.. to_doc

18.05
===============================

.. announce_start

Enhancements
-------------------------------

* Allow user authentication using OpenID Connect protocol
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 4474`_, `Pull Request 5908`_, `Pull Request 5906`_
* Add basic `cgroup <https://en.wikipedia.org/wiki/Cgroups>`__ metric collection
  easing the collection of job memory data
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 5610`_
* Enhance Galaxy's API and test framework to allow running tool tests on running
  Galaxy instances. Check out the new Ephemeris functionality it is powering
  `here <https://github.com/galaxyproject/ephemeris/pull/81>`__.
  `Pull Request 5628`_, `Pull Request 5667`_
* Global and profile-bound language configuration
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 5282`_
* Tool that adds/sets tags for collection elements from a file
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 5462`_
* Implement an extension point during workflow running to describe site
  specific job scheduling parameters
  (thanks to `@JeffreyThiessen <https://github.com/JeffreyThiessen>`__).
  `Pull Request 4830`_
* Update Dynamic Tool Destinations with configurable priorities and better
  validation
  (thanks to `@tizzir <https://github.com/tizzir>`__).
  `Pull Request 5645`_
* More great `Kubernetes <https://kubernetes.io/>`__ job runner enhancements to improve robustness and configurability
  (thanks to `@pcm32 <https://github.com/pcm32>`__ and the `PhenoMeNal project <https://phenomenal-h2020.eu/home/>`__).
  `Pull Request 5760`_, `Pull Request 5761`_
* Documentation version selector on
  `docs.galaxyproject.org <https://docs.galaxyproject.org/en/master/>`__.
  `Pull Request 5334`_
* Update sort tool to allow ignoring headers
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 4235`_
* Add ``GALAXY_MEMORY_MB_PER_SLOT`` environment variable to job environment
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 5625`_
* Allow sending slow request timing to `Sentry <https://sentry.io/>`__.
  `Pull Request 5479`_
* Allow formatting `StatsD <https://github.com/etsy/statsd>`__ data for
  `InfluxDB <https://github.com/influxdata/influxdb>`__
  (thanks to `@erasche <https://github.com/erasche>`__).
  `Pull Request 5742`_
* Tool versions should follow `PEP 440 <https://www.python.org/dev/peps/pep-0440/>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5746`_
* Expand `pipenv <https://docs.pipenv.org/>`__ dependency management to include all
  Python dependencies
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5786`_
* Sniffing framework with constrained memory and I/O.
  `Pull Request 5793`_
* Infrastructure for dynamic compressed datatypes.
  `Pull Request 5794`_
* Capture more HDA state transitions in the history panel.
  `Pull Request 5749`_
* Add script for propagating hashtags in a Galaxy history
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 5669`_
* Add proteomics proBAM and proBED datatypes
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 5360`_
* Add fasta.gz datatype.
  `Pull Request 5553`_
* Add genbank.gz datatype
  (thanks to `@Delphine-L <https://github.com/Delphine-L>`__).
  `Pull Request 5772`_
* Add RDS object and SingleCellExperiment datatypes
  (thanks to `@mtekman <https://github.com/mtekman>`__).
  `Pull Request 5716`_
* Allow registration with empty email
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 5320`_
* Avoid silent tool upgrades during workflow imports.
  `Pull Request 5821`_
* Many awesome Python 3 related fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__ and
  `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 5359`_, `Pull Request 5422`_, `Pull Request 5453`_,
  `Pull Request 5461`_, `Pull Request 5492`_, `Pull Request 5494`_,
  `Pull Request 5458`_, `Pull Request 5636`_,`Pull Request 5642`_,
  `Pull Request 5427`_, `Pull Request 5451`_
* Install `Node.js`_ and `Yarn <https://yarnpkg.com/en/>`__ on startup if running a non-release branch.
  `Pull Request 5375`_
* Add ``--skip_flakey_fails`` flag to CI script for API tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5388`_
* Remove unused mapping code.
  `Pull Request 5450`_
* Show parameter name in ``DataToolParameter`` exception
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 5465`_
* Unify config-rebuild ``Makefile`` targets
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5488`_
* Rev `SQLAlchemy <https://www.sqlalchemy.org/>`__ from 1.0.15 to 1.2.2.
