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galaxy/doc/source/releases/18.01.rst
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Nicola Soranzo 46b3539a35 Fix doc bugs 
Use proper cross-referencing with `:doc:`.
2019-01-14 22:45:34 +00:00

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.. to_doc
18.01
===============================
.. announce_start
Enhancements
-------------------------------
.. major_feature
.. _list of related performance pull requests:
* Performance and User Experience Improvements
`Pull Request 5514`_, `Pull Request 5515`_, `Pull Request 5542`_,
`Pull Request 5574`_, `Pull Request 5576`_, `Pull Request 5582`_,
`Pull Request 5533`_, `Pull Request 5615`_, `Pull Request 5616`_
.. _list of related client pull requests:
* Client Architecture
`Pull Request 4435`_, `Pull Request 4978`_, `Pull Request 4436`_, `Pull Request 5173`_
`Pull Request 5293`_, `Pull Request 5191`_, `Pull Request 5190`_,
`Pull Request 4827`_, `Pull Request 4964`_, `Pull Request 5371`_,
`Pull Request 5128`_, `Pull Request 5262`_, `Pull Request 5081`_, `Pull Request 5054`_
`Pull Request 5093`_, `Pull Request 5001`_, `Pull Request 5261`_, `Pull Request 5278`_,
`Pull Request 5294`_
.. feature
* Add option to clone tool steps in the workflow editor
(thanks to `@anatskiy <https://github.com/anatskiy>`__).
`Pull Request 5087`_, `Pull Request 5124`_, `Pull Request 5185`_
* Implement a generic Cloud ObjectStore using multi-cloud support from
`cloudbridge <https://github.com/gvlproject/cloudbridge>`__
(thanks to `@VJalili <https://github.com/VJalili>`__).
`Pull Request 4487`_
* Reload tools immediately if a macro changes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4635`_
* Add an interactive environment for `AskOmics <https://github.com/askomics/askomics>`__
a visual SPARQL query builder for RDF databases
(thanks to `@xgaia <https://github.com/xgaia>`__).
`Pull Request 4737`_
* Implement a Github error report backend for
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4765`_
* Add maintenance script to simplify setting up a cleanup cron job
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 4916`_
* Create the ``$GALAXY_MEMORY_MB`` job environment variable for tools.
`Pull Request 4958`_
* Improved home and temp directory handling for tools and jobs.
`Pull Request 5193`_
* Tool-based annotation of out of memory errors.
`Pull Request 5196`_
* Added support for recursively discovering output datasets
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 5240`_
* Add an API endpoint that allows admins to decode galaxy object IDs.
`Pull Request 5018`_
* Add sorting options for data library folders.
`Pull Request 4877`_
* Add option to auto create ``user_library_import_dir`` directories upon user
login.
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 5138`_
* Add option to check file permissions for the user library imports
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 5154`_
* Add an admin form to pre-populate an LDAP user
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 5238`_
* Add a CRAM to BAM datatype converter
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4939`_
* Add infernal-cm datatype
(thanks to `@mmiladi <https://github.com/mmiladi>`__).
`Pull Request 4977`_
* Add ICM datatype for glimmer
(thanks to `@abretaud <https://github.com/abretaud>`__).
`Pull Request 5042`_
* Add Analyze75 datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 4841`_
* Add Classical linkage and haplotype datatypes
(thanks to `@mtekman <https://github.com/mtekman>`__).
`Pull Request 4894`_
* Add ideaspre datatype
(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
`Pull Request 5445`_
* Add compressed fasta support.
`Pull Request 5561`_
* Add ``cool`` datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 5023`_
* Add neostore zip datatype
(thanks to `@zipho <https://github.com/zipho>`__).
`Pull Request 4178`_
* Add fast5_archive datatype
(thanks to `@jvolkening <https://github.com/jvolkening>`__).
`Pull Request 4569`_
* Add postgresql datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 4730`_
* Add IQtree datatypes
(thanks to `@mtekman <https://github.com/mtekman>`__).
`Pull Request 4849`_
* Add Phylip datatype
(thanks to `@khillion <https://github.com/khillion>`__).
`Pull Request 5301`_
.. enhancement
* Option to group Galaxy Tours for viewing clarity
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 4829`_
* Allow users to upload multiple FTP files within a single request
`Pull Request 4513`_
* Replaces the admin form builder grid and forms
`Pull Request 4480`_
* Update pysam dependency to 0.14 and eliminate the need to have
samtools on Galaxy's ``PATH`` (with huge help from `@mvdbeek
<https://github.com/mvdbeek>`__)
`Pull Request 4497`_, `Pull Request 5512`_, `Pull Request 5037`_
* Expand and improve Selenium testing of the web UI (with help from
`@anatskiy <https://github.com/anatskiy>`__).
`Pull Request 4543`_, `Pull Request 4655`_, `Pull Request 4676`_,
`Pull Request 4753`_, `Pull Request 4732`_, `Pull Request 4909`_,
`Pull Request 4935`_, `Pull Request 4925`_,
`Pull Request 4687`_, `Pull Request 4660`_, `Pull Request 5333`_,
`Pull Request 5068`_, `Pull Request 4757`_, `Pull Request 4971`_,
`Pull Request 4653`_
* Allow multiple simultaneous uploads via single POST.
`Pull Request 4563`_
* Various bits of proactive security-related hardening
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4604`_
* Move test helper ``wait_for_dataset_collection`` for reuse
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4658`_
* Extend job search for hdcas
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4665`_
* Add a custom ``TRACE`` log level for even more verbosity.
`Pull Request 4672`_
* Migrate various mako templates to modern JavaScript driven views.
`Pull Request 4681`_, `Pull Request 4682`_, `Pull Request 4711`_,
`Pull Request 4755`_, `Pull Request 4661`_, `Pull Request 4993`_,
`Pull Request 4664`_, `Pull Request 4996`_, `Pull Request 5014`_,
`Pull Request 4833`_, `Pull Request 5212`_, `Pull Request 5114`_
* More HDCA copying tests, add option to copy HDAs into new history.
`Pull Request 5004`_
* Use only latest publication in ``CITATION``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4688`_
* Nicer logging message for sentry
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4693`_
* Use enumeration to provide history input index names.
`Pull Request 4700`_
* Cleanup delayed action in ``history-view.js``.
`Pull Request 4704`_
* Add logging during for script integrity exceptions
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4720`_
* Fix to respect ``galaxy.json`` supplied metadata for empty outputs.
`Pull Request 4722`_
* Update ``reports.md`` with a link to the community hub
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 4723`_
* Typo fixes and small cleanups
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4725`_
* Fix that implements stricter checks for SDF datatype sniffing
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4729`_
* When reloading the toolbox, use the existing dependency manager if possible
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4739`_
* Many more upload tests - big improvements to uploads will be coming to Galaxy 18.05.
`Pull Request 4746`_, `Pull Request 4762`_, `Pull Request 4790`_,
`Pull Request 4863`_, `Pull Request 5266`_, `Pull Request 5209`_
* Kubernetes resources requests/limits support
(thanks to `@pcm32 <https://github.com/pcm32>`__ and the `@phnmnl <https://github.com/phnmnl>`__ project).
`Pull Request 4751`_
* Send all influxdb stats to a single bucket
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4758`_
* PEP-8 fixes in random doctests.
`Pull Request 4764`_
* Avoid circular import when determining max metadata value size.
`Pull Request 4770`_
* Remove unused concept of dataset children.
`Pull Request 4771`_
* Allow dataset attribute changes without refreshing the page.
`Pull Request 4779`_
* Include check for updates to dependencies in tox, Makefile, Travis.
`Pull Request 4788`_
* Add labels to selection options of the collection flattening tool.
`Pull Request 4791`_
* Expose ``state``, ``stdout``, ``stderr``, ``uuid`` in the library API
`Pull Request 4839`_
* Significant improvements to client QUnit tests including new
`Karma <https://karma-runner.github.io/>`__ based test driver.
