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.. to_doc
18.09
===============================
.. announce_start
Enhancements
-------------------------------
.. feature
* Allow selecting subset of collection by group tag
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/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 <https://github.com/bernt-matthias>`__).
`Pull Request 6313`_
* Allows DatasetMatcher to use multiple filters
(thanks to `@ebolyen <https://github.com/ebolyen>`__).
`Pull Request 6443`_
* Adding 4 new GROMACS datatypes: cpt, xtc, top, and gro
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 6655`_
* Implement runtime parameters for subworkflows.
`Pull Request 6664`_
* Expose workflow versions
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6013`_
* Add hostname metric
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6021`_
* Pause jobs with invalid inputs
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6072`_
* Add blib datatype for Mass Spectrometry spectral library
(thanks to `@jj-umn <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6135`_
* Make workflow editor ``toolTitle`` link include the tools description
(thanks to `@scrathat <https://github.com/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 <https://github.com/hexylena>`__).
`Pull Request 6200`_
* Add the newick extension for the Newick datatype,
(thanks to `@gregvonkuster <https://github.com/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 <https://github.com/hexylena>`__).
`Pull Request 6221`_
* Workflow submit text links
`Pull Request 6240`_
* Password encoding improvements
(thanks to `@nsoranzo <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6273`_
* Consolidate use of ``get_repo_for_repository()`` and ``clone_repository()``
(thanks to `@nsoranzo <https://github.com/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 <https://github.com/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 <https://github.com/rhpvorderman>`__).
`Pull Request 6305`_
* More use of Mercurial CLI instead of API
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6307`_
* Lists-as-tuples collection operations
`Pull Request 6312`_
* Replace unmaintained pycrypto dependency with pycryptodome
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6324`_
* Add py34-first_startup to Travis and default tox tests
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6325`_
* Visualization static staging
`Pull Request 6344`_
* Add period to the list of allowed characters in user names
(thanks to `@moskalenko <https://github.com/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 <https://github.com/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 <https://github.com/qiagu>`__).
`Pull Request 6388`_
* Client library upgrades.
`Pull Request 6400`_
* Allow resource selection for data managers
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6402`_
* Update dev dependencies
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6403`_
* Add py34-unit (allowed to fail) job to Travis
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6406`_
* Allow supplying name of pasted data
(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
`Pull Request 6415`_
* Fixes for uploading empty files to Galaxy.
`Pull Request 6418`_
* Remove installation of python-lzo system dependencies
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6425`_
* Citation style work
`Pull Request 6427`_
* Run workflows from published workflows menu
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6428`_
* Fix a few tool_deps test errors
(thanks to `@bgruening <https://github.com/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 <https://github.com/almahmoud>`__).
`Pull Request 6447`_
* Let data managers also use conda python.
(thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
`Pull Request 6466`_
* Make upload tool python3 compatible
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6467`_
* Allow including paths in inputs json files.
`Pull Request 6468`_
* Update cliff and other related dependencies
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6469`_
* Fix bug noticed in sentry
(thanks to `@hexylena <https://github.com/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 <https://github.com/hexylena>`__).
`Pull Request 6480`_
* Use bootstrap vue classes for workflow import form
`Pull Request 6489`_
* Small improvement to the tool xsd docs regarding ``discovered_datasets``
(thanks to `@bernt-matthias <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/bgruening>`__).
`Pull Request 6596`_
* Add trr datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 6597`_
* Refresh an expired OIDC ID token
`Pull Request 6606`_
* Handle driver shutdown, show all tests in pytest
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6608`_
* Add dcd datatype for molecular dynamics
(thanks to `@chrisbarnettster <https://github.com/chrisbarnettster>`__).
`Pull Request 6613`_
* Py3 testing cleanups
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6616`_
* Integration test for job recovery.
`Pull Request 6620`_
* Update all dependencies
(thanks to `@nsoranzo <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6630`_
* Testing framework improvements
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/mblue9>`__).
