galaxy/doc/source/releases/17.09.rst

.. to_doc

17.09
===============================

.. announce_start

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

.. major_feature


.. feature

* Galaxy Workflow support for GenomeSpace
  (thanks to `@nuwang <https://github.com/nuwang>`__ and
  `@gvlproject <https://github.com/gvlproject>`__).
  `Pull Request 1814`_
* Support tags (including new "name" tags) in data libraries.
  (thanks to `@bwlang <https://github.com/bwlang>`__).
  `Pull Request 4262`_
* HiCBrowser as Galaxy IE
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3330`_
* Synnefo/Pithos+ object store backend
  (thanks to `@saxtouri <https://github.com/saxtouri>`__).
  `Pull Request 3611`_
* Add job runner for `Chronos <https://mesos.github.io/chronos/>`__
  (thanks to `@theosotr <https://github.com/theosotr>`__).
  `Pull Request 3946`_, `Pull Request 4120`_
* Many improvements to the shell job runner (including a new Paramiko based
  runner with retry support)
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4358`_, `Pull Request 4599`_, `Pull Request 4343`_
* Add entry for ``empty_extra_files_path`` validator
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 3994`_
* Extend async data sources to support dataset collections
  (thanks to `@fabio-cumbo <https://github.com/fabio-cumbo>`__).
  `Pull Request 4198`_
* Add a repository uninstall endpoint to the tool dependency API
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4248`_
* Display preview feature for Bam datatype
  (thanks to `@ashvark <https://github.com/ashvark>`__).
  `Pull Request 4279`_
* Add Unipept taxonomy viewer plugin
  (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
  `Pull Request 4310`_
* Created alphabetic and numerical sort tool for collection operations
  (thanks to `@glormph <https://github.com/glormph>`__).
  `Pull Request 4329`_
* Prevent loading tools that require a newer galaxy
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4382`_
* Add explicit support for gzipped VCF files
  (thanks to `@ffinfo <https://github.com/ffinfo>`__).
  `Pull Request 4254`_
* Add ptkscmp datatype
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 4259`_
* Add imzML datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4370`_
* Add deepTools datatypes to Galaxy
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4392`_
* Add support for the MEME psp format
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 4430`_
* Add biom2 datatype
  (thanks to `@shiltemann <https://github.com/shiltemann>`__).
  `Pull Request 4519`_
* Add Excel97 Datatype
  `Pull Request 4410`_
* Add mz5 datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4466`_
* Refactor tool error reporting into plugins and implement a new
  plugin for `influxdb <https://www.influxdata.com/>`__
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4305`_, `Pull Request 4533`_
* Implement second toolshed installation UX targetting the API.
  `Pull Request 3626`_
* Tool-Describing-Tours
  (thanks to `@anatskiy <https://github.com/anatskiy>`__).
  `Pull Request 4019`_