`Pull Request 4855`_, `Pull Request 5066`_, `Pull Request 5063`_,
`Pull Request 5074`_
* Remove tool reloading buttons and packaging endpoint, revise admin labels
`Pull Request 4866`_
* Add various elements to the Tool XML doc page
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4871`_
* Absolute pins on linting dependencies.
`Pull Request 4876`_
* Update various Galaxy requirements.
`Pull Request 4884`_
* Updates and enhancements for the testing ``Dockerfile``.
`Pull Request 4885`_, `Pull Request 4879`_, `Pull Request 4900`_
* Add nicer composite dataset names by default
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 4886`_
* Improved initialization and isolation of Postgres databases used in integration testing.
`Pull Request 4887`_, `Pull Request 4914`_
* Rework dev dependencies to be Pipfile generated, locked, and hashed.
`Pull Request 4891`_
* Install dev and regular dependencies at the same time.
`Pull Request 4903`_
* More structured app shutdown.
`Pull Request 4910`_
* Touch up issue labels in repository procedures document.
`Pull Request 4912`_
* Improve error handling for incorrect datatype upload.
`Pull Request 4922`_
* Activate mulled dependencies once per job
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4945`_
* Remove invalid user preferences beta (no longer a beta, always enabled)
`Pull Request 4957`_
* Add ``DELETE /api/jobs/<job_id>`` as a job cancellation API endpoint.
`Pull Request 4961`_
* Kill off processes when stopping the local job runner.
`Pull Request 4962`_
* Test both endpoints for collection creation in history contents API.
`Pull Request 4965`_
* Add @flakey test annotation and "skip" them if the fail on Jenkins.
`Pull Request 4972`_
* Include path in job script integrity errors
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4991`_
* Fix tox envlist to contain all envs that should pass
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4992`_
* Changes made while working on uWSGI mules that don't belong in the mules PR
`Pull Request 4994`_
* Add warning for sort-of-defunct workflow options in galaxy.ini.
`Pull Request 5002`_
* Fix Python import order everywhere
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4697`_, `Pull Request 5005`_
* dataset info: present decoded IDs for admins and add peek
`Pull Request 5006`_
* Removed unneeded skip_install tags in tox.ini.
`Pull Request 5011`_
* Add metric to the core plugin to collect $GALAXY_MEMORY_MB
`Pull Request 5016`_
* Test renaming multiple different outputs in workflows.
`Pull Request 5017`_
* Render arbitrarily nested lists in the UI
`Pull Request 5038`_
* Expose proper element_identifier in tool action template expansions
`Pull Request 5049`_
* Document fastest way to iterate on client & client tests together.
`Pull Request 5051`_
* Support separate DSN for job sentry error reports
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 5056`_
* Build endpoint separation
`Pull Request 5058`_
* Remove ``wchartype`` dependency and ``is_multi_byte`` attribute
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5062`_, `Pull Request 5088`_
* Implement multilingualization support on workflow page
(thanks to `@manabuishii <https://github.com/manabuishii>`__).
`Pull Request 5077`_
* Update Jupyter IE default image
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 5095`_
* Determine dynamically if an extension corresponds to an unsniffable binary
datatype
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5109`_
* Update to flake8-import-order 0.16
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4869`_, `Pull Request 5110`_
* Change the default to not add tags based on filename
`Pull Request 5115`_
* Improve tool validation and metadata generation
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5119`_
* Download button fixes.
`Pull Request 5125`_
* Datatype conversion check optimization
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5137`_
* Test resubmit for dynamic JobDestination structures.
`Pull Request 5139`_
* Various dataset hashtag display improvements.
`Pull Request 5155`_
* i18n improvements for French localization
(thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
`Pull Request 5089`_, `Pull Request 5157`_
* Change hicexplorer image name
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 5177`_
* Fix `#3002 <https://github.com/galaxyproject/galaxy/issues/3002>`__ with update to
newer version of virtualenv.
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 5202`_
* Huge steps toward Python 3 compatiblity
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5215`_, `Pull Request 5221`_, `Pull Request 5225`_, `Pull Request 5228`_,
`Pull Request 5200`_, `Pull Request 5199`_, `Pull Request 4799`_, `Pull Request 4811`_
* Add chinese support
(thanks to `@istevenshen <https://github.com/istevenshen>`__).
`Pull Request 5232`_
* Make ``pam`` a conditional dependency
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5251`_
* Update api quickstart doc to use default port, with a little bit of extra
guidance.
`Pull Request 5260`_
* Allow sorting collection elements based on file
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5273`_
* Add Biostar configuration options to the configuration sample file.
`Pull Request 5276`_
* Update Japanese translation
(thanks to `@istevenshen <https://github.com/istevenshen>`__).
`Pull Request 5288`_
* Improve the migration message when having to downgrade the database
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5299`_
* Allow ``message`` attribute to be modified on a library dataset.
`Pull Request 5312`_
* Enforce a size constraint on the tag editor.
`Pull Request 5337`_
* Various webhooks improvements.
`Pull Request 5342`_
* Make ``TabularToolDataTable._deduplicate_data()`` faster
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5383`_
* Add ``--skip_flakey_fails`` flag to CI script for API tests
`Pull Request 5455`_
* Fix for toolbox filters
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 5526`_
* Fix missing job stdout/stderr on Pulsar transfer failures.
`Pull Request 5535`_
* Optimization to fix repeated fetching dataset permissions in dynamic output collection.
`Pull Request 5578`_
* Backport toolbox cache
`Pull Request 5583`_
* Replace distutils.version with packaging.version (fixing lineage handling for
freebayes among other things).
`Pull Request 5588`_
* Move the cache from toolbox level to the tool level.
`Pull Request 5600`_
.. small_enhancement
* Removes Sample request and External services makos/controllers
`Pull Request 4526`_, `Pull Request 4872`_, `Pull Request 5103`_,
`Pull Request 5204`_
* Remove unused abstraction layers from Visualizations Registry.
`Pull Request 4620`_
* Visible keys standardization in model classes.
`Pull Request 4744`_
* Remove legacy library interface
`Pull Request 4908`_
* ES6 client/galaxy/scripts/utils/ajax-queue.js
`Pull Request 4933`_
* Remove unused galaxy-side set_tool_version code
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4986`_
* Fix ``allow-register`` option in ``auth`` module
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4989`_
* Tried to fix issue with Conda environment building failing jobs that
had to be rolled back.
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5036`_, `Pull Request 5470`_
* Add packed symlink back pending a deprecation cycle.
`Pull Request 5094`_
* Onload webhook toggles.
`Pull Request 5116`_
* Re-organize edge case upload options for greater readability.
`Pull Request 5206`_
* Refactor ``upload.py`` toward reuse.
`Pull Request 5229`_
* JavaScript router cleanup.
`Pull Request 5235`_
* Comment PlantTribes datatypes
(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
`Pull Request 5254`_
* Dataset error interface cleanup.
`Pull Request 5279`_
* Mention how to specify the config file location
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5297`_
* Uninstall a tool by default (vs. deactivating it).
`Pull Request 5300`_
Fixes
-------------------------------
.. major_bug
.. bug
* Allow mapping over collections when discovering dataset collections in tools
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5413`_
* Make liftover tool use data tables
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4645`_
* Pass job output file unqualified names to Pulsar so that it can create them
before running the job.
`Pull Request 4662`_
* Fix transiently failing saved histories due to success message disappearing.
`Pull Request 4669`_
* Update CITATION file with 2016 paper
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4686`_
* Stop running common_startup.sh twice when starting from run.sh
`Pull Request 4759`_
* Fix docstring linting.
`Pull Request 4766`_
* Mothur.freq sniffer more stringent
(thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__).
`Pull Request 4781`_
* MacOS X fix for a test tool.
`Pull Request 4806`_
* Minor architecture slides fixes for typos/grammar.
