Pull Request 6532: https://github.com/galaxyproject/galaxy/pull/6532 .. _Pull Request 6533: https://github.com/galaxyproject/galaxy/pull/6533 .. _Pull Request 6538: https://github.com/galaxyproject/galaxy/pull/6538 .. _Pull Request 6539: https://github.com/galaxyproject/galaxy/pull/6539 .. _Pull Request 6541: https://github.com/galaxyproject/galaxy/pull/6541 .. _Pull Request 6542: https://github.com/galaxyproject/galaxy/pull/6542 .. _Pull Request 6544: https://github.com/galaxyproject/galaxy/pull/6544 .. _Pull Request 6545: https://github.com/galaxyproject/galaxy/pull/6545 .. _Pull Request 6546: https://github.com/galaxyproject/galaxy/pull/6546 .. _Pull Request 6550: https://github.com/galaxyproject/galaxy/pull/6550 .. _Pull Request 6551: https://github.com/galaxyproject/galaxy/pull/6551 .. _Pull Request 6552: https://github.com/galaxyproject/galaxy/pull/6552 .. _Pull Request 6553: https://github.com/galaxyproject/galaxy/pull/6553 .. _Pull Request 6554: https://github.com/galaxyproject/galaxy/pull/6554 .. _Pull Request 6555: https://github.com/galaxyproject/galaxy/pull/6555 .. _Pull Request 6557: https://github.com/galaxyproject/galaxy/pull/6557 .. _Pull Request 6561: https://github.com/galaxyproject/galaxy/pull/6561 .. _Pull Request 6562: https://github.com/galaxyproject/galaxy/pull/6562 .. _Pull Request 6564: https://github.com/galaxyproject/galaxy/pull/6564 .. _Pull Request 6565: https://github.com/galaxyproject/galaxy/pull/6565 .. _Pull Request 6567: https://github.com/galaxyproject/galaxy/pull/6567 .. _Pull Request 6568: https://github.com/galaxyproject/galaxy/pull/6568 .. _Pull Request 6570: https://github.com/galaxyproject/galaxy/pull/6570 .. _Pull Request 6571: https://github.com/galaxyproject/galaxy/pull/6571 .. _Pull Request 6572: https://github.com/galaxyproject/galaxy/pull/6572 .. _Pull Request 6575: https://github.com/galaxyproject/galaxy/pull/6575 .. _Pull Request 6578: https://github.com/galaxyproject/galaxy/pull/6578 .. _Pull Request 6580: https://github.com/galaxyproject/galaxy/pull/6580 .. _Pull Request 6582: https://github.com/galaxyproject/galaxy/pull/6582 .. _Pull Request 6586: https://github.com/galaxyproject/galaxy/pull/6586 .. _Pull Request 6587: https://github.com/galaxyproject/galaxy/pull/6587 .. _Pull Request 6588: https://github.com/galaxyproject/galaxy/pull/6588 .. _Pull Request 6591: https://github.com/galaxyproject/galaxy/pull/6591 .. _Pull Request 6592: https://github.com/galaxyproject/galaxy/pull/6592 .. _Pull Request 6593: https://github.com/galaxyproject/galaxy/pull/6593 .. _Pull Request 6594: https://github.com/galaxyproject/galaxy/pull/6594 .. _Pull Request 6595: https://github.com/galaxyproject/galaxy/pull/6595 .. _Pull Request 6596: https://github.com/galaxyproject/galaxy/pull/6596 .. _Pull Request 6597: https://github.com/galaxyproject/galaxy/pull/6597 .. _Pull Request 6602: https://github.com/galaxyproject/galaxy/pull/6602 .. _Pull Request 6605: https://github.com/galaxyproject/galaxy/pull/6605 .. _Pull Request 6606: https://github.com/galaxyproject/galaxy/pull/6606 .. _Pull Request 6608: https://github.com/galaxyproject/galaxy/pull/6608 .. _Pull Request 6609: https://github.com/galaxyproject/galaxy/pull/6609 .. _Pull Request 6610: https://github.com/galaxyproject/galaxy/pull/6610 .. _Pull Request 6611: https://github.com/galaxyproject/galaxy/pull/6611 .. _Pull Request 6613: https://github.com/galaxyproject/galaxy/pull/6613 .. _Pull Request 6616: https://github.com/galaxyproject/galaxy/pull/6616 .. _Pull Request 6620: https://github.com/galaxyproject/galaxy/pull/6620 .. _Pull Request 6622: https://github.com/galaxyproject/galaxy/pull/6622 .. _Pull Request 6623: https://github.com/galaxyproject/galaxy/pull/6623 .. _Pull Request 6627: https://github.com/galaxyproject/galaxy/pull/6627 .. _Pull Request 6628: https://github.com/galaxyproject/galaxy/pull/6628 .. _Pull Request 6629: https://github.com/galaxyproject/galaxy/pull/6629 .. _Pull Request 6630: https://github.com/galaxyproject/galaxy/pull/6630 .. _Pull Request 6631: https://github.com/galaxyproject/galaxy/pull/6631 .. _Pull Request 6632: https://github.com/galaxyproject/galaxy/pull/6632 .. _Pull Request 6633: https://github.com/galaxyproject/galaxy/pull/6633 .. _Pull Request 6635: https://github.com/galaxyproject/galaxy/pull/6635 .. _Pull Request 6636: https://github.com/galaxyproject/galaxy/pull/6636 .. _Pull Request 6638: https://github.com/galaxyproject/galaxy/pull/6638 .. _Pull Request 6639: https://github.com/galaxyproject/galaxy/pull/6639 .. _Pull Request 6641: https://github.com/galaxyproject/galaxy/pull/6641 .. _Pull Request 6642: https://github.com/galaxyproject/galaxy/pull/6642 .. _Pull Request 6643: https://github.com/galaxyproject/galaxy/pull/6643 .. _Pull Request 6644: https://github.com/galaxyproject/galaxy/pull/6644 .. _Pull Request 6647: https://github.com/galaxyproject/galaxy/pull/6647 .. _Pull Request 6648: https://github.com/galaxyproject/galaxy/pull/6648 .. _Pull Request 6651: https://github.com/galaxyproject/galaxy/pull/6651 .. _Pull Request 6655: https://github.com/galaxyproject/galaxy/pull/6655 .. _Pull Request 6656: https://github.com/galaxyproject/galaxy/pull/6656 .. _Pull Request 6659: https://github.com/galaxyproject/galaxy/pull/6659 .. _Pull Request 6660: https://github.com/galaxyproject/galaxy/pull/6660 .. _Pull Request 6661: https://github.com/galaxyproject/galaxy/pull/6661 .. _Pull Request 6662: https://github.com/galaxyproject/galaxy/pull/6662 .. _Pull Request 6664: https://github.com/galaxyproject/galaxy/pull/6664 .. _Pull Request 6668: https://github.com/galaxyproject/galaxy/pull/6668 .. _Pull Request 6669: https://github.com/galaxyproject/galaxy/pull/6669 .. _Pull Request 6670: https://github.com/galaxyproject/galaxy/pull/6670 .. _Pull Request 6672: https://github.com/galaxyproject/galaxy/pull/6672 .. _Pull Request 6676: https://github.com/galaxyproject/galaxy/pull/6676 .. _Pull Request 6677: https://github.com/galaxyproject/galaxy/pull/6677 .. _Pull Request 6678: https://github.com/galaxyproject/galaxy/pull/6678 .. _Pull Request 6680: https://github.com/galaxyproject/galaxy/pull/6680 .. _Pull Request 6681: https://github.com/galaxyproject/galaxy/pull/6681 .. _Pull Request 6683: https://github.com/galaxyproject/galaxy/pull/6683 .. _Pull Request 6687: https://github.com/galaxyproject/galaxy/pull/6687 .. _Pull Request 6692: https://github.com/galaxyproject/galaxy/pull/6692 .. _Pull Request 6695: https://github.com/galaxyproject/galaxy/pull/6695 .. _Pull Request 6703: https://github.com/galaxyproject/galaxy/pull/6703 .. _Pull Request 6705: https://github.com/galaxyproject/galaxy/pull/6705 .. _Pull Request 6707: https://github.com/galaxyproject/galaxy/pull/6707 .. _Pull Request 6711: https://github.com/galaxyproject/galaxy/pull/6711 .. _Pull Request 6723: https://github.com/galaxyproject/galaxy/pull/6723 .. _Pull Request 6725: https://github.com/galaxyproject/galaxy/pull/6725 .. _Pull Request 6726: https://github.com/galaxyproject/galaxy/pull/6726 .. _Pull Request 6728: https://github.com/galaxyproject/galaxy/pull/6728 .. _Pull Request 6730: https://github.com/galaxyproject/galaxy/pull/6730 .. _Pull Request 6733: https://github.com/galaxyproject/galaxy/pull/6733 .. _Pull Request 6737: https://github.com/galaxyproject/galaxy/pull/6737 .. _Pull Request 6739: https://github.com/galaxyproject/galaxy/pull/6739 .. _Pull Request 6741: https://github.com/galaxyproject/galaxy/pull/6741 .. _Pull Request 6742: https://github.com/galaxyproject/galaxy/pull/6742 .. _Pull Request 6743: https://github.com/galaxyproject/galaxy/pull/6743 .. _Pull Request 6744: https://github.com/galaxyproject/galaxy/pull/6744 .. _Pull Request 6745: https://github.com/galaxyproject/galaxy/pull/6745 .. _Pull Request 6747: https://github.com/galaxyproject/galaxy/pull/6747 .. _Pull Request 6748: https://github.com/galaxyproject/galaxy/pull/6748 .. _Pull Request 6749: https://github.com/galaxyproject/galaxy/pull/6749 .. _Pull Request 6750: https://github.com/galaxyproject/galaxy/pull/6750 .. _Pull Request 6753: https://github.com/galaxyproject/galaxy/pull/6753 .. _Pull Request 6755: https://github.com/galaxyproject/galaxy/pull/6755 .. _Pull Request 6760: https://github.com/galaxyproject/galaxy/pull/6760 .. _Pull Request 6761: https://github.com/galaxyproject/galaxy/pull/6761 .. _Pull Request 6765: https://github.com/galaxyproject/galaxy/pull/6765 .. _Pull Request 6766: https://github.com/galaxyproject/galaxy/pull/6766 .. _Pull Request 6768: https://github.com/galaxyproject/galaxy/pull/6768 .. _Pull Request 6771: https://github.com/galaxyproject/galaxy/pull/6771 .. _Pull Request 6774: https://github.com/galaxyproject/galaxy/pull/6774 .. _Pull Request 6780: https://github.com/galaxyproject/galaxy/pull/6780 .. _Pull Request 6782: https://github.com/galaxyproject/galaxy/pull/6782 .. _Pull Request 6785: https://github.com/galaxyproject/galaxy/pull/6785 .. _Pull Request 6789: https://github.com/galaxyproject/galaxy/pull/6789 .. _Pull Request 6791: https://github.com/galaxyproject/galaxy/pull/6791 .. _Pull Request 6793: https://github.com/galaxyproject/galaxy/pull/6793 .. _Pull Request 6796: https://github.com/galaxyproject/galaxy/pull/6796 .. _Pull Request 6798: https://github.com/galaxyproject/galaxy/pull/6798 .. _Pull Request 6799: https://github.com/galaxyproject/galaxy/pull/6799 .. _Pull Request 6802: https://github.com/galaxyproject/galaxy/pull/6802 .. _Pull Request 6803: https://github.com/galaxyproject/galaxy/pull/6803 .. _Pull Request 6805: https://github.com/galaxyproject/galaxy/pull/6805 .. _Pull Request 6808: https://github.com/galaxyproject/galaxy/pull/6808 .. _Pull Request 6809: https://github.com/galaxyproject/galaxy/pull/6809 .. _Pull Request 6810: https://github.com/galaxyproject/galaxy/pull/6810 .. _Pull Request 6823: https://github.com/galaxyproject/galaxy/pull/6823 .. _Pull Request 6828: https://github.com/galaxyproject/galaxy/pull/6828 .. _Pull Request 6830: https://github.com/galaxyproject/galaxy/pull/6830 .. _Pull Request 6836: https://github.com/galaxyproject/galaxy/pull/6836 .. _Pull Request 6839: https://github.com/galaxyproject/galaxy/pull/6839 .. _Pull Request 6845: https://github.com/galaxyproject/galaxy/pull/6845 .. _Pull Request 6859: https://github.com/galaxyproject/galaxy/pull/6859 .. _Pull Request 6863: https://github.com/galaxyproject/galaxy/pull/6863 .. _Pull Request 6867: https://github.com/galaxyproject/galaxy/pull/6867 .. _Pull Request 6875: https://github.com/galaxyproject/galaxy/pull/6875 .. _Pull Request 6885: https://github.com/galaxyproject/galaxy/pull/6885 .. _Pull Request 6904: https://github.com/galaxyproject/galaxy/pull/6904 .. _Pull Request 6908: https://github.com/galaxyproject/galaxy/pull/6908 .. _Pull Request 6912: https://github.com/galaxyproject/galaxy/pull/6912 .. _Pull Request 6932: https://github.com/galaxyproject/galaxy/pull/6932