  `Pull Request 5538`_
* Add middleware and instrumentation to allow per-request SQL debugging.
  `Pull Request 5539`_
* Overhaul UCSC tools with more specific, working Conda compatible requirements
  (with help from `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5544`_, `Pull Request 5973`_
* More and more robust Selenium tests.
  `Pull Request 5559`_, `Pull Request 5882`_, `Pull Request 5886`_,
  `Pull Request 5876`_, `Pull Request 5836`_, `Pull Request 5701`_,
  `Pull Request 5771`_, `Pull Request 5754`_, `Pull Request 5714`_, `Pull Request 5705`_,
  `Pull Request 5708`_, `Pull Request 5710`_, `Pull Request 5706`_, `Pull Request 5707`_
* Implement basic cache on toolbox ``to_dict`` objects.
  `Pull Request 5570`_
* Log errors from external chown script.
  (thanks to `@Petraea <https://github.com/Petraea>`__).
  `Pull Request 5581`_
* Updates against `galaxy-lib <https://github.com/galaxyproject/galaxy-lib>`__ changes.
  `Pull Request 5602`_, `Pull Request 5621`_, `Pull Request 5936`_, `Pull Request 5653`_
* Performance optimization to avoid producing deep-copies of tool input dictionaries.
  `Pull Request 5646`_
* Disable tool input datatype validation for dropped history items.
  `Pull Request 5657`_
* Add a script for dumping library file paths for backup.
  `Pull Request 5436`_
* Rebuild client only if there are changes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5679`_
* Populate column selector for datasets which are not ready yet.
  `Pull Request 5680`_
* Fix role handling library manager.
  `Pull Request 5681`_
* GFF updates to handle ``##FASTA`` directive.
  `Pull Request 5686`_
* Memory and performance fixes for upload tool.
  `Pull Request 5689`_
* Fixes for testing ``Dockerfile`` recipe.
  `Pull Request 5693`_
* Various improvements for API tests.
  `Pull Request 5697`_, `Pull Request 5699`_
* Small log level improvement
  (thanks to `@erasche <https://github.com/erasche>`__).
  `Pull Request 5715`_
* Swap password checking for the constant time comparison algorithm
  (thanks to `@erasche <https://github.com/erasche>`__).
  `Pull Request 5719`_
* Upgrade clone failure logging to error
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 5724`_
* Improve galaxy update commands, update some bootstrap checkpoints.
  `Pull Request 5731`_
* Remove ``extract_genomic_dna`` tool from tool sample.
  `Pull Request 5741`_
* Revise `uWSGI <https://uwsgi-docs.readthedocs.io/en/latest/>`__ defaults and display.
  `Pull Request 5743`_
* Documentation typo fixes and small refactors
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5747`_
* More backend speed ups for user's workflow index query.
  `Pull Request 5755`_
* Fix all bundled scripts for the switch to YAML configuration.
  `Pull Request 5769`_
* Rev and re-lock Galaxy dependencies
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5776`_
* Lock pysam to 0.14.1 in Pipfile.
  `Pull Request 5798`_
* Client related readme and ``Makefile`` clarifications.
  `Pull Request 5800`_
* Use `VueJS <https://vuejs.org/>`__ and API to handle workflow imports.
  `Pull Request 5804`_
* Add link that explains quota management to quota indicator.
  `Pull Request 5811`_
* Improve startup interoperability with Conda.
  `Pull Request 5854`_
* Implement the API version of the Docker containers interface.
  `Pull Request 5861`_
* Use ``extras`` to specify additional social_auth_core dependencies
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5877`_
* Update cluster docs for a Virtualenv issue in DRMAA real user jobs
  (thanks to `@moskalenko <https://github.com/moskalenko>`__).
  `Pull Request 5881`_
* Add Mocha/Chai client test framework.
  `Pull Request 5888`_
* Small fix to run more integration tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5892`_
* Use random password generation function of user class
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 5904`_
* Remove unused client route.
  `Pull Request 5907`_
* Fix to provide ``ToolDataTableManager`` class for backwards compatibility
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 5924`_
* Document Github bug reporter
  (thanks to `@erasche <https://github.com/erasche>`__).
  `Pull Request 5928`_
* Rewrite history structure display in `VueJS <https://vuejs.org/>`__
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 5317`_
* Remove ``static/scripts/*`` from the dev branch, add to .gitignore.