`Pull Request 4822`_
* Fix two invalid targets in dataset list item.
`Pull Request 4823`_
* Fix double return in form-parameters.
`Pull Request 4826`_
* Fix the case where 'Labels' in a docker node inspect exists but is null.
`Pull Request 4838`_
* Fix all E722 errors and ignore E741
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4847`_
* Fix jsutils time - fixes charts visualize.
`Pull Request 4852`_
* Bugfix during error handling with linked files during upload
(thanks to `@ieguinoa <https://github.com/ieguinoa>`__).
`Pull Request 4858`_
* Add a gulp plumber.
`Pull Request 4867`_
* Minor admin panel fixes.
`Pull Request 4895`_
* Fix list collection creator dragdrop event bindings.
`Pull Request 4901`_
* Fix status handling for grids.
`Pull Request 4913`_
* Fix revision selection during (beta) repository installation
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4944`_
* Fix Trackster styles bleeding into the app (the slightly off-center upload
.icon buttons).
`Pull Request 4948`_
* Fix multiple selections for grid operations redirecting to center panel.
`Pull Request 4951`_
* Fix visualization link in import success message.
`Pull Request 4952`_
* Fix up reports JavaScript.
`Pull Request 4967`_
* Run ``hg clone`` in a subprocess instead of using the Mercurial API
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4979`_
* Tolerate ``IOError`` in tool and data table watcher
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4981`_
* Install numpy before bx-python in case you are installing from sdists
`Pull Request 4982`_
* Specify ``TagAssociation`` class when copying a tag
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4984`_
* Fix initialization of named ajax queue.
`Pull Request 4985`_
* Encode file content with utf-8
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4987`_
* Revert export to file.
`Pull Request 4988`_
* Remove extraneous subclass for DMND datatype
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4990`_
* Fix to allow ``get_history`` calls with ``create=False`` when evaluating workflows.
`Pull Request 4997`_
* Add missing ``ipaddress`` requirement
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5000`_
* Use github instead of NCBI for problematic data manager test FASTA.
`Pull Request 5007`_
* Fix for history contents API to remove the default flag override.
`Pull Request 5008`_
* Fix to avoid visiting child inputs of invalid conditionals.
`Pull Request 5010`_
* Fix for ``parse_interpreter`` - log a warning only if interpreter is set
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5015`_
* Fix a few stray wiki links.
`Pull Request 5020`_
* Workflow editor outputs fixes.
`Pull Request 5021`_
* Fix workflow editor output attributes.
`Pull Request 5022`_
* Metadata parameters rely on their own optional setting not on the field
attribute.
`Pull Request 5027`_
* A Python 3 fix for the gsummary tool
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 5043`_
* Cleanup SA objects between workflow invocation scheduling attempts.
`Pull Request 5045`_
* Safely handle possible ``None`` value encountered in processing and execution of
post-job action arguments
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 5050`_
* Restore admin form routes.
`Pull Request 5065`_
* Fixes galaxy startup when ``LC_TYPE=UTF-8`` on OS X
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5070`_
* Ignore ``OSError`` when chmod'ing integrated_tool_panel_conf.xml
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5071`_
* Fix metadata setting for ``otu`` datatypes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5072`_
* Fix exception in admin panel
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5079`_
* Always fill ``message`` to avoid ``KeyError`` for sentry ``ERROR_TEMPLATE``
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5086`_
* Attempt to make data manager integration test more robust.
`Pull Request 5098`_
* Toolshed install stability improvements
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5099`_
* Fix Trackster link to custom builds view.
`Pull Request 5104`_
* Improve resilience of filter detection, add error messages, fix identifiers.
`Pull Request 5106`_
* Fix ICM datatype sniffer config
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5121`_
* Fix attribute error that was missed during refactor of sentry
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 5122`_
* Fix connecting non-input modules to subworkflow inputs.
`Pull Request 5140`_
* Fix for history copy.
`Pull Request 5144`_
* Fixes for handling delayed steps within subworkflows.
`Pull Request 5145`_
* Fix localization and build client.
`Pull Request 5156`_
* Resolve broken link for "all workflows"
(thanks to `@mmiladi <https://github.com/mmiladi>`__).
`Pull Request 5161`_
* Fix workflow collection attachments.
`Pull Request 5166`_
* Provide UI collection output information for subworkflows.
`Pull Request 5172`_
* Remove legacy request controller from reports app.
`Pull Request 5182`_
* Fixes genome decode handling.
`Pull Request 5198`_
* Remove broken Yahoo OpenID support
(thanks to `@VJalili <https://github.com/VJalili>`__).
`Pull Request 5208`_
* Force window jQuery access for charts.
`Pull Request 5210`_
* Mark transiently failing ``test_run_data`` as flakey.
`Pull Request 5211`_
* Fail job if tools that use ``galaxy.json`` write to stderr
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5217`_
* Allow shell plugins with different parameters to co-exist
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5223`_
* paster.pid/log to galaxy.pid/log reference update
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5226`_
* Refine Conda version numbers allowed for using ``--offline`` flag again
(thanks to `@NCEichner <https://github.com/NCEichner>`__).
`Pull Request 5233`_
* Workflow list show-in-tool-panel callback bugfix.
`Pull Request 5234`_
* Fix image proxy prefix in tool form.
`Pull Request 5237`_
* Fix wrong tool id after switching versions
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5249`_
* Catch and display error when displaying broken BAM file
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5253`_
* Fix for getmicrobedata tool
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 5258`_
* Adjust note about nginx enabled sites configuration
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 5259`_
* Mark the test ``rerun_with_use_cached_job`` as flakey
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5286`_
* Fix dataset edit link.
`Pull Request 5289`_
* Fix link to getgalaxy.org
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 5295`_
* Fix tool report submission with sentry
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5303`_
* Fix ``common_startup.sh`` bash-isms
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5304`_
* Fix Galaxy instance startup error
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 5306`_
* Fix link to library from history structure view.
`Pull Request 5327`_
* Prevent reloading when data table is being modified
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5331`_
* Work around (temporarily) wrong ``getsize()`` output
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5335`_
* Disable galaxy tour 'path' navigation.
`Pull Request 5340`_
* Fix ``tool-shed-config-validate`` ``Makefile`` target.
(thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
`Pull Request 5343`_
* History import fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5344`_
* Fix dataset purging, dataset cleanup script and db_shell script
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5346`_
* Fix BAM conversion test tool
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5351`_
* Remove charlimit for fetching URLs.
`Pull Request 5353`_
* Use ``print()`` function in common_startup.sh
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5357`_
* Handle ``None`` in job owner in API
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 5358`_
* Fix form logic in deactivate or uninstall.
`Pull Request 5363`_
* History multipanel fixes.
`Pull Request 5364`_
* Remove additional checkbox workarounds.
`Pull Request 5367`_
* Workflow tool menu fix for deleted workflows.
`Pull Request 5368`_
* Bump conditional ``Pygments`` version to 2.2.0 so it matches the dev.
`Pull Request 5376`_
* Fix ``make docs`` when the virtualenv is not ``.venv`` .
`Pull Request 5377`_
* Force a fixed node image version when building client for Jenkins.
`Pull Request 5382`_
* Install latest Conda and don't use ``shell=True``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5397`_
* Fix for subworkflow creation
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5398`_
* Follow IUC and drop ``r`` channel from the default Conda channels
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5406`_
* Implement workaround for extra metadata revision creation.
`Pull Request 5433`_
* Don't silently fail rest of multi-action queue when attempting to purge a
collection.
`Pull Request 5443`_
* Ensure ``jobStateSummariesCollection`` exists.
`Pull Request 5444`_
* Fix ``server_name`` when config is a ``dict``.
`Pull Request 5447`_
* Fixes for workflow sharing links.
`Pull Request 5467`_
* Fix workflow execution post action - rename
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 5485`_
* Fix ``common_startup.sh`` for galaxy tarballs
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5491`_
* Close ``tempfile`` handles.