`Pull Request 6648`_
* Allow group tag selection also for multiple="true" inputs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6661`_
* Various link and documentation fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6662`_
* Upgraded genomespaceclient to newer version
(thanks to `@gvlproject <https://github.com/gvlproject>`__).
`Pull Request 6668`_
* Workflow replacement parameters polish.
`Pull Request 6678`_
* Keep newly broken tool in toolbox
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6805`_
* Allow testing tags in input collections.
`Pull Request 6823`_
.. small_enhancement
* Remove duplicate metric sending
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6011`_
* This strips the graphite-specific middleware
`Pull Request 6018`_
* Make ``interactor._{get,post,put,...}`` less repetitive
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6070`_
* Workflow and remote-user related refactoring and a bug fix
`Pull Request 6076`_
* Drop unused files
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6315`_
* Rewrite admin data types as vue component
(thanks to `@scrathat <https://github.com/scrathat>`__).
`Pull Request 6383`_
* Some style cleanup.
`Pull Request 6386`_
* py3 compat
(thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
`Pull Request 6434`_
* Python3: Encode return values of JSON encoder
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6439`_
* Python3: Drop ``json_fix``, doesn't seem to be necessary and fixes workflow
unit tests
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6446`_
* py3: fixes ``test_DatasetManager.py:DatasetManagerTestCase``
(thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
`Pull Request 6452`_
* Fix test_toolbox for python 3
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6561`_
* Setup py3 test job
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6595`_
* Enable and fix framework py3 tests
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6605`_
* Order data parameters before unlinked multiplication
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6609`_
* Fix remaining selenium py3 test failures
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6627`_
* Tweak conda_* setting in test driver
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6633`_
* Move tests to pytest setup
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6669`_
* Fix remaining selenium py3 errors
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/galaxyproject>`__).
`Pull Request 6009`_
* Fix some imports
(thanks to `@nsoranzo <https://github.com/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 <https://github.com/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 <https://github.com/abretaud>`__).
`Pull Request 6211`_
* Fix ``optional="True"`` inputs
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/ValentinChCloud>`__).
`Pull Request 6228`_
* Fix file type error in RuleCollectionBuilder.
`Pull Request 6231`_
* Fix non-strict tabular relabel operation
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6234`_
* Hack paster args to not duplicate pid file stuff for RUN_ALL.
(thanks to `@lparsons <https://github.com/lparsons>`__).
`Pull Request 6239`_
* Backport of Workflow Execution Text Fixup
`Pull Request 6243`_
* Hyperlink DOIs against preferred resolver
(thanks to `@katrinleinweber <https://github.com/katrinleinweber>`__).
`Pull Request 6244`_
* Check context for textable mode of select fields
`Pull Request 6251`_
* Mapping over ``from_param`` fixes
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6262`_
* Fix dataset sizes in GRT export script
(thanks to `@atyryshkina <https://github.com/atyryshkina>`__).
`Pull Request 6263`_
* Allow invalid optional param values for tools profile versions < 18.09
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6264`_
* Python3 fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6265`_
* Fixes for phenotype association tools
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6269`_
* Fix link to workflow list
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 6270`_
* Fix help text for renaming operation in workflows
`Pull Request 6274`_
* Various fixes for mapping over collections
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6278`_
* Fix tool search overlay selector
(thanks to `@scrathat <https://github.com/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 <https://github.com/hrhotz>`__).
`Pull Request 6292`_
* Strip a spurious Slurm warning from job stderr
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6293`_
* Fix ``GALAXY_RUN_ALL=1 ./run.sh --daemon``
(thanks to `@nsoranzo <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6304`_
* Fix undefined ``success_message``
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6316`_
* Allow ``#if $datasets #end if`` pattern for file lists
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6317`_
* Fix target update for rule collection builder after input selection
(thanks to `@scrathat <https://github.com/scrathat>`__).
`Pull Request 6326`_
* Added missing level ``fatal_oom`` to galaxy.xsd
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 6341`_
* Update description for installing pbs-python
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/dpryan79>`__).