  `Pull Request 5434`_
* History contents client code refactoring.
  `Pull Request 5448`_
* Drop short-lived ``make client-production`` warning from build scripts.
  `Pull Request 5508`_
* Use ``with`` statement in ``lib/galaxy/datatypes/``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5623`_
* Update tool conf samples for recent changes.
  `Pull Request 5637`_
* Extend grid framework with formal support for delayed columns.
  `Pull Request 5789`_
* Fixes for plugin directory staging.
  `Pull Request 5810`_
* Remove defunct CasperJS tests.
  `Pull Request 5567`_
* Eliminate unused pre-created datasets concept in upload API.
  `Pull Request 5604`_


Fixes
-------------------------------

.. major_bug


.. bug

* Fix workflow step cloning.
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 6085`_
* Fix tool state performance for large collections.
  `Pull Request 5997`_
* Fix overly strict sanitizing in the filter tool
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 5872`_
* Allow whitelisted symlinks to be imported
  (thanks to `@bwlang <https://github.com/bwlang>`__).
  `Pull Request 5596`_
* Fix no dataset found issue
  (thanks to `@osallou <https://github.com/osallou>`__).
  `Pull Request 5829`_
* Fix active tab highlighting
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 5675`_
* Fix initial binding for slow query logging.
  `Pull Request 5401`_
* Default slow request tracking to disabled.
  `Pull Request 5513`_
* Fixed stale link
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 5548`_
* Fix active tab highlighting issue `#4846
  <https://github.com/galaxyproject/galaxy/issues/4846>`__
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 5593`_
* Small misc fixes and cleanups
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5638`_
* Fix for running `Yarn <https://yarnpkg.com/en/>`__ in Docker for tests that do not need it.
  `Pull Request 5690`_
* Various test fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5691`_
* Hack to fix bug in uploader where it sometimes posts with empty "file_type".
  `Pull Request 5692`_
* Bump `psycopg2 <http://initd.org/psycopg/docs/>`__ to 2.7.4.
  `Pull Request 5698`_, `Pull Request 5825`_
* Do not show composite datatypes for regular dataset upload
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5700`_
* Relax validation condition for dynamic parameters.
  `Pull Request 5702`_
* Fix issue where some elements of collections wouldn't render in the UI.
  `Pull Request 5703`_
* Fix default role type on auto created roles
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 5709`_
* Fix to properly order ``@flakey`` and ``@selenium_test`` Selenium test decorators
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5711`_
* Clarify that `nginx-extras <https://packages.debian.org/sid/nginx-extras>`__ needs to be install for the upload_store documentation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 5717`_
* Remove ``subclass="true"`` from Phylip datatype definition
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5718`_
* `Sentry <https://sentry.io/>`__ bug reports working for anonymous users
  (thanks to `@erasche <https://github.com/erasche>`__).
  `Pull Request 5721`_
* Add Galaxy `lib` directory to Python path for 2 scripts
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5725`_
* Fix LDAP when ``role_search_attribute`` is not defined
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5732`_
* Fix mulled Docker caching.
  `Pull Request 5735`_
* Drop old charts building from makefile/package scripts
  `Pull Request 5737`_
* Configuration fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5745`_
* Add additional validation to numeric input element.
  `Pull Request 5750`_
* Various scatterplot fixes.
  `Pull Request 5752`_
* Fix linking option for library dataset uploads
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5758`_
* Fix copying tags for collections when copying histories.
  `Pull Request 5766`_
* Fix ``/api/whoami`` API endpoint for master key.
  `Pull Request 5773`_
* Log the pid of the first `uWSGI <https://uwsgi-docs.readthedocs.io/en/latest/>`__ process
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5774`_
* Fix SQL query for "workflows shared with me" as part of workflow index.
  `Pull Request 5782`_
* Fix model operation tools that produce standalone datasets.
  `Pull Request 5784`_
* Fix missing "from Import Directory" button in data libraries
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5797`_
* Fix metadata setting for CRAM files
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 5805`_
* Use ``app.datatypes_registry`` in ``ValidationContext.from_app()``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5806`_
* Fix ``upload_common.py`` ensure hda is added to a session.
  `Pull Request 5816`_
* Exclude the JS GIE proxy's `Node.js`_ modules from linting.