`Pull Request 5506`_, `Pull Request 5552`_
* Do not allow ``codefiles`` during tool shed tool loading.
`Pull Request 5510`_
* Fix for GenomeSpace importer/exporter
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 5528`_
* Fix search overlay JS errors
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 5531`_
* Allow LDAP options not starting with ``OPT_``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5556`_
* Fix broken admin ``create new user`` when ``registration =='challenge'``
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 5569`_
* Do not remove external path files during library uploads
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5573`_
* Bump sqlite3 dependency for web proxy.
`Pull Request 5575`_
* Fix small bam (header-only) infinite fetching.
`Pull Request 5579`_
* Fix migration 0137's downgrade.
`Pull Request 5605`_
* Conda fix for commands using stdout redirection.
`Pull Request 5620`_
* Move `Extract genomic DNA 1` to list of versioned galaxy tools requiring
galaxy to be importable
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5626`_
* Changed GenomeSpace token handling to use manual OpenID association only.
`Pull Request 5631`_
* Use sample file path when adding missing indexes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5650`_
* Fix exception if user preference value undefined
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5662`_
* Fix exception if email is not specified or email is wrong
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5663`_
* Show error message if user tries purging datasets
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5664`_
* Show error message if history structure can't be shown
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5665`_
* Consistent sniffing regardless of in_place.
`Pull Request 5643`_
.. github_links
.. _Pull Request 4178: https://github.com/galaxyproject/galaxy/pull/4178
.. _Pull Request 4435: https://github.com/galaxyproject/galaxy/pull/4435
.. _Pull Request 4436: https://github.com/galaxyproject/galaxy/pull/4436
.. _Pull Request 4475: https://github.com/galaxyproject/galaxy/pull/4475
.. _Pull Request 4480: https://github.com/galaxyproject/galaxy/pull/4480
.. _Pull Request 4487: https://github.com/galaxyproject/galaxy/pull/4487
.. _Pull Request 4497: https://github.com/galaxyproject/galaxy/pull/4497
.. _Pull Request 4513: https://github.com/galaxyproject/galaxy/pull/4513
.. _Pull Request 4526: https://github.com/galaxyproject/galaxy/pull/4526
.. _Pull Request 4543: https://github.com/galaxyproject/galaxy/pull/4543
.. _Pull Request 4563: https://github.com/galaxyproject/galaxy/pull/4563
.. _Pull Request 4569: https://github.com/galaxyproject/galaxy/pull/4569
.. _Pull Request 4604: https://github.com/galaxyproject/galaxy/pull/4604
.. _Pull Request 4620: https://github.com/galaxyproject/galaxy/pull/4620
.. _Pull Request 4635: https://github.com/galaxyproject/galaxy/pull/4635
.. _Pull Request 4645: https://github.com/galaxyproject/galaxy/pull/4645
.. _Pull Request 4649: https://github.com/galaxyproject/galaxy/pull/4649
.. _Pull Request 4653: https://github.com/galaxyproject/galaxy/pull/4653
.. _Pull Request 4655: https://github.com/galaxyproject/galaxy/pull/4655
.. _Pull Request 4658: https://github.com/galaxyproject/galaxy/pull/4658
.. _Pull Request 4660: https://github.com/galaxyproject/galaxy/pull/4660
.. _Pull Request 4661: https://github.com/galaxyproject/galaxy/pull/4661
.. _Pull Request 4662: https://github.com/galaxyproject/galaxy/pull/4662
.. _Pull Request 4664: https://github.com/galaxyproject/galaxy/pull/4664
.. _Pull Request 4665: https://github.com/galaxyproject/galaxy/pull/4665
.. _Pull Request 4669: https://github.com/galaxyproject/galaxy/pull/4669
.. _Pull Request 4672: https://github.com/galaxyproject/galaxy/pull/4672
.. _Pull Request 4673: https://github.com/galaxyproject/galaxy/pull/4673
.. _Pull Request 4676: https://github.com/galaxyproject/galaxy/pull/4676
.. _Pull Request 4679: https://github.com/galaxyproject/galaxy/pull/4679
.. _Pull Request 4681: https://github.com/galaxyproject/galaxy/pull/4681
.. _Pull Request 4682: https://github.com/galaxyproject/galaxy/pull/4682
.. _Pull Request 4686: https://github.com/galaxyproject/galaxy/pull/4686
.. _Pull Request 4687: https://github.com/galaxyproject/galaxy/pull/4687
.. _Pull Request 4688: https://github.com/galaxyproject/galaxy/pull/4688
.. _Pull Request 4689: https://github.com/galaxyproject/galaxy/pull/4689
.. _Pull Request 4690: https://github.com/galaxyproject/galaxy/pull/4690
.. _Pull Request 4693: https://github.com/galaxyproject/galaxy/pull/4693
.. _Pull Request 4697: https://github.com/galaxyproject/galaxy/pull/4697
.. _Pull Request 4699: https://github.com/galaxyproject/galaxy/pull/4699
.. _Pull Request 4700: https://github.com/galaxyproject/galaxy/pull/4700
.. _Pull Request 4704: https://github.com/galaxyproject/galaxy/pull/4704
.. _Pull Request 4711: https://github.com/galaxyproject/galaxy/pull/4711
.. _Pull Request 4720: https://github.com/galaxyproject/galaxy/pull/4720
.. _Pull Request 4722: https://github.com/galaxyproject/galaxy/pull/4722
.. _Pull Request 4723: https://github.com/galaxyproject/galaxy/pull/4723
.. _Pull Request 4725: https://github.com/galaxyproject/galaxy/pull/4725
.. _Pull Request 4729: https://github.com/galaxyproject/galaxy/pull/4729
.. _Pull Request 4730: https://github.com/galaxyproject/galaxy/pull/4730
.. _Pull Request 4732: https://github.com/galaxyproject/galaxy/pull/4732
.. _Pull Request 4737: https://github.com/galaxyproject/galaxy/pull/4737
.. _Pull Request 4739: https://github.com/galaxyproject/galaxy/pull/4739
.. _Pull Request 4744: https://github.com/galaxyproject/galaxy/pull/4744
.. _Pull Request 4746: https://github.com/galaxyproject/galaxy/pull/4746
.. _Pull Request 4751: https://github.com/galaxyproject/galaxy/pull/4751
.. _Pull Request 4753: https://github.com/galaxyproject/galaxy/pull/4753
.. _Pull Request 4755: https://github.com/galaxyproject/galaxy/pull/4755
.. _Pull Request 4757: https://github.com/galaxyproject/galaxy/pull/4757
.. _Pull Request 4758: https://github.com/galaxyproject/galaxy/pull/4758
.. _Pull Request 4759: https://github.com/galaxyproject/galaxy/pull/4759
.. _Pull Request 4762: https://github.com/galaxyproject/galaxy/pull/4762
.. _Pull Request 4764: https://github.com/galaxyproject/galaxy/pull/4764
.. _Pull Request 4765: https://github.com/galaxyproject/galaxy/pull/4765
.. _Pull Request 4766: https://github.com/galaxyproject/galaxy/pull/4766
.. _Pull Request 4770: https://github.com/galaxyproject/galaxy/pull/4770