`Pull Request 6349`_
* Fix the ``--log-file`` option in the job handlers
(thanks to `@dpryan79 <https://github.com/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 <https://github.com/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 <https://github.com/qiagu>`__).
`Pull Request 6389`_
* Optimize setting large numbers of HIDs for collection outputs.
`Pull Request 6394`_
* Fixing ``<conditional>`` XML example
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 6399`_
* Fix positioning for tool search box.
`Pull Request 6416`_
* Removing binary as input for python compatibility
(thanks to `@eslerm <https://github.com/eslerm>`__).
`Pull Request 6417`_
* GCC2018 python3 unit-test fixes
(thanks to `@ycgong <https://github.com/ycgong>`__).
`Pull Request 6419`_
* Python 3 porting
(thanks to `@caleb-easterly <https://github.com/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 <https://github.com/johnbradley>`__).
`Pull Request 6429`_
* Unit testing with Python 3
(thanks to `@NicHerndon <https://github.com/NicHerndon>`__).
`Pull Request 6430`_
* Do not encode a rendered Mako template
(thanks to `@nsoranzo <https://github.com/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 <https://github.com/caleb-easterly>`__).
`Pull Request 6438`_
* py3 compat: fixes test_vcf, test_sniff_compressed*
(thanks to `@caleb-easterly <https://github.com/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 <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6453`_
* py3: replace e.message with str(e)
(thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
`Pull Request 6454`_
* Various Python 3 fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6455`_
* GIE static url
(thanks to `@thobalose <https://github.com/thobalose>`__).
`Pull Request 6460`_
* Update common_startup_functions.sh
(thanks to `@nagoue <https://github.com/nagoue>`__).
`Pull Request 6481`_
* Fix for show params server error
`Pull Request 6486`_
* Fix ``ftp_upload_purge`` in galaxy.yml
(thanks to `@phac-nml <https://github.com/phac-nml>`__).
`Pull Request 6494`_
* Fix resume from history panel
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6498`_
* Fix bam to bigwig error detection.
(thanks to `@pvanheus <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6594`_
* Fix Location of Plugin Static Content In Documentation for 18.05
(thanks to `@phac-nml <https://github.com/phac-nml>`__).
`Pull Request 6602`_
* Fix cron/build_chrom_db.py and update UCSC builds
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6623`_
* Fix for workflow extraction cleanup routine.
`Pull Request 6636`_
* Row ids that are all numeric become ints...
(thanks to `@bwlang <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6659`_
* Update bx-python to 0.8.2
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6670`_
* Serialize select field options, fixes beta install
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6677`_
* Fix wf-editor when loading subworkflow with parenthesis in label
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6737`_
* Fix and test anonymous error reports
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/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 <https://github.com/mvdbeek>`__).
`Pull Request 6771`_
* Update name of ``Workflow`` when updating ``StoredWorkflow`` name
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6774`_
* All extracted datasets should be visible
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6780`_
* Fix ``__encode_invocation`` signature
`Pull Request 6782`_
* Strip all control characters from rules
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6785`_
* Fix bam upload resulting in 'auto' datatype
(thanks to `@mvdbeek <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/nsoranzo>`__).
`Pull Request 6830`_
* Register job monitor thread as postfork function
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6836`_
* Unified panel style bottom padding fix
`Pull Request 6839`_
* Fix slurm cli on secure shell
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6845`_
* update paramiko dep
`Pull Request 6859`_
* Fix ``LocalShell`` doctest
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6863`_
* Keep xlsx files compressed
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6867`_
* Do not traceback when uploading a TS repo with no changes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6875`_
* Create composite file archives in new_file_path instead of TMP
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6885`_
* Fix pretty printing of shed_tool_conf.xml file
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6904`_
* Fix ``make config-validate``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6908`_
* Fix stopping DRMAA jobs
`Pull Request 6912`_
* Fix toolshed error in display_tool if tool is invalid
(thanks to `@mvdbeek <https://github.com/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
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