  `Pull Request 5826`_
* Do not append '/' to 'js' in GIE static path, this breaks `uWSGI <https://uwsgi-docs.readthedocs.io/en/latest/>`__ static
  routing.
  `Pull Request 5859`_
* Fix conditional parameter handling.
  `Pull Request 5864`_
* Increase `Yarn's <https://yarnpkg.com/en/>`__ network timeout.
  `Pull Request 5870`_
* Move the memory statement below _galaxy_setup_environment
  (thanks to `@moskalenko <https://github.com/moskalenko>`__).
  `Pull Request 5880`_
* Remove deprecated controller endpoint and link to preferred implementation.
  `Pull Request 5887`_
* Fix update_repository when hg repo has local modifications
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5890`_
* Fix admin data library dataset permissions.
  `Pull Request 5899`_
* Fix display of the tour index names.
  `Pull Request 5900`_
* Fix Trackster links.
  `Pull Request 5916`_
* Fix uploads of link-only datasets to data library
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 5917`_
* Correct signal number in admin documentation
  (thanks to `@erasche <https://github.com/erasche>`__).
  `Pull Request 5921`_
* Fix error with data managers when trying to move_merge nonexistent
  extra_files dir
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 5922`_
* Fix bug with removing workflow outputs from a node.
  `Pull Request 5935`_
* Fix for running in containers when ``job_tmp`` is set in ``job_conf.xml``.
  `Pull Request 5937`_
* Fix for running jobs in containers.
  `Pull Request 5938`_
* Fix dropdown click and highlighting behavior.
  `Pull Request 5945`_
* Resort to ``os.path.exists()`` also for paths not ending in ``.loc``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5947`_
* Remove ini config parameter from cleanup scripts
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 5956`_
* Fix shared history list bug.
  `Pull Request 5962`_
* Pin the version of `Node.js`_ used in CI.
  `Pull Request 5972`_
* Fix 2 typos in the docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 5986`_

.. github_links
.. _`Node.js`: https://nodejs.org/en/
.. _Pull Request 4235: https://github.com/galaxyproject/galaxy/pull/4235
.. _Pull Request 4474: https://github.com/galaxyproject/galaxy/pull/4474
.. _Pull Request 4830: https://github.com/galaxyproject/galaxy/pull/4830
.. _Pull Request 5220: https://github.com/galaxyproject/galaxy/pull/5220
.. _Pull Request 5282: https://github.com/galaxyproject/galaxy/pull/5282
.. _Pull Request 5317: https://github.com/galaxyproject/galaxy/pull/5317
.. _Pull Request 5320: https://github.com/galaxyproject/galaxy/pull/5320
.. _Pull Request 5334: https://github.com/galaxyproject/galaxy/pull/5334
.. _Pull Request 5359: https://github.com/galaxyproject/galaxy/pull/5359
.. _Pull Request 5360: https://github.com/galaxyproject/galaxy/pull/5360
.. _Pull Request 5365: https://github.com/galaxyproject/galaxy/pull/5365
.. _Pull Request 5375: https://github.com/galaxyproject/galaxy/pull/5375
.. _Pull Request 5386: https://github.com/galaxyproject/galaxy/pull/5386
.. _Pull Request 5388: https://github.com/galaxyproject/galaxy/pull/5388
.. _Pull Request 5392: https://github.com/galaxyproject/galaxy/pull/5392
.. _Pull Request 5401: https://github.com/galaxyproject/galaxy/pull/5401
.. _Pull Request 5422: https://github.com/galaxyproject/galaxy/pull/5422
.. _Pull Request 5427: https://github.com/galaxyproject/galaxy/pull/5427
.. _Pull Request 5434: https://github.com/galaxyproject/galaxy/pull/5434
.. _Pull Request 5436: https://github.com/galaxyproject/galaxy/pull/5436