.. enhancement

* Revamp configuration and default server for tool shed and Galaxy reports application
  (these now use a uwsgi server by default configured with a YAML configuration file).
  `Pull Request 3179`_
* Speed up and optimize the process of identifying public libraries.
  `Pull Request 4640`_
* Numerous data library fixes and improvements - both to the frontend and backend.
  `Pull Request 4568`_, `Pull Request 4595`_,
  `Pull Request 4594`_, `Pull Request 4579`_, `Pull Request 4560`_
  `Pull Request 4512`_, `Pull Request 4621`_, `Pull Request 4752`_
* Enhance workflow import API endpoint to allow admins to install repositories corresponding
  to a supplied workflow
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 3064`_
* GFF3 support in filter by attribute
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 3076`_
* Add extension point for user preferences
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3383`_
* Respect ``expose_user_email`` configuration in data libraries permissions list.
  `Pull Request 4611`_
* Explicitly include PyPI as an ``--extra-index-url`` to pip.
  `Pull Request 4674`_
* Improved Kubernetes support (non-privileged filesystem access, updated k8s Job API target)
  (thanks to `@phnmnl <https://github.com/phnmnl>`__).
  `Pull Request 3972`_
* New Dependency resolver for the LMOD environment modules system
  (thanks to `@arbernard <https://github.com/arbernard>`__).
  `Pull Request 4489`_
* Nicer tool click targets for toolbox
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4470`_
* Implement a "plain" bootstrap theme for the UX
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4470`_
* Add Selenium tests for the "saved histories", "published histories", and
  "custom builds"
  (thanks to `@anatskiy <https://github.com/anatskiy>`__).
  `Pull Request 4587`_, `Pull Request 4502`_, `Pull Request 4641`_,
* Dozens of Selenium functional test enhancements and fixes
  `Pull Request 3993`_, `Pull Request 4523`_, `Pull Request 4524`_, `Pull Request 4549`_,
  `Pull Request 4588`_, `Pull Request 4589`_, `Pull Request 4647`_,
  `Pull Request 3992`_, `Pull Request 4003`_, `Pull Request 4053`_,
  `Pull Request 4576`_, `Pull Request 4561`_, `Pull Request 4531`_, `Pull Request 4564`_,
  `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_, `Pull Request 4042`_
* Prevent graphite from dying loudly
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4036`_
* Updated parameters check for OpenID
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 4039`_
* Tooltip translation . Add Deutsch,Spanish
  (thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
  `Pull Request 4045`_
* New Workflow Management Screen UI using JavaScript
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4047`_
* Improve release checklist
  `Pull Request 4077`_
* Fix French translation errors
  (thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
  `Pull Request 4080`_
* remove the content alert from TS response
  `Pull Request 4082`_
* Touchup .gitignore to not ignore new bundles.
  `Pull Request 4091`_
* New Configure Workflow Menu UI
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4092`_
* get real user name from username and email (for submission as real user with
  drmaa)
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 4096`_
* Security policy
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4113`_
* Improved styling of workflow list.
  `Pull Request 4138`_
* Swap over all URLs to new wiki location
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4141`_
* Documentation fixes and improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4146`_
* Slider enhancement, shared event listeners
  `Pull Request 4149`_
* Add the ability to control job conf plugin loading from environment
  variables.
  `Pull Request 4154`_
* Replace various mako templates with client side JavaScript rendering.
  `Pull Request 4157`_, `Pull Request 4167`_, `Pull Request 4169`_,
  `Pull Request 4201`_, `Pull Request 4311`_, `Pull Request 4377`_,
  `Pull Request 4411`_, `Pull Request 4334`_, `Pull Request 4305`_,
  `Pull Request 4067`_, `Pull Request 4327`_
* Related to the above mako transition, rework various "grid" rendering code
  to do more on the client side as well.
  `Pull Request 4302`_, `Pull Request 4291`_, `Pull Request 4293`_,
  `Pull Request 4385`_, `Pull Request 4405`_, 
  `Pull Request 4449`_, `Pull Request 4263`_, `Pull Request 4341`_,
  `Pull Request 4163`_, `Pull Request 4101`_
* Set content type to application/json for JSON text types.
  `Pull Request 4160`_
* Assorted enhancements for container support (both for mulled container generation
  and fetching as well as to new Singularity support).
  `Pull Request 4173`_, `Pull Request 4179`_, `Pull Request 4180`_,
  `Pull Request 4185`_
* Make updateucsc.sh.sample usable without any change
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4192`_
* deals with .xls older file extension
  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
  `Pull Request 4200`_
* add dev requirement
  `Pull Request 4008`_
* Improve search plugin
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4213`_
* Upgrading Neo4j IE to 3.1
  (thanks to `@thobalose <https://github.com/thobalose>`__).
  `Pull Request 4216`_
* Running a word count on a compressed fastq file now runs wc on the un…
  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
  `Pull Request 4226`_
* "Join two Datasets" (join1) preserve column headers
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 4229`_
* Add public-only filter for data libraries
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 4232`_
* Fix import order and Python3 compatibility for 51 files
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4236`_
* Sniff fastqsanger and prefer it over fastq if the quality scores match
  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
  `Pull Request 4237`_
* Enable skipping comment lines while sniffing files
  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
  `Pull Request 4239`_
* Expose 4 more rows from the galaxy_user table to help out sys admins
  (thanks to `@XDtim <https://github.com/XDtim>`__).
  `Pull Request 4255`_
* Change 'register or login' to just 'login' if 'allow_user_creation=False'
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 4258`_
* Keep tool parameters when rerunning a job
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4271`_