.. _Pull Request 4771: https://github.com/galaxyproject/galaxy/pull/4771
.. _Pull Request 4778: https://github.com/galaxyproject/galaxy/pull/4778
.. _Pull Request 4779: https://github.com/galaxyproject/galaxy/pull/4779
.. _Pull Request 4781: https://github.com/galaxyproject/galaxy/pull/4781
.. _Pull Request 4787: https://github.com/galaxyproject/galaxy/pull/4787
.. _Pull Request 4788: https://github.com/galaxyproject/galaxy/pull/4788
.. _Pull Request 4789: https://github.com/galaxyproject/galaxy/pull/4789
.. _Pull Request 4790: https://github.com/galaxyproject/galaxy/pull/4790
.. _Pull Request 4791: https://github.com/galaxyproject/galaxy/pull/4791
.. _Pull Request 4792: https://github.com/galaxyproject/galaxy/pull/4792
.. _Pull Request 4796: https://github.com/galaxyproject/galaxy/pull/4796
.. _Pull Request 4799: https://github.com/galaxyproject/galaxy/pull/4799
.. _Pull Request 4806: https://github.com/galaxyproject/galaxy/pull/4806
.. _Pull Request 4811: https://github.com/galaxyproject/galaxy/pull/4811
.. _Pull Request 4814: https://github.com/galaxyproject/galaxy/pull/4814
.. _Pull Request 4822: https://github.com/galaxyproject/galaxy/pull/4822
.. _Pull Request 4823: https://github.com/galaxyproject/galaxy/pull/4823
.. _Pull Request 4826: https://github.com/galaxyproject/galaxy/pull/4826
.. _Pull Request 4827: https://github.com/galaxyproject/galaxy/pull/4827
.. _Pull Request 4829: https://github.com/galaxyproject/galaxy/pull/4829
.. _Pull Request 4833: https://github.com/galaxyproject/galaxy/pull/4833
.. _Pull Request 4838: https://github.com/galaxyproject/galaxy/pull/4838
.. _Pull Request 4839: https://github.com/galaxyproject/galaxy/pull/4839
.. _Pull Request 4841: https://github.com/galaxyproject/galaxy/pull/4841
.. _Pull Request 4847: https://github.com/galaxyproject/galaxy/pull/4847
.. _Pull Request 4849: https://github.com/galaxyproject/galaxy/pull/4849
.. _Pull Request 4850: https://github.com/galaxyproject/galaxy/pull/4850
.. _Pull Request 4852: https://github.com/galaxyproject/galaxy/pull/4852
.. _Pull Request 4855: https://github.com/galaxyproject/galaxy/pull/4855
.. _Pull Request 4858: https://github.com/galaxyproject/galaxy/pull/4858
.. _Pull Request 4863: https://github.com/galaxyproject/galaxy/pull/4863
.. _Pull Request 4866: https://github.com/galaxyproject/galaxy/pull/4866
.. _Pull Request 4867: https://github.com/galaxyproject/galaxy/pull/4867
.. _Pull Request 4869: https://github.com/galaxyproject/galaxy/pull/4869
.. _Pull Request 4871: https://github.com/galaxyproject/galaxy/pull/4871
.. _Pull Request 4872: https://github.com/galaxyproject/galaxy/pull/4872
.. _Pull Request 4876: https://github.com/galaxyproject/galaxy/pull/4876
.. _Pull Request 4877: https://github.com/galaxyproject/galaxy/pull/4877
.. _Pull Request 4879: https://github.com/galaxyproject/galaxy/pull/4879
.. _Pull Request 4884: https://github.com/galaxyproject/galaxy/pull/4884
.. _Pull Request 4885: https://github.com/galaxyproject/galaxy/pull/4885
.. _Pull Request 4886: https://github.com/galaxyproject/galaxy/pull/4886
.. _Pull Request 4887: https://github.com/galaxyproject/galaxy/pull/4887
.. _Pull Request 4891: https://github.com/galaxyproject/galaxy/pull/4891
.. _Pull Request 4894: https://github.com/galaxyproject/galaxy/pull/4894
.. _Pull Request 4895: https://github.com/galaxyproject/galaxy/pull/4895
.. _Pull Request 4900: https://github.com/galaxyproject/galaxy/pull/4900
.. _Pull Request 4901: https://github.com/galaxyproject/galaxy/pull/4901
.. _Pull Request 4903: https://github.com/galaxyproject/galaxy/pull/4903
.. _Pull Request 4908: https://github.com/galaxyproject/galaxy/pull/4908
.. _Pull Request 4909: https://github.com/galaxyproject/galaxy/pull/4909
.. _Pull Request 4910: https://github.com/galaxyproject/galaxy/pull/4910
.. _Pull Request 4912: https://github.com/galaxyproject/galaxy/pull/4912
.. _Pull Request 4913: https://github.com/galaxyproject/galaxy/pull/4913
.. _Pull Request 4914: https://github.com/galaxyproject/galaxy/pull/4914
.. _Pull Request 4916: https://github.com/galaxyproject/galaxy/pull/4916
.. _Pull Request 4917: https://github.com/galaxyproject/galaxy/pull/4917
.. _Pull Request 4922: https://github.com/galaxyproject/galaxy/pull/4922
.. _Pull Request 4925: https://github.com/galaxyproject/galaxy/pull/4925
.. _Pull Request 4933: https://github.com/galaxyproject/galaxy/pull/4933
.. _Pull Request 4934: https://github.com/galaxyproject/galaxy/pull/4934
.. _Pull Request 4935: https://github.com/galaxyproject/galaxy/pull/4935
.. _Pull Request 4939: https://github.com/galaxyproject/galaxy/pull/4939
.. _Pull Request 4942: https://github.com/galaxyproject/galaxy/pull/4942
.. _Pull Request 4944: https://github.com/galaxyproject/galaxy/pull/4944
.. _Pull Request 4945: https://github.com/galaxyproject/galaxy/pull/4945
.. _Pull Request 4948: https://github.com/galaxyproject/galaxy/pull/4948
.. _Pull Request 4951: https://github.com/galaxyproject/galaxy/pull/4951
.. _Pull Request 4952: https://github.com/galaxyproject/galaxy/pull/4952
.. _Pull Request 4957: https://github.com/galaxyproject/galaxy/pull/4957
.. _Pull Request 4958: https://github.com/galaxyproject/galaxy/pull/4958
.. _Pull Request 4961: https://github.com/galaxyproject/galaxy/pull/4961
.. _Pull Request 4962: https://github.com/galaxyproject/galaxy/pull/4962
.. _Pull Request 4964: https://github.com/galaxyproject/galaxy/pull/4964
.. _Pull Request 4965: https://github.com/galaxyproject/galaxy/pull/4965
.. _Pull Request 4967: https://github.com/galaxyproject/galaxy/pull/4967
.. _Pull Request 4968: https://github.com/galaxyproject/galaxy/pull/4968
.. _Pull Request 4971: https://github.com/galaxyproject/galaxy/pull/4971
.. _Pull Request 4972: https://github.com/galaxyproject/galaxy/pull/4972
.. _Pull Request 4977: https://github.com/galaxyproject/galaxy/pull/4977
.. _Pull Request 4978: https://github.com/galaxyproject/galaxy/pull/4978
.. _Pull Request 4979: https://github.com/galaxyproject/galaxy/pull/4979
.. _Pull Request 4981: https://github.com/galaxyproject/galaxy/pull/4981
.. _Pull Request 4982: https://github.com/galaxyproject/galaxy/pull/4982
.. _Pull Request 4984: https://github.com/galaxyproject/galaxy/pull/4984
.. _Pull Request 4985: https://github.com/galaxyproject/galaxy/pull/4985
.. _Pull Request 4986: https://github.com/galaxyproject/galaxy/pull/4986
.. _Pull Request 4987: https://github.com/galaxyproject/galaxy/pull/4987
.. _Pull Request 4988: https://github.com/galaxyproject/galaxy/pull/4988
.. _Pull Request 4989: https://github.com/galaxyproject/galaxy/pull/4989