.. _Pull Request 5448: https://github.com/galaxyproject/galaxy/pull/5448
.. _Pull Request 5450: https://github.com/galaxyproject/galaxy/pull/5450
.. _Pull Request 5451: https://github.com/galaxyproject/galaxy/pull/5451
.. _Pull Request 5453: https://github.com/galaxyproject/galaxy/pull/5453
.. _Pull Request 5458: https://github.com/galaxyproject/galaxy/pull/5458
.. _Pull Request 5461: https://github.com/galaxyproject/galaxy/pull/5461
.. _Pull Request 5462: https://github.com/galaxyproject/galaxy/pull/5462
.. _Pull Request 5465: https://github.com/galaxyproject/galaxy/pull/5465
.. _Pull Request 5479: https://github.com/galaxyproject/galaxy/pull/5479
.. _Pull Request 5487: https://github.com/galaxyproject/galaxy/pull/5487
.. _Pull Request 5488: https://github.com/galaxyproject/galaxy/pull/5488
.. _Pull Request 5492: https://github.com/galaxyproject/galaxy/pull/5492
.. _Pull Request 5494: https://github.com/galaxyproject/galaxy/pull/5494
.. _Pull Request 5505: https://github.com/galaxyproject/galaxy/pull/5505
.. _Pull Request 5508: https://github.com/galaxyproject/galaxy/pull/5508
.. _Pull Request 5513: https://github.com/galaxyproject/galaxy/pull/5513
.. _Pull Request 5516: https://github.com/galaxyproject/galaxy/pull/5516
.. _Pull Request 5538: https://github.com/galaxyproject/galaxy/pull/5538
.. _Pull Request 5539: https://github.com/galaxyproject/galaxy/pull/5539
.. _Pull Request 5540: https://github.com/galaxyproject/galaxy/pull/5540
.. _Pull Request 5544: https://github.com/galaxyproject/galaxy/pull/5544
.. _Pull Request 5548: https://github.com/galaxyproject/galaxy/pull/5548
.. _Pull Request 5553: https://github.com/galaxyproject/galaxy/pull/5553
.. _Pull Request 5559: https://github.com/galaxyproject/galaxy/pull/5559
.. _Pull Request 5567: https://github.com/galaxyproject/galaxy/pull/5567
.. _Pull Request 5570: https://github.com/galaxyproject/galaxy/pull/5570
.. _Pull Request 5581: https://github.com/galaxyproject/galaxy/pull/5581
.. _Pull Request 5593: https://github.com/galaxyproject/galaxy/pull/5593
.. _Pull Request 5596: https://github.com/galaxyproject/galaxy/pull/5596
.. _Pull Request 5602: https://github.com/galaxyproject/galaxy/pull/5602
.. _Pull Request 5604: https://github.com/galaxyproject/galaxy/pull/5604
.. _Pull Request 5610: https://github.com/galaxyproject/galaxy/pull/5610
.. _Pull Request 5621: https://github.com/galaxyproject/galaxy/pull/5621
.. _Pull Request 5623: https://github.com/galaxyproject/galaxy/pull/5623
.. _Pull Request 5625: https://github.com/galaxyproject/galaxy/pull/5625
.. _Pull Request 5628: https://github.com/galaxyproject/galaxy/pull/5628
.. _Pull Request 5630: https://github.com/galaxyproject/galaxy/pull/5630
.. _Pull Request 5633: https://github.com/galaxyproject/galaxy/pull/5633
.. _Pull Request 5636: https://github.com/galaxyproject/galaxy/pull/5636
.. _Pull Request 5637: https://github.com/galaxyproject/galaxy/pull/5637
.. _Pull Request 5638: https://github.com/galaxyproject/galaxy/pull/5638
.. _Pull Request 5642: https://github.com/galaxyproject/galaxy/pull/5642
.. _Pull Request 5645: https://github.com/galaxyproject/galaxy/pull/5645
.. _Pull Request 5646: https://github.com/galaxyproject/galaxy/pull/5646
.. _Pull Request 5653: https://github.com/galaxyproject/galaxy/pull/5653
.. _Pull Request 5657: https://github.com/galaxyproject/galaxy/pull/5657
.. _Pull Request 5658: https://github.com/galaxyproject/galaxy/pull/5658
.. _Pull Request 5667: https://github.com/galaxyproject/galaxy/pull/5667
.. _Pull Request 5669: https://github.com/galaxyproject/galaxy/pull/5669