* More uniform backend code for generating page titles
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4272`_, `Pull Request 4578`_
* Fix blockquote>p sizing
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4273`_
* Expose more user properties to admins via the API.
  `Pull Request 4274`_
* Ensure tags are copied and presented when moving collections
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 4277`_
* Add ``test_errors`` to .gitignore.
  `Pull Request 4278`_
* Implement package locking for node modules.
  `Pull Request 4283`_
* Enhancement for Phylocanvas plugin
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4284`_
* Improve security via local network access restrictions
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4289`_
* Enhancement for Phyloviz viz plugin
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4292`_
* Allow submitting the galaxy jobs as a predefined system user using
  ``real_system_username``
  (thanks to `@ashvark <https://github.com/ashvark>`__).
  `Pull Request 4294`_
* Update Japanese translation
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 4304`_
* Allow localization of more UI strings
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 4306`_, `Pull Request 4307`_
* Allow import of history archives via simple file upload
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4326`_
* Fix some French errors
  (thanks to `@loraine-gueguen <https://github.com/loraine-gueguen>`__).
  `Pull Request 4337`_
* Updated the version requirements
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 4342`_
* CSRF protection for login, logout, and user registration (most parts of the
  Galaxy UI still don't have explicit CSRF protection).
  `Pull Request 4365`_, `Pull Request 4710`_
* Implement ``default_identifier_source`` for tool collection outputs and sort
  input keys by default
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4368`_, `Pull Request 4380`_
* Galactic Radio Telescope Update
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4376`_
* Show minimum required galaxy version in tool shed and galaxy installation
  process
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4386`_
* Cleanup of Unit Test Code for Loading Tools
  `Pull Request 4387`_
* Refactor ToolOutputCollectionStructure...
  `Pull Request 4389`_
* Slightly improve workflow warnings/errors logging.
  `Pull Request 4396`_
* Better Error Summaries for API Tests
  `Pull Request 4397`_
* Fix import order and Python3 compatibility for lib/galaxy/web/base/
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4403`_
* Generalize allow_library_path_paste to allow_path_paste.
  `Pull Request 4404`_
* Small GRT bugfixes
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4408`_
* Update conda channel order to sync with Bioconda
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4409`_
* Fixes and enhancements for the upload API
  `Pull Request 4417`_
* Avoid adding `(imported from API)` to workflows
  (thanks to `@chambm <https://github.com/chambm>`__).
  `Pull Request 4434`_
* Enhanced tool options for dataset discovery
  `Pull Request 4437`_
* Augment form module separation
  `Pull Request 4438`_
* Fix E201 and E202 style errors
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4440`_
* Add autopep8 script to help rebasing branches after `#4440
  <https://github.com/galaxyproject/galaxy/issues/4440>`__.
  `Pull Request 4447`_
* Uniform indentation of multiline if conditionals
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4455`_
* Small logging improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4456`_
* Improvements to `Sentry <https://sentry.io/welcome/>`__ integration
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4457`_, `Pull Request 4471`_
* Fix for GIEs to not automatically uppercase environment variables
  (thanks to `@xgaia <https://github.com/xgaia>`__).
  `Pull Request 4458`_, `Pull Request 4454`_
* Fix security checking of WorkflowInvocation for published workflows
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4465`_
* Show more items per page in saved history view and directly show tags
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4467`_
* A variety of usability improvements to the workflow index page (show tags,
  allow import by drag-and-drop, and avoid unneeded page refreshs)
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4476`_, `Pull Request 4369`_
* Use pysam instead of samtools binary when discovering BAM metadata in one
  place (samtools is still required by Galaxy)
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4479`_
* Replace exclamation with a clock icon for "new" datasets in the history panel.
  `Pull Request 4485`_
* Minor copy datasets dialog improvement.
  `Pull Request 4486`_
* 41% reduction in freiburg galaxy startup time
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4495`_
* Allow paramiko cli to recover from ssh timeout
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4503`_
* Tests and clarifications for composite uploads.
  `Pull Request 4505`_
* Load tools with collection type source attributes into the workflow editor
  `Pull Request 4514`_
* Display d3 hierarchy datatype in upload interface
  `Pull Request 4522`_
* Sync non-CWL galaxy-lib changes.
  `Pull Request 4535`_
* Add a small howto on profiling galaxy code
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4542`_
* allow linking, posix and spaces conversions in datalib imports
  `Pull Request 4547`_
* Allow exporting workflows when tool is uninstalled
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4553`_
* Lower threshold for auto-matching dataset pairs in the collection builder
  `Pull Request 4555`_
* Allow working with pbzip2 compressed files
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4559`_
* add logging to ts index building
  `Pull Request 4567`_
* Add show/hide deleted/hidden links when history is filtered...
  (thanks to `@chambm <https://github.com/chambm>`__).
  `Pull Request 4581`_
* Python 3 fixes for set_metadata.py
  `Pull Request 4607`_
* Allow adding new data tables without restart
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4617`_
* remove .git and .hg from recursive file search
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4636`_
* Better handling of long id secrets when generating per-kind encryption keys.
  `Pull Request 4713`_