.. _Pull Request 4990: https://github.com/galaxyproject/galaxy/pull/4990
.. _Pull Request 4991: https://github.com/galaxyproject/galaxy/pull/4991
.. _Pull Request 4992: https://github.com/galaxyproject/galaxy/pull/4992
.. _Pull Request 4993: https://github.com/galaxyproject/galaxy/pull/4993
.. _Pull Request 4994: https://github.com/galaxyproject/galaxy/pull/4994
.. _Pull Request 4996: https://github.com/galaxyproject/galaxy/pull/4996
.. _Pull Request 4997: https://github.com/galaxyproject/galaxy/pull/4997
.. _Pull Request 4998: https://github.com/galaxyproject/galaxy/pull/4998
.. _Pull Request 5000: https://github.com/galaxyproject/galaxy/pull/5000
.. _Pull Request 5001: https://github.com/galaxyproject/galaxy/pull/5001
.. _Pull Request 5002: https://github.com/galaxyproject/galaxy/pull/5002
.. _Pull Request 5004: https://github.com/galaxyproject/galaxy/pull/5004
.. _Pull Request 5005: https://github.com/galaxyproject/galaxy/pull/5005
.. _Pull Request 5006: https://github.com/galaxyproject/galaxy/pull/5006
.. _Pull Request 5007: https://github.com/galaxyproject/galaxy/pull/5007
.. _Pull Request 5008: https://github.com/galaxyproject/galaxy/pull/5008
.. _Pull Request 5010: https://github.com/galaxyproject/galaxy/pull/5010
.. _Pull Request 5011: https://github.com/galaxyproject/galaxy/pull/5011
.. _Pull Request 5013: https://github.com/galaxyproject/galaxy/pull/5013
.. _Pull Request 5014: https://github.com/galaxyproject/galaxy/pull/5014
.. _Pull Request 5015: https://github.com/galaxyproject/galaxy/pull/5015
.. _Pull Request 5016: https://github.com/galaxyproject/galaxy/pull/5016
.. _Pull Request 5017: https://github.com/galaxyproject/galaxy/pull/5017
.. _Pull Request 5018: https://github.com/galaxyproject/galaxy/pull/5018
.. _Pull Request 5020: https://github.com/galaxyproject/galaxy/pull/5020
.. _Pull Request 5021: https://github.com/galaxyproject/galaxy/pull/5021
.. _Pull Request 5022: https://github.com/galaxyproject/galaxy/pull/5022
.. _Pull Request 5023: https://github.com/galaxyproject/galaxy/pull/5023
.. _Pull Request 5027: https://github.com/galaxyproject/galaxy/pull/5027
.. _Pull Request 5036: https://github.com/galaxyproject/galaxy/pull/5036
.. _Pull Request 5037: https://github.com/galaxyproject/galaxy/pull/5037
.. _Pull Request 5038: https://github.com/galaxyproject/galaxy/pull/5038
.. _Pull Request 5042: https://github.com/galaxyproject/galaxy/pull/5042
.. _Pull Request 5043: https://github.com/galaxyproject/galaxy/pull/5043
.. _Pull Request 5045: https://github.com/galaxyproject/galaxy/pull/5045
.. _Pull Request 5049: https://github.com/galaxyproject/galaxy/pull/5049
.. _Pull Request 5050: https://github.com/galaxyproject/galaxy/pull/5050
.. _Pull Request 5051: https://github.com/galaxyproject/galaxy/pull/5051
.. _Pull Request 5054: https://github.com/galaxyproject/galaxy/pull/5054
.. _Pull Request 5056: https://github.com/galaxyproject/galaxy/pull/5056
.. _Pull Request 5058: https://github.com/galaxyproject/galaxy/pull/5058
.. _Pull Request 5062: https://github.com/galaxyproject/galaxy/pull/5062
.. _Pull Request 5063: https://github.com/galaxyproject/galaxy/pull/5063
.. _Pull Request 5065: https://github.com/galaxyproject/galaxy/pull/5065
.. _Pull Request 5066: https://github.com/galaxyproject/galaxy/pull/5066
.. _Pull Request 5068: https://github.com/galaxyproject/galaxy/pull/5068
.. _Pull Request 5070: https://github.com/galaxyproject/galaxy/pull/5070
.. _Pull Request 5071: https://github.com/galaxyproject/galaxy/pull/5071
.. _Pull Request 5072: https://github.com/galaxyproject/galaxy/pull/5072
.. _Pull Request 5073: https://github.com/galaxyproject/galaxy/pull/5073
.. _Pull Request 5074: https://github.com/galaxyproject/galaxy/pull/5074
.. _Pull Request 5077: https://github.com/galaxyproject/galaxy/pull/5077
.. _Pull Request 5078: https://github.com/galaxyproject/galaxy/pull/5078
.. _Pull Request 5079: https://github.com/galaxyproject/galaxy/pull/5079
.. _Pull Request 5080: https://github.com/galaxyproject/galaxy/pull/5080
.. _Pull Request 5081: https://github.com/galaxyproject/galaxy/pull/5081
.. _Pull Request 5086: https://github.com/galaxyproject/galaxy/pull/5086
.. _Pull Request 5087: https://github.com/galaxyproject/galaxy/pull/5087
.. _Pull Request 5088: https://github.com/galaxyproject/galaxy/pull/5088
.. _Pull Request 5089: https://github.com/galaxyproject/galaxy/pull/5089
.. _Pull Request 5091: https://github.com/galaxyproject/galaxy/pull/5091
.. _Pull Request 5092: https://github.com/galaxyproject/galaxy/pull/5092
.. _Pull Request 5093: https://github.com/galaxyproject/galaxy/pull/5093
.. _Pull Request 5094: https://github.com/galaxyproject/galaxy/pull/5094
.. _Pull Request 5095: https://github.com/galaxyproject/galaxy/pull/5095
.. _Pull Request 5098: https://github.com/galaxyproject/galaxy/pull/5098
.. _Pull Request 5099: https://github.com/galaxyproject/galaxy/pull/5099
.. _Pull Request 5103: https://github.com/galaxyproject/galaxy/pull/5103
.. _Pull Request 5104: https://github.com/galaxyproject/galaxy/pull/5104
.. _Pull Request 5105: https://github.com/galaxyproject/galaxy/pull/5105
.. _Pull Request 5106: https://github.com/galaxyproject/galaxy/pull/5106
.. _Pull Request 5108: https://github.com/galaxyproject/galaxy/pull/5108
.. _Pull Request 5109: https://github.com/galaxyproject/galaxy/pull/5109
.. _Pull Request 5110: https://github.com/galaxyproject/galaxy/pull/5110
.. _Pull Request 5114: https://github.com/galaxyproject/galaxy/pull/5114
.. _Pull Request 5115: https://github.com/galaxyproject/galaxy/pull/5115
.. _Pull Request 5116: https://github.com/galaxyproject/galaxy/pull/5116
.. _Pull Request 5119: https://github.com/galaxyproject/galaxy/pull/5119
.. _Pull Request 5121: https://github.com/galaxyproject/galaxy/pull/5121
.. _Pull Request 5122: https://github.com/galaxyproject/galaxy/pull/5122
.. _Pull Request 5124: https://github.com/galaxyproject/galaxy/pull/5124
.. _Pull Request 5125: https://github.com/galaxyproject/galaxy/pull/5125
.. _Pull Request 5128: https://github.com/galaxyproject/galaxy/pull/5128
.. _Pull Request 5135: https://github.com/galaxyproject/galaxy/pull/5135
.. _Pull Request 5137: https://github.com/galaxyproject/galaxy/pull/5137
.. _Pull Request 5138: https://github.com/galaxyproject/galaxy/pull/5138
.. _Pull Request 5139: https://github.com/galaxyproject/galaxy/pull/5139
.. _Pull Request 5140: https://github.com/galaxyproject/galaxy/pull/5140
.. _Pull Request 5143: https://github.com/galaxyproject/galaxy/pull/5143
.. _Pull Request 5144: https://github.com/galaxyproject/galaxy/pull/5144