.. _Pull Request 5675: https://github.com/galaxyproject/galaxy/pull/5675
.. _Pull Request 5679: https://github.com/galaxyproject/galaxy/pull/5679
.. _Pull Request 5680: https://github.com/galaxyproject/galaxy/pull/5680
.. _Pull Request 5681: https://github.com/galaxyproject/galaxy/pull/5681
.. _Pull Request 5683: https://github.com/galaxyproject/galaxy/pull/5683
.. _Pull Request 5686: https://github.com/galaxyproject/galaxy/pull/5686
.. _Pull Request 5689: https://github.com/galaxyproject/galaxy/pull/5689
.. _Pull Request 5690: https://github.com/galaxyproject/galaxy/pull/5690
.. _Pull Request 5691: https://github.com/galaxyproject/galaxy/pull/5691
.. _Pull Request 5692: https://github.com/galaxyproject/galaxy/pull/5692
.. _Pull Request 5693: https://github.com/galaxyproject/galaxy/pull/5693
.. _Pull Request 5697: https://github.com/galaxyproject/galaxy/pull/5697
.. _Pull Request 5698: https://github.com/galaxyproject/galaxy/pull/5698
.. _Pull Request 5699: https://github.com/galaxyproject/galaxy/pull/5699
.. _Pull Request 5700: https://github.com/galaxyproject/galaxy/pull/5700
.. _Pull Request 5701: https://github.com/galaxyproject/galaxy/pull/5701
.. _Pull Request 5702: https://github.com/galaxyproject/galaxy/pull/5702
.. _Pull Request 5703: https://github.com/galaxyproject/galaxy/pull/5703
.. _Pull Request 5705: https://github.com/galaxyproject/galaxy/pull/5705
.. _Pull Request 5706: https://github.com/galaxyproject/galaxy/pull/5706
.. _Pull Request 5707: https://github.com/galaxyproject/galaxy/pull/5707
.. _Pull Request 5708: https://github.com/galaxyproject/galaxy/pull/5708
.. _Pull Request 5709: https://github.com/galaxyproject/galaxy/pull/5709
.. _Pull Request 5710: https://github.com/galaxyproject/galaxy/pull/5710
.. _Pull Request 5711: https://github.com/galaxyproject/galaxy/pull/5711
.. _Pull Request 5714: https://github.com/galaxyproject/galaxy/pull/5714
.. _Pull Request 5715: https://github.com/galaxyproject/galaxy/pull/5715
.. _Pull Request 5716: https://github.com/galaxyproject/galaxy/pull/5716
.. _Pull Request 5717: https://github.com/galaxyproject/galaxy/pull/5717
.. _Pull Request 5718: https://github.com/galaxyproject/galaxy/pull/5718
.. _Pull Request 5719: https://github.com/galaxyproject/galaxy/pull/5719
.. _Pull Request 5721: https://github.com/galaxyproject/galaxy/pull/5721
.. _Pull Request 5724: https://github.com/galaxyproject/galaxy/pull/5724
.. _Pull Request 5725: https://github.com/galaxyproject/galaxy/pull/5725
.. _Pull Request 5731: https://github.com/galaxyproject/galaxy/pull/5731
.. _Pull Request 5732: https://github.com/galaxyproject/galaxy/pull/5732
.. _Pull Request 5735: https://github.com/galaxyproject/galaxy/pull/5735
.. _Pull Request 5737: https://github.com/galaxyproject/galaxy/pull/5737
.. _Pull Request 5740: https://github.com/galaxyproject/galaxy/pull/5740
.. _Pull Request 5741: https://github.com/galaxyproject/galaxy/pull/5741
.. _Pull Request 5742: https://github.com/galaxyproject/galaxy/pull/5742
.. _Pull Request 5743: https://github.com/galaxyproject/galaxy/pull/5743
.. _Pull Request 5745: https://github.com/galaxyproject/galaxy/pull/5745
.. _Pull Request 5746: https://github.com/galaxyproject/galaxy/pull/5746
.. _Pull Request 5747: https://github.com/galaxyproject/galaxy/pull/5747
.. _Pull Request 5749: https://github.com/galaxyproject/galaxy/pull/5749
.. _Pull Request 5750: https://github.com/galaxyproject/galaxy/pull/5750
.. _Pull Request 5752: https://github.com/galaxyproject/galaxy/pull/5752
.. _Pull Request 5754: https://github.com/galaxyproject/galaxy/pull/5754