.. small_enhancement

* Add test case clarifying datasets do get "renamed" by rename PJA in
  collections.
  `Pull Request 3983`_
* Add some test tools for collection job failures.
  `Pull Request 4044`_
* Merge ShedToolLineage and StockLineage to ToolLineage
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4119`_
* Move PlantTribes datatypes to a separate file with enhancements and fixes
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 4137`_
* Move ``galaxy.tools.toolbox.cache`` to ``galaxy.tools.cache``.
  `Pull Request 4155`_
* Small code style and error message fixes for data library code
  (thanks to `@bwlang <https://github.com/bwlang>`__).
  `Pull Request 4250`_
* Refactors tag manager to not consume the unneeded ``app`` argument
  (thanks to `@bwlang <https://github.com/bwlang>`__).
  `Pull Request 4253`_
* Use contextmanager when using ``compression_util.get_fileobj()``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4270`_
* Swap the deprecated ``unescape()`` for ``decodeURIComponent``.
  `Pull Request 4321`_
* More consistent formatting for model mapping code
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 4333`_
* Merge configure menu with main workflow view
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4353`_
* Delete ``conda_exec_home`` instead of ``env['HOME']``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4360`_
* Replace list with generator when iterating headers in datatypes code
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4388`_
* Get tools with ``tool_version`` in more places
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4391`_
* Fix issues identified by the JavaScript linting application
  `lgtm <https://github.com/lgtmco/lgtm>`__.
  (thanks to `@xiemaisi <https://github.com/xiemaisi>`__).
  `Pull Request 4421`_
* Remove /mobile and associated templates (the code was unused and broken).
  `Pull Request 4494`_
* Workflow loading speedup
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4500`_
* Prevent transient job state API test failures from failing the build.
  `Pull Request 4510`_
* More robust workflow invocation testing.
  `Pull Request 4530`_
* Refactor history import/export tests to allow collection testing.
  `Pull Request 4534`_
* Refactor test modules toward cleaner dependencies
  `Pull Request 4536`_
* Prevent in-place editing of uploaded files if files are imported from the
  FTP folder
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4539`_
* Speedup toolform building
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4541`_
* Check user roles only once if user has no roles
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4546`_
* Remove unused bam to bai converter
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4598`_
* Remove various unreachable statements
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4603`_
* Refactored a dataset variable to HDA
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 4630`_
* Disable MacOS tests on TravisCI.
  `Pull Request 4631`_