.. _Pull Request 5145: https://github.com/galaxyproject/galaxy/pull/5145
.. _Pull Request 5147: https://github.com/galaxyproject/galaxy/pull/5147
.. _Pull Request 5154: https://github.com/galaxyproject/galaxy/pull/5154
.. _Pull Request 5155: https://github.com/galaxyproject/galaxy/pull/5155
.. _Pull Request 5156: https://github.com/galaxyproject/galaxy/pull/5156
.. _Pull Request 5157: https://github.com/galaxyproject/galaxy/pull/5157
.. _Pull Request 5161: https://github.com/galaxyproject/galaxy/pull/5161
.. _Pull Request 5166: https://github.com/galaxyproject/galaxy/pull/5166
.. _Pull Request 5170: https://github.com/galaxyproject/galaxy/pull/5170
.. _Pull Request 5172: https://github.com/galaxyproject/galaxy/pull/5172
.. _Pull Request 5173: https://github.com/galaxyproject/galaxy/pull/5173
.. _Pull Request 5177: https://github.com/galaxyproject/galaxy/pull/5177
.. _Pull Request 5180: https://github.com/galaxyproject/galaxy/pull/5180
.. _Pull Request 5182: https://github.com/galaxyproject/galaxy/pull/5182
.. _Pull Request 5185: https://github.com/galaxyproject/galaxy/pull/5185
.. _Pull Request 5190: https://github.com/galaxyproject/galaxy/pull/5190
.. _Pull Request 5191: https://github.com/galaxyproject/galaxy/pull/5191
.. _Pull Request 5193: https://github.com/galaxyproject/galaxy/pull/5193
.. _Pull Request 5196: https://github.com/galaxyproject/galaxy/pull/5196
.. _Pull Request 5197: https://github.com/galaxyproject/galaxy/pull/5197
.. _Pull Request 5198: https://github.com/galaxyproject/galaxy/pull/5198
.. _Pull Request 5199: https://github.com/galaxyproject/galaxy/pull/5199
.. _Pull Request 5200: https://github.com/galaxyproject/galaxy/pull/5200
.. _Pull Request 5202: https://github.com/galaxyproject/galaxy/pull/5202
.. _Pull Request 5204: https://github.com/galaxyproject/galaxy/pull/5204
.. _Pull Request 5206: https://github.com/galaxyproject/galaxy/pull/5206
.. _Pull Request 5208: https://github.com/galaxyproject/galaxy/pull/5208
.. _Pull Request 5209: https://github.com/galaxyproject/galaxy/pull/5209
.. _Pull Request 5210: https://github.com/galaxyproject/galaxy/pull/5210
.. _Pull Request 5211: https://github.com/galaxyproject/galaxy/pull/5211
.. _Pull Request 5212: https://github.com/galaxyproject/galaxy/pull/5212
.. _Pull Request 5215: https://github.com/galaxyproject/galaxy/pull/5215
.. _Pull Request 5217: https://github.com/galaxyproject/galaxy/pull/5217
.. _Pull Request 5221: https://github.com/galaxyproject/galaxy/pull/5221
.. _Pull Request 5223: https://github.com/galaxyproject/galaxy/pull/5223
.. _Pull Request 5225: https://github.com/galaxyproject/galaxy/pull/5225
.. _Pull Request 5226: https://github.com/galaxyproject/galaxy/pull/5226
.. _Pull Request 5228: https://github.com/galaxyproject/galaxy/pull/5228
.. _Pull Request 5229: https://github.com/galaxyproject/galaxy/pull/5229
.. _Pull Request 5230: https://github.com/galaxyproject/galaxy/pull/5230
.. _Pull Request 5232: https://github.com/galaxyproject/galaxy/pull/5232
.. _Pull Request 5233: https://github.com/galaxyproject/galaxy/pull/5233
.. _Pull Request 5234: https://github.com/galaxyproject/galaxy/pull/5234
.. _Pull Request 5235: https://github.com/galaxyproject/galaxy/pull/5235
.. _Pull Request 5237: https://github.com/galaxyproject/galaxy/pull/5237
.. _Pull Request 5238: https://github.com/galaxyproject/galaxy/pull/5238
.. _Pull Request 5240: https://github.com/galaxyproject/galaxy/pull/5240
.. _Pull Request 5247: https://github.com/galaxyproject/galaxy/pull/5247
.. _Pull Request 5249: https://github.com/galaxyproject/galaxy/pull/5249
.. _Pull Request 5251: https://github.com/galaxyproject/galaxy/pull/5251
.. _Pull Request 5253: https://github.com/galaxyproject/galaxy/pull/5253
.. _Pull Request 5254: https://github.com/galaxyproject/galaxy/pull/5254
.. _Pull Request 5258: https://github.com/galaxyproject/galaxy/pull/5258
.. _Pull Request 5259: https://github.com/galaxyproject/galaxy/pull/5259
.. _Pull Request 5260: https://github.com/galaxyproject/galaxy/pull/5260
.. _Pull Request 5261: https://github.com/galaxyproject/galaxy/pull/5261
.. _Pull Request 5262: https://github.com/galaxyproject/galaxy/pull/5262
.. _Pull Request 5264: https://github.com/galaxyproject/galaxy/pull/5264
.. _Pull Request 5266: https://github.com/galaxyproject/galaxy/pull/5266
.. _Pull Request 5270: https://github.com/galaxyproject/galaxy/pull/5270
.. _Pull Request 5272: https://github.com/galaxyproject/galaxy/pull/5272
.. _Pull Request 5273: https://github.com/galaxyproject/galaxy/pull/5273
.. _Pull Request 5276: https://github.com/galaxyproject/galaxy/pull/5276
.. _Pull Request 5278: https://github.com/galaxyproject/galaxy/pull/5278
.. _Pull Request 5279: https://github.com/galaxyproject/galaxy/pull/5279
.. _Pull Request 5286: https://github.com/galaxyproject/galaxy/pull/5286
.. _Pull Request 5288: https://github.com/galaxyproject/galaxy/pull/5288
.. _Pull Request 5289: https://github.com/galaxyproject/galaxy/pull/5289
.. _Pull Request 5293: https://github.com/galaxyproject/galaxy/pull/5293
.. _Pull Request 5294: https://github.com/galaxyproject/galaxy/pull/5294
.. _Pull Request 5295: https://github.com/galaxyproject/galaxy/pull/5295
.. _Pull Request 5297: https://github.com/galaxyproject/galaxy/pull/5297
.. _Pull Request 5299: https://github.com/galaxyproject/galaxy/pull/5299
.. _Pull Request 5300: https://github.com/galaxyproject/galaxy/pull/5300
.. _Pull Request 5301: https://github.com/galaxyproject/galaxy/pull/5301
.. _Pull Request 5303: https://github.com/galaxyproject/galaxy/pull/5303
.. _Pull Request 5304: https://github.com/galaxyproject/galaxy/pull/5304
.. _Pull Request 5306: https://github.com/galaxyproject/galaxy/pull/5306
.. _Pull Request 5311: https://github.com/galaxyproject/galaxy/pull/5311
.. _Pull Request 5312: https://github.com/galaxyproject/galaxy/pull/5312
.. _Pull Request 5321: https://github.com/galaxyproject/galaxy/pull/5321
.. _Pull Request 5327: https://github.com/galaxyproject/galaxy/pull/5327
.. _Pull Request 5331: https://github.com/galaxyproject/galaxy/pull/5331
.. _Pull Request 5333: https://github.com/galaxyproject/galaxy/pull/5333
.. _Pull Request 5335: https://github.com/galaxyproject/galaxy/pull/5335
.. _Pull Request 5337: https://github.com/galaxyproject/galaxy/pull/5337
.. _Pull Request 5340: https://github.com/galaxyproject/galaxy/pull/5340
.. _Pull Request 5342: https://github.com/galaxyproject/galaxy/pull/5342
.. _Pull Request 5343: https://github.com/galaxyproject/galaxy/pull/5343
.. _Pull Request 5344: https://github.com/galaxyproject/galaxy/pull/5344
.. _Pull Request 5346: https://github.com/galaxyproject/galaxy/pull/5346