.. _Pull Request 5755: https://github.com/galaxyproject/galaxy/pull/5755
.. _Pull Request 5758: https://github.com/galaxyproject/galaxy/pull/5758
.. _Pull Request 5759: https://github.com/galaxyproject/galaxy/pull/5759
.. _Pull Request 5760: https://github.com/galaxyproject/galaxy/pull/5760
.. _Pull Request 5761: https://github.com/galaxyproject/galaxy/pull/5761
.. _Pull Request 5766: https://github.com/galaxyproject/galaxy/pull/5766
.. _Pull Request 5769: https://github.com/galaxyproject/galaxy/pull/5769
.. _Pull Request 5771: https://github.com/galaxyproject/galaxy/pull/5771
.. _Pull Request 5772: https://github.com/galaxyproject/galaxy/pull/5772
.. _Pull Request 5773: https://github.com/galaxyproject/galaxy/pull/5773
.. _Pull Request 5774: https://github.com/galaxyproject/galaxy/pull/5774
.. _Pull Request 5776: https://github.com/galaxyproject/galaxy/pull/5776
.. _Pull Request 5782: https://github.com/galaxyproject/galaxy/pull/5782
.. _Pull Request 5784: https://github.com/galaxyproject/galaxy/pull/5784
.. _Pull Request 5786: https://github.com/galaxyproject/galaxy/pull/5786
.. _Pull Request 5788: https://github.com/galaxyproject/galaxy/pull/5788
.. _Pull Request 5789: https://github.com/galaxyproject/galaxy/pull/5789
.. _Pull Request 5793: https://github.com/galaxyproject/galaxy/pull/5793
.. _Pull Request 5794: https://github.com/galaxyproject/galaxy/pull/5794
.. _Pull Request 5797: https://github.com/galaxyproject/galaxy/pull/5797
.. _Pull Request 5798: https://github.com/galaxyproject/galaxy/pull/5798
.. _Pull Request 5799: https://github.com/galaxyproject/galaxy/pull/5799
.. _Pull Request 5800: https://github.com/galaxyproject/galaxy/pull/5800
.. _Pull Request 5804: https://github.com/galaxyproject/galaxy/pull/5804
.. _Pull Request 5805: https://github.com/galaxyproject/galaxy/pull/5805
.. _Pull Request 5806: https://github.com/galaxyproject/galaxy/pull/5806
.. _Pull Request 5807: https://github.com/galaxyproject/galaxy/pull/5807
.. _Pull Request 5810: https://github.com/galaxyproject/galaxy/pull/5810
.. _Pull Request 5811: https://github.com/galaxyproject/galaxy/pull/5811
.. _Pull Request 5814: https://github.com/galaxyproject/galaxy/pull/5814
.. _Pull Request 5815: https://github.com/galaxyproject/galaxy/pull/5815
.. _Pull Request 5816: https://github.com/galaxyproject/galaxy/pull/5816
.. _Pull Request 5819: https://github.com/galaxyproject/galaxy/pull/5819
.. _Pull Request 5821: https://github.com/galaxyproject/galaxy/pull/5821
.. _Pull Request 5823: https://github.com/galaxyproject/galaxy/pull/5823
.. _Pull Request 5825: https://github.com/galaxyproject/galaxy/pull/5825
.. _Pull Request 5826: https://github.com/galaxyproject/galaxy/pull/5826
.. _Pull Request 5829: https://github.com/galaxyproject/galaxy/pull/5829
.. _Pull Request 5836: https://github.com/galaxyproject/galaxy/pull/5836
.. _Pull Request 5839: https://github.com/galaxyproject/galaxy/pull/5839
.. _Pull Request 5854: https://github.com/galaxyproject/galaxy/pull/5854
.. _Pull Request 5859: https://github.com/galaxyproject/galaxy/pull/5859
.. _Pull Request 5861: https://github.com/galaxyproject/galaxy/pull/5861
.. _Pull Request 5864: https://github.com/galaxyproject/galaxy/pull/5864
.. _Pull Request 5869: https://github.com/galaxyproject/galaxy/pull/5869
.. _Pull Request 5870: https://github.com/galaxyproject/galaxy/pull/5870
.. _Pull Request 5872: https://github.com/galaxyproject/galaxy/pull/5872
.. _Pull Request 5876: https://github.com/galaxyproject/galaxy/pull/5876