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

.. major_bug

.. bug

* Various hashtag (or name tag) fixes (also backported to 17.05).
  `Pull Request 4139`_, `Pull Request 4188`_
* Simplify RC creation in Makefile.
  `Pull Request 4011`_
* Do not recurse in ``ensure_installed()``
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 4049`_
* Minor fixes for new locales, rebuild of client.
  `Pull Request 4050`_
* French translation error
  (thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
  `Pull Request 4051`_
* Minor history tour tweaks.
  `Pull Request 4061`_
* Improve tour button logic
  (thanks to `@bagnacan <https://github.com/bagnacan>`__).
  `Pull Request 4062`_
* Bug fix to prevent fetching the file path of purged files
  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
  `Pull Request 4066`_
* ToolShed tool dependency install fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4105`_
* Fix legacy Python path for genome diversity tools from miller lab.
  `Pull Request 4117`_
* Avoid locale specific string.letters for job_name
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 4121`_
* Fix typo in job_conf.xml.sample
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 4126`_
* Hide error highlighting if user interacts with highlighted field
  `Pull Request 4147`_
* Fix webhooks loading URL.
  `Pull Request 4158`_
* Fix older GIE config sample description.
  `Pull Request 4164`_
* Fix `#3990 <https://github.com/galaxyproject/galaxy/issues/3990>`__, don't
  chown non-galaxy files
  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
  `Pull Request 4186`_
* Debug of script library_upload_dir.py
  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
  `Pull Request 4199`_
* Correct name of neo4j datatype class
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 4223`_
* Fix ``Registry.get_datatype_by_extension()`` to return ``None`` if ``ext`` is unknown
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4224`_
* Avoid broken version of Mercurial in conda
  (thanks to `@bwlang <https://github.com/bwlang>`__).
  `Pull Request 4227`_
* Fix empty tabular output error when using discover_datasets.
  (thanks to `@pkrog <https://github.com/pkrog>`__).
  `Pull Request 4240`_
* Fix importing old exported histories.
  (thanks to `@cche <https://github.com/cche>`__).
  `Pull Request 4268`_
* Update ``tool_conf.xml.main`` to reflect usegalaxy.org's current state.
  `Pull Request 4295`_
* Fix ``TypeError`` when uploading large files from FTP to S3.
  (thanks to `@jlhg <https://github.com/jlhg>`__).
  `Pull Request 4315`_
* Fix for loading tools when ``tool.lineage is None``.
  `Pull Request 4317`_
* Fix for the caching of location filenames when they are broken symlinks.
  `Pull Request 4318`_
* Remove print debug option from toolshed.
  `Pull Request 4332`_
* Fix default output labels for subworkflows
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4346`_
* Search overlay plugin bug fix
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4348`_
* Tool version and lineage fixes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4375`_
* Fix bug in ``scripts/extract_dataset_part.py`` during task splitting.
  `Pull Request 4383`_
* Fix ``get_tool`` returning list when it shouldn't.
  `Pull Request 4390`_
* Bug fix for loading subworkflows from workflow descriptions.
  `Pull Request 4394`_
* Bug fix ``__str__`` method on tool parsers that previously would throw an ``Exception``.
  `Pull Request 4395`_
* Add missing chemical formats to ``datatypes_conf.xml.sample``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4413`_
* Don't cast ``tool_version`` to string if ``tool_version`` is None-type
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4420`_
* Some unicoding for local runner
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4426`_
* Break connection in workflow editor if necessary
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4431`_
* Fix private role validation.
  `Pull Request 4432`_
* Remove print of non-existent attribute 'content'
  (thanks to `@chambm <https://github.com/chambm>`__).
  `Pull Request 4439`_
* Fix quota function name
  `Pull Request 4469`_
* Fixes for VCF/BCF datatypes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4477`_
* Validate workflow step after step argument injection.
  `Pull Request 4483`_
* Fix drag and drop from history for Firefox
  `Pull Request 4496`_
* 2017-08 Security Patch
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4501`_
* Fix history import if using symlink in database directory
  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
  `Pull Request 4511`_
* Fix missing tools in the workflow editor
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4552`_
* Prevent unbound variable error history controller.
  `Pull Request 4557`_
* Backport uwsgi fix from `#2836
  <https://github.com/galaxyproject/galaxy/issues/2836>`__.
  `Pull Request 4565`_
* Bug fix startup of galaxy when webhooks dir is empty
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4570`_
* Fix delete option in history menu.
  `Pull Request 4574`_
* Cancel workflow invocations when histories are deleted.
  `Pull Request 4580`_
* Multiview missing histories fix
  `Pull Request 4610`_
* Fix virtualenv activation for some scripts
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4616`_
* Pulsar remote metadata fixes
  `Pull Request 4622`_
* Swap sanitize whitelist form to use a post.
  `Pull Request 4625`_
* Fix various spelling and grammatical error fixes.
  `Pull Request 4626`_
* Typo fix
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 4628`_
* Updated function description and fix some typos
  (thanks to `@VJalili <https://github.com/VJalili>`__).
  `Pull Request 4629`_
* Fix display of data in "custom builds" page
  (thanks to `@anatskiy <https://github.com/anatskiy>`__).
  `Pull Request 4634`_
* Do not wrap lines in the upload URL fetch.
  `Pull Request 4639`_
* Explicitly write registry.xml when creating a job for the upload tool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4644`_, `Pull Request 4600`_
* Fix links on workflow, history items.
  `Pull Request 4656`_
* Fix for modules resolver.
  `Pull Request 4663`_
* Remove overly chatty debug statement.
  `Pull Request 4671`_
* Client side fixes for GIEs.
  `Pull Request 4680`_
* Update target versions of conda and conda-build
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 4701`_
* Correct base route for workflows, allowing proxy-prefix to work.
  `Pull Request 4705`_
* Cachebust IE require'd files (jupyter.js, etc).
  `Pull Request 4714`_
* Add message (error and info) display to workflows display list.
  `Pull Request 4716`_
* If the newest version of a tool is hidden, load the newest older version, if
  any, into the tool panel.
  `Pull Request 4726`_
* Fix missing support for command_inject when using containers lib in GIEs.
  `Pull Request 4740`_
* Fix t, a, g, s returned in to_dict() method
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4742`_
* Fix joiner tool to inherit datatype from the input format
  `Pull Request 4745`_
* Fix auth with ``ldaps://``
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 4748`_
* Force onload webhooks to wait for Galaxy object (and root) resolution.
  `Pull Request 4750`_
* GIEs: Grandfather automatic uppercasing of some env_override variables
  `Pull Request 4760`_