.. _Pull Request 5351: https://github.com/galaxyproject/galaxy/pull/5351
.. _Pull Request 5353: https://github.com/galaxyproject/galaxy/pull/5353
.. _Pull Request 5357: https://github.com/galaxyproject/galaxy/pull/5357
.. _Pull Request 5358: https://github.com/galaxyproject/galaxy/pull/5358
.. _Pull Request 5363: https://github.com/galaxyproject/galaxy/pull/5363
.. _Pull Request 5364: https://github.com/galaxyproject/galaxy/pull/5364
.. _Pull Request 5367: https://github.com/galaxyproject/galaxy/pull/5367
.. _Pull Request 5368: https://github.com/galaxyproject/galaxy/pull/5368
.. _Pull Request 5371: https://github.com/galaxyproject/galaxy/pull/5371
.. _Pull Request 5373: https://github.com/galaxyproject/galaxy/pull/5373
.. _Pull Request 5376: https://github.com/galaxyproject/galaxy/pull/5376
.. _Pull Request 5377: https://github.com/galaxyproject/galaxy/pull/5377
.. _Pull Request 5382: https://github.com/galaxyproject/galaxy/pull/5382
.. _Pull Request 5383: https://github.com/galaxyproject/galaxy/pull/5383
.. _Pull Request 5387: https://github.com/galaxyproject/galaxy/pull/5387
.. _Pull Request 5390: https://github.com/galaxyproject/galaxy/pull/5390
.. _Pull Request 5395: https://github.com/galaxyproject/galaxy/pull/5395
.. _Pull Request 5397: https://github.com/galaxyproject/galaxy/pull/5397
.. _Pull Request 5398: https://github.com/galaxyproject/galaxy/pull/5398
.. _Pull Request 5403: https://github.com/galaxyproject/galaxy/pull/5403
.. _Pull Request 5406: https://github.com/galaxyproject/galaxy/pull/5406
.. _Pull Request 5413: https://github.com/galaxyproject/galaxy/pull/5413
.. _Pull Request 5414: https://github.com/galaxyproject/galaxy/pull/5414
.. _Pull Request 5416: https://github.com/galaxyproject/galaxy/pull/5416
.. _Pull Request 5418: https://github.com/galaxyproject/galaxy/pull/5418
.. _Pull Request 5426: https://github.com/galaxyproject/galaxy/pull/5426
.. _Pull Request 5433: https://github.com/galaxyproject/galaxy/pull/5433
.. _Pull Request 5440: https://github.com/galaxyproject/galaxy/pull/5440
.. _Pull Request 5441: https://github.com/galaxyproject/galaxy/pull/5441
.. _Pull Request 5442: https://github.com/galaxyproject/galaxy/pull/5442
.. _Pull Request 5443: https://github.com/galaxyproject/galaxy/pull/5443
.. _Pull Request 5444: https://github.com/galaxyproject/galaxy/pull/5444
.. _Pull Request 5445: https://github.com/galaxyproject/galaxy/pull/5445
.. _Pull Request 5447: https://github.com/galaxyproject/galaxy/pull/5447
.. _Pull Request 5449: https://github.com/galaxyproject/galaxy/pull/5449
.. _Pull Request 5455: https://github.com/galaxyproject/galaxy/pull/5455
.. _Pull Request 5456: https://github.com/galaxyproject/galaxy/pull/5456
.. _Pull Request 5460: https://github.com/galaxyproject/galaxy/pull/5460
.. _Pull Request 5467: https://github.com/galaxyproject/galaxy/pull/5467
.. _Pull Request 5470: https://github.com/galaxyproject/galaxy/pull/5470
.. _Pull Request 5482: https://github.com/galaxyproject/galaxy/pull/5482
.. _Pull Request 5485: https://github.com/galaxyproject/galaxy/pull/5485
.. _Pull Request 5491: https://github.com/galaxyproject/galaxy/pull/5491
.. _Pull Request 5506: https://github.com/galaxyproject/galaxy/pull/5506
.. _Pull Request 5510: https://github.com/galaxyproject/galaxy/pull/5510
.. _Pull Request 5512: https://github.com/galaxyproject/galaxy/pull/5512
.. _Pull Request 5514: https://github.com/galaxyproject/galaxy/pull/5514
.. _Pull Request 5515: https://github.com/galaxyproject/galaxy/pull/5515
.. _Pull Request 5521: https://github.com/galaxyproject/galaxy/pull/5521
.. _Pull Request 5526: https://github.com/galaxyproject/galaxy/pull/5526
.. _Pull Request 5528: https://github.com/galaxyproject/galaxy/pull/5528
.. _Pull Request 5531: https://github.com/galaxyproject/galaxy/pull/5531
.. _Pull Request 5532: https://github.com/galaxyproject/galaxy/pull/5532
.. _Pull Request 5533: https://github.com/galaxyproject/galaxy/pull/5533
.. _Pull Request 5535: https://github.com/galaxyproject/galaxy/pull/5535
.. _Pull Request 5542: https://github.com/galaxyproject/galaxy/pull/5542
.. _Pull Request 5552: https://github.com/galaxyproject/galaxy/pull/5552
.. _Pull Request 5556: https://github.com/galaxyproject/galaxy/pull/5556
.. _Pull Request 5558: https://github.com/galaxyproject/galaxy/pull/5558
.. _Pull Request 5561: https://github.com/galaxyproject/galaxy/pull/5561
.. _Pull Request 5566: https://github.com/galaxyproject/galaxy/pull/5566
.. _Pull Request 5569: https://github.com/galaxyproject/galaxy/pull/5569
.. _Pull Request 5573: https://github.com/galaxyproject/galaxy/pull/5573
.. _Pull Request 5574: https://github.com/galaxyproject/galaxy/pull/5574
.. _Pull Request 5575: https://github.com/galaxyproject/galaxy/pull/5575
.. _Pull Request 5576: https://github.com/galaxyproject/galaxy/pull/5576
.. _Pull Request 5578: https://github.com/galaxyproject/galaxy/pull/5578
.. _Pull Request 5579: https://github.com/galaxyproject/galaxy/pull/5579
.. _Pull Request 5582: https://github.com/galaxyproject/galaxy/pull/5582
.. _Pull Request 5583: https://github.com/galaxyproject/galaxy/pull/5583
.. _Pull Request 5588: https://github.com/galaxyproject/galaxy/pull/5588
.. _Pull Request 5589: https://github.com/galaxyproject/galaxy/pull/5589
.. _Pull Request 5600: https://github.com/galaxyproject/galaxy/pull/5600
.. _Pull Request 5605: https://github.com/galaxyproject/galaxy/pull/5605
.. _Pull Request 5615: https://github.com/galaxyproject/galaxy/pull/5615
.. _Pull Request 5616: https://github.com/galaxyproject/galaxy/pull/5616
.. _Pull Request 5620: https://github.com/galaxyproject/galaxy/pull/5620
.. _Pull Request 5626: https://github.com/galaxyproject/galaxy/pull/5626
.. _Pull Request 5631: https://github.com/galaxyproject/galaxy/pull/5631
.. _Pull Request 5634: https://github.com/galaxyproject/galaxy/pull/5634
.. _Pull Request 5635: https://github.com/galaxyproject/galaxy/pull/5635
.. _Pull Request 5643: https://github.com/galaxyproject/galaxy/pull/5643
.. _Pull Request 5644: https://github.com/galaxyproject/galaxy/pull/5644
.. _Pull Request 5650: https://github.com/galaxyproject/galaxy/pull/5650
.. _Pull Request 5662: https://github.com/galaxyproject/galaxy/pull/5662
.. _Pull Request 5663: https://github.com/galaxyproject/galaxy/pull/5663
.. _Pull Request 5664: https://github.com/galaxyproject/galaxy/pull/5664
.. _Pull Request 5665: https://github.com/galaxyproject/galaxy/pull/5665
.. _Pull Request 5674: https://github.com/galaxyproject/galaxy/pull/5674
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