.. _Pull Request 5877: https://github.com/galaxyproject/galaxy/pull/5877
.. _Pull Request 5878: https://github.com/galaxyproject/galaxy/pull/5878
.. _Pull Request 5880: https://github.com/galaxyproject/galaxy/pull/5880
.. _Pull Request 5881: https://github.com/galaxyproject/galaxy/pull/5881
.. _Pull Request 5882: https://github.com/galaxyproject/galaxy/pull/5882
.. _Pull Request 5886: https://github.com/galaxyproject/galaxy/pull/5886
.. _Pull Request 5887: https://github.com/galaxyproject/galaxy/pull/5887
.. _Pull Request 5888: https://github.com/galaxyproject/galaxy/pull/5888
.. _Pull Request 5890: https://github.com/galaxyproject/galaxy/pull/5890
.. _Pull Request 5892: https://github.com/galaxyproject/galaxy/pull/5892
.. _Pull Request 5896: https://github.com/galaxyproject/galaxy/pull/5896
.. _Pull Request 5899: https://github.com/galaxyproject/galaxy/pull/5899
.. _Pull Request 5900: https://github.com/galaxyproject/galaxy/pull/5900
.. _Pull Request 5902: https://github.com/galaxyproject/galaxy/pull/5902
.. _Pull Request 5904: https://github.com/galaxyproject/galaxy/pull/5904
.. _Pull Request 5906: https://github.com/galaxyproject/galaxy/pull/5906
.. _Pull Request 5907: https://github.com/galaxyproject/galaxy/pull/5907
.. _Pull Request 5908: https://github.com/galaxyproject/galaxy/pull/5908
.. _Pull Request 5909: https://github.com/galaxyproject/galaxy/pull/5909
.. _Pull Request 5913: https://github.com/galaxyproject/galaxy/pull/5913
.. _Pull Request 5914: https://github.com/galaxyproject/galaxy/pull/5914
.. _Pull Request 5916: https://github.com/galaxyproject/galaxy/pull/5916
.. _Pull Request 5917: https://github.com/galaxyproject/galaxy/pull/5917
.. _Pull Request 5921: https://github.com/galaxyproject/galaxy/pull/5921
.. _Pull Request 5922: https://github.com/galaxyproject/galaxy/pull/5922
.. _Pull Request 5924: https://github.com/galaxyproject/galaxy/pull/5924
.. _Pull Request 5928: https://github.com/galaxyproject/galaxy/pull/5928
.. _Pull Request 5929: https://github.com/galaxyproject/galaxy/pull/5929
.. _Pull Request 5935: https://github.com/galaxyproject/galaxy/pull/5935
.. _Pull Request 5936: https://github.com/galaxyproject/galaxy/pull/5936
.. _Pull Request 5937: https://github.com/galaxyproject/galaxy/pull/5937
.. _Pull Request 5938: https://github.com/galaxyproject/galaxy/pull/5938
.. _Pull Request 5940: https://github.com/galaxyproject/galaxy/pull/5940
.. _Pull Request 5945: https://github.com/galaxyproject/galaxy/pull/5945
.. _Pull Request 5947: https://github.com/galaxyproject/galaxy/pull/5947
.. _Pull Request 5956: https://github.com/galaxyproject/galaxy/pull/5956
.. _Pull Request 5962: https://github.com/galaxyproject/galaxy/pull/5962
.. _Pull Request 5965: https://github.com/galaxyproject/galaxy/pull/5965
.. _Pull Request 5968: https://github.com/galaxyproject/galaxy/pull/5968
.. _Pull Request 5969: https://github.com/galaxyproject/galaxy/pull/5969
.. _Pull Request 5972: https://github.com/galaxyproject/galaxy/pull/5972
.. _Pull Request 5973: https://github.com/galaxyproject/galaxy/pull/5973
.. _Pull Request 5980: https://github.com/galaxyproject/galaxy/pull/5980
.. _Pull Request 5986: https://github.com/galaxyproject/galaxy/pull/5986
.. _Pull Request 5991: https://github.com/galaxyproject/galaxy/pull/5991
.. _Pull Request 5997: https://github.com/galaxyproject/galaxy/pull/5997
.. _Pull Request 6007: https://github.com/galaxyproject/galaxy/pull/6007
.. _Pull Request 6069: https://github.com/galaxyproject/galaxy/pull/6069
.. _Pull Request 6085: https://github.com/galaxyproject/galaxy/pull/6085