.. github_links
.. _Pull Request 1814: https://github.com/galaxyproject/galaxy/pull/1814
.. _Pull Request 3064: https://github.com/galaxyproject/galaxy/pull/3064
.. _Pull Request 3076: https://github.com/galaxyproject/galaxy/pull/3076
.. _Pull Request 3179: https://github.com/galaxyproject/galaxy/pull/3179
.. _Pull Request 3330: https://github.com/galaxyproject/galaxy/pull/3330
.. _Pull Request 3383: https://github.com/galaxyproject/galaxy/pull/3383
.. _Pull Request 3611: https://github.com/galaxyproject/galaxy/pull/3611
.. _Pull Request 3626: https://github.com/galaxyproject/galaxy/pull/3626
.. _Pull Request 3946: https://github.com/galaxyproject/galaxy/pull/3946
.. _Pull Request 3972: https://github.com/galaxyproject/galaxy/pull/3972
.. _Pull Request 3983: https://github.com/galaxyproject/galaxy/pull/3983
.. _Pull Request 3992: https://github.com/galaxyproject/galaxy/pull/3992
.. _Pull Request 3993: https://github.com/galaxyproject/galaxy/pull/3993
.. _Pull Request 3994: https://github.com/galaxyproject/galaxy/pull/3994
.. _Pull Request 3995: https://github.com/galaxyproject/galaxy/pull/3995
.. _Pull Request 4003: https://github.com/galaxyproject/galaxy/pull/4003
.. _Pull Request 4008: https://github.com/galaxyproject/galaxy/pull/4008
.. _Pull Request 4010: https://github.com/galaxyproject/galaxy/pull/4010
.. _Pull Request 4011: https://github.com/galaxyproject/galaxy/pull/4011
.. _Pull Request 4019: https://github.com/galaxyproject/galaxy/pull/4019
.. _Pull Request 4036: https://github.com/galaxyproject/galaxy/pull/4036
.. _Pull Request 4039: https://github.com/galaxyproject/galaxy/pull/4039
.. _Pull Request 4042: https://github.com/galaxyproject/galaxy/pull/4042
.. _Pull Request 4044: https://github.com/galaxyproject/galaxy/pull/4044
.. _Pull Request 4045: https://github.com/galaxyproject/galaxy/pull/4045
.. _Pull Request 4047: https://github.com/galaxyproject/galaxy/pull/4047
.. _Pull Request 4049: https://github.com/galaxyproject/galaxy/pull/4049
.. _Pull Request 4050: https://github.com/galaxyproject/galaxy/pull/4050
.. _Pull Request 4051: https://github.com/galaxyproject/galaxy/pull/4051
.. _Pull Request 4053: https://github.com/galaxyproject/galaxy/pull/4053
.. _Pull Request 4061: https://github.com/galaxyproject/galaxy/pull/4061
.. _Pull Request 4062: https://github.com/galaxyproject/galaxy/pull/4062
.. _Pull Request 4066: https://github.com/galaxyproject/galaxy/pull/4066
.. _Pull Request 4067: https://github.com/galaxyproject/galaxy/pull/4067
.. _Pull Request 4077: https://github.com/galaxyproject/galaxy/pull/4077
.. _Pull Request 4080: https://github.com/galaxyproject/galaxy/pull/4080
.. _Pull Request 4081: https://github.com/galaxyproject/galaxy/pull/4081
.. _Pull Request 4082: https://github.com/galaxyproject/galaxy/pull/4082
.. _Pull Request 4087: https://github.com/galaxyproject/galaxy/pull/4087
.. _Pull Request 4088: https://github.com/galaxyproject/galaxy/pull/4088
.. _Pull Request 4091: https://github.com/galaxyproject/galaxy/pull/4091
.. _Pull Request 4092: https://github.com/galaxyproject/galaxy/pull/4092
.. _Pull Request 4093: https://github.com/galaxyproject/galaxy/pull/4093
.. _Pull Request 4096: https://github.com/galaxyproject/galaxy/pull/4096
.. _Pull Request 4098: https://github.com/galaxyproject/galaxy/pull/4098
.. _Pull Request 4101: https://github.com/galaxyproject/galaxy/pull/4101
.. _Pull Request 4105: https://github.com/galaxyproject/galaxy/pull/4105
.. _Pull Request 4112: https://github.com/galaxyproject/galaxy/pull/4112
.. _Pull Request 4113: https://github.com/galaxyproject/galaxy/pull/4113
.. _Pull Request 4117: https://github.com/galaxyproject/galaxy/pull/4117
.. _Pull Request 4119: https://github.com/galaxyproject/galaxy/pull/4119
.. _Pull Request 4120: https://github.com/galaxyproject/galaxy/pull/4120
.. _Pull Request 4121: https://github.com/galaxyproject/galaxy/pull/4121
.. _Pull Request 4124: https://github.com/galaxyproject/galaxy/pull/4124
.. _Pull Request 4126: https://github.com/galaxyproject/galaxy/pull/4126
.. _Pull Request 4137: https://github.com/galaxyproject/galaxy/pull/4137
.. _Pull Request 4138: https://github.com/galaxyproject/galaxy/pull/4138
.. _Pull Request 4139: https://github.com/galaxyproject/galaxy/pull/4139
.. _Pull Request 4141: https://github.com/galaxyproject/galaxy/pull/4141
.. _Pull Request 4146: https://github.com/galaxyproject/galaxy/pull/4146
.. _Pull Request 4147: https://github.com/galaxyproject/galaxy/pull/4147
.. _Pull Request 4149: https://github.com/galaxyproject/galaxy/pull/4149
.. _Pull Request 4154: https://github.com/galaxyproject/galaxy/pull/4154
.. _Pull Request 4155: https://github.com/galaxyproject/galaxy/pull/4155
.. _Pull Request 4156: https://github.com/galaxyproject/galaxy/pull/4156
.. _Pull Request 4157: https://github.com/galaxyproject/galaxy/pull/4157
.. _Pull Request 4158: https://github.com/galaxyproject/galaxy/pull/4158
.. _Pull Request 4160: https://github.com/galaxyproject/galaxy/pull/4160
.. _Pull Request 4163: https://github.com/galaxyproject/galaxy/pull/4163
.. _Pull Request 4164: https://github.com/galaxyproject/galaxy/pull/4164
.. _Pull Request 4167: https://github.com/galaxyproject/galaxy/pull/4167
.. _Pull Request 4169: https://github.com/galaxyproject/galaxy/pull/4169
.. _Pull Request 4173: https://github.com/galaxyproject/galaxy/pull/4173
.. _Pull Request 4175: https://github.com/galaxyproject/galaxy/pull/4175
.. _Pull Request 4179: https://github.com/galaxyproject/galaxy/pull/4179
.. _Pull Request 4180: https://github.com/galaxyproject/galaxy/pull/4180
.. _Pull Request 4185: https://github.com/galaxyproject/galaxy/pull/4185
.. _Pull Request 4186: https://github.com/galaxyproject/galaxy/pull/4186
.. _Pull Request 4188: https://github.com/galaxyproject/galaxy/pull/4188
.. _Pull Request 4192: https://github.com/galaxyproject/galaxy/pull/4192
.. _Pull Request 4198: https://github.com/galaxyproject/galaxy/pull/4198
.. _Pull Request 4199: https://github.com/galaxyproject/galaxy/pull/4199
.. _Pull Request 4200: https://github.com/galaxyproject/galaxy/pull/4200
.. _Pull Request 4201: https://github.com/galaxyproject/galaxy/pull/4201
.. _Pull Request 4207: https://github.com/galaxyproject/galaxy/pull/4207
.. _Pull Request 4208: https://github.com/galaxyproject/galaxy/pull/4208
.. _Pull Request 4210: https://github.com/galaxyproject/galaxy/pull/4210
.. _Pull Request 4213: https://github.com/galaxyproject/galaxy/pull/4213
.. _Pull Request 4216: https://github.com/galaxyproject/galaxy/pull/4216
.. _Pull Request 4223: https://github.com/galaxyproject/galaxy/pull/4223
.. _Pull Request 4224: https://github.com/galaxyproject/galaxy/pull/4224
.. _Pull Request 4226: https://github.com/galaxyproject/galaxy/pull/4226
.. _Pull Request 4227: https://github.com/galaxyproject/galaxy/pull/4227
.. _Pull Request 4229: https://github.com/galaxyproject/galaxy/pull/4229
.. _Pull Request 4232: https://github.com/galaxyproject/galaxy/pull/4232
.. _Pull Request 4236: https://github.com/galaxyproject/galaxy/pull/4236
.. _Pull Request 4237: https://github.com/galaxyproject/galaxy/pull/4237
.. _Pull Request 4239: https://github.com/galaxyproject/galaxy/pull/4239
.. _Pull Request 4240: https://github.com/galaxyproject/galaxy/pull/4240
.. _Pull Request 4248: https://github.com/galaxyproject/galaxy/pull/4248
.. _Pull Request 4250: https://github.com/galaxyproject/galaxy/pull/4250
.. _Pull Request 4253: https://github.com/galaxyproject/galaxy/pull/4253
.. _Pull Request 4254: https://github.com/galaxyproject/galaxy/pull/4254
.. _Pull Request 4255: https://github.com/galaxyproject/galaxy/pull/4255
.. _Pull Request 4258: https://github.com/galaxyproject/galaxy/pull/4258
.. _Pull Request 4259: https://github.com/galaxyproject/galaxy/pull/4259
.. _Pull Request 4262: https://github.com/galaxyproject/galaxy/pull/4262
.. _Pull Request 4263: https://github.com/galaxyproject/galaxy/pull/4263
.. _Pull Request 4268: https://github.com/galaxyproject/galaxy/pull/4268
.. _Pull Request 4270: https://github.com/galaxyproject/galaxy/pull/4270
.. _Pull Request 4271: https://github.com/galaxyproject/galaxy/pull/4271
.. _Pull Request 4272: https://github.com/galaxyproject/galaxy/pull/4272
.. _Pull Request 4273: https://github.com/galaxyproject/galaxy/pull/4273
.. _Pull Request 4274: https://github.com/galaxyproject/galaxy/pull/4274
.. _Pull Request 4277: https://github.com/galaxyproject/galaxy/pull/4277
.. _Pull Request 4278: https://github.com/galaxyproject/galaxy/pull/4278
.. _Pull Request 4279: https://github.com/galaxyproject/galaxy/pull/4279
.. _Pull Request 4281: https://github.com/galaxyproject/galaxy/pull/4281
.. _Pull Request 4283: https://github.com/galaxyproject/galaxy/pull/4283
.. _Pull Request 4284: https://github.com/galaxyproject/galaxy/pull/4284
.. _Pull Request 4285: https://github.com/galaxyproject/galaxy/pull/4285
.. _Pull Request 4289: https://github.com/galaxyproject/galaxy/pull/4289
.. _Pull Request 4291: https://github.com/galaxyproject/galaxy/pull/4291
.. _Pull Request 4292: https://github.com/galaxyproject/galaxy/pull/4292
.. _Pull Request 4293: https://github.com/galaxyproject/galaxy/pull/4293
.. _Pull Request 4294: https://github.com/galaxyproject/galaxy/pull/4294
.. _Pull Request 4295: https://github.com/galaxyproject/galaxy/pull/4295
.. _Pull Request 4302: https://github.com/galaxyproject/galaxy/pull/4302
.. _Pull Request 4304: https://github.com/galaxyproject/galaxy/pull/4304
.. _Pull Request 4305: https://github.com/galaxyproject/galaxy/pull/4305
.. _Pull Request 4306: https://github.com/galaxyproject/galaxy/pull/4306
.. _Pull Request 4307: https://github.com/galaxyproject/galaxy/pull/4307
.. _Pull Request 4309: https://github.com/galaxyproject/galaxy/pull/4309
.. _Pull Request 4310: https://github.com/galaxyproject/galaxy/pull/4310
.. _Pull Request 4311: https://github.com/galaxyproject/galaxy/pull/4311
.. _Pull Request 4315: https://github.com/galaxyproject/galaxy/pull/4315
.. _Pull Request 4317: https://github.com/galaxyproject/galaxy/pull/4317
.. _Pull Request 4318: https://github.com/galaxyproject/galaxy/pull/4318
.. _Pull Request 4321: https://github.com/galaxyproject/galaxy/pull/4321
.. _Pull Request 4326: https://github.com/galaxyproject/galaxy/pull/4326
.. _Pull Request 4327: https://github.com/galaxyproject/galaxy/pull/4327
.. _Pull Request 4329: https://github.com/galaxyproject/galaxy/pull/4329
.. _Pull Request 4332: https://github.com/galaxyproject/galaxy/pull/4332
.. _Pull Request 4333: https://github.com/galaxyproject/galaxy/pull/4333
.. _Pull Request 4334: https://github.com/galaxyproject/galaxy/pull/4334
.. _Pull Request 4337: https://github.com/galaxyproject/galaxy/pull/4337
.. _Pull Request 4341: https://github.com/galaxyproject/galaxy/pull/4341
.. _Pull Request 4342: https://github.com/galaxyproject/galaxy/pull/4342
.. _Pull Request 4343: https://github.com/galaxyproject/galaxy/pull/4343
.. _Pull Request 4346: https://github.com/galaxyproject/galaxy/pull/4346
.. _Pull Request 4348: https://github.com/galaxyproject/galaxy/pull/4348
.. _Pull Request 4353: https://github.com/galaxyproject/galaxy/pull/4353
.. _Pull Request 4357: https://github.com/galaxyproject/galaxy/pull/4357
.. _Pull Request 4358: https://github.com/galaxyproject/galaxy/pull/4358
.. _Pull Request 4360: https://github.com/galaxyproject/galaxy/pull/4360
.. _Pull Request 4365: https://github.com/galaxyproject/galaxy/pull/4365
.. _Pull Request 4368: https://github.com/galaxyproject/galaxy/pull/4368
.. _Pull Request 4369: https://github.com/galaxyproject/galaxy/pull/4369
.. _Pull Request 4370: https://github.com/galaxyproject/galaxy/pull/4370
.. _Pull Request 4371: https://github.com/galaxyproject/galaxy/pull/4371
.. _Pull Request 4373: https://github.com/galaxyproject/galaxy/pull/4373
.. _Pull Request 4375: https://github.com/galaxyproject/galaxy/pull/4375
.. _Pull Request 4376: https://github.com/galaxyproject/galaxy/pull/4376
.. _Pull Request 4377: https://github.com/galaxyproject/galaxy/pull/4377
.. _Pull Request 4380: https://github.com/galaxyproject/galaxy/pull/4380
.. _Pull Request 4382: https://github.com/galaxyproject/galaxy/pull/4382
.. _Pull Request 4383: https://github.com/galaxyproject/galaxy/pull/4383
.. _Pull Request 4385: https://github.com/galaxyproject/galaxy/pull/4385
.. _Pull Request 4386: https://github.com/galaxyproject/galaxy/pull/4386
.. _Pull Request 4387: https://github.com/galaxyproject/galaxy/pull/4387
.. _Pull Request 4388: https://github.com/galaxyproject/galaxy/pull/4388
.. _Pull Request 4389: https://github.com/galaxyproject/galaxy/pull/4389
.. _Pull Request 4390: https://github.com/galaxyproject/galaxy/pull/4390
.. _Pull Request 4391: https://github.com/galaxyproject/galaxy/pull/4391
.. _Pull Request 4392: https://github.com/galaxyproject/galaxy/pull/4392
.. _Pull Request 4394: https://github.com/galaxyproject/galaxy/pull/4394
.. _Pull Request 4395: https://github.com/galaxyproject/galaxy/pull/4395
.. _Pull Request 4396: https://github.com/galaxyproject/galaxy/pull/4396
.. _Pull Request 4397: https://github.com/galaxyproject/galaxy/pull/4397
.. _Pull Request 4403: https://github.com/galaxyproject/galaxy/pull/4403
.. _Pull Request 4404: https://github.com/galaxyproject/galaxy/pull/4404
.. _Pull Request 4405: https://github.com/galaxyproject/galaxy/pull/4405
.. _Pull Request 4408: https://github.com/galaxyproject/galaxy/pull/4408
.. _Pull Request 4409: https://github.com/galaxyproject/galaxy/pull/4409
.. _Pull Request 4410: https://github.com/galaxyproject/galaxy/pull/4410
.. _Pull Request 4411: https://github.com/galaxyproject/galaxy/pull/4411
.. _Pull Request 4413: https://github.com/galaxyproject/galaxy/pull/4413
.. _Pull Request 4417: https://github.com/galaxyproject/galaxy/pull/4417
.. _Pull Request 4420: https://github.com/galaxyproject/galaxy/pull/4420
.. _Pull Request 4421: https://github.com/galaxyproject/galaxy/pull/4421
.. _Pull Request 4426: https://github.com/galaxyproject/galaxy/pull/4426
.. _Pull Request 4427: https://github.com/galaxyproject/galaxy/pull/4427
.. _Pull Request 4430: https://github.com/galaxyproject/galaxy/pull/4430
.. _Pull Request 4431: https://github.com/galaxyproject/galaxy/pull/4431
.. _Pull Request 4432: https://github.com/galaxyproject/galaxy/pull/4432
.. _Pull Request 4434: https://github.com/galaxyproject/galaxy/pull/4434
.. _Pull Request 4437: https://github.com/galaxyproject/galaxy/pull/4437
.. _Pull Request 4438: https://github.com/galaxyproject/galaxy/pull/4438
.. _Pull Request 4439: https://github.com/galaxyproject/galaxy/pull/4439
.. _Pull Request 4440: https://github.com/galaxyproject/galaxy/pull/4440
.. _Pull Request 4445: https://github.com/galaxyproject/galaxy/pull/4445
.. _Pull Request 4446: https://github.com/galaxyproject/galaxy/pull/4446
.. _Pull Request 4447: https://github.com/galaxyproject/galaxy/pull/4447
.. _Pull Request 4449: https://github.com/galaxyproject/galaxy/pull/4449
.. _Pull Request 4454: https://github.com/galaxyproject/galaxy/pull/4454
.. _Pull Request 4455: https://github.com/galaxyproject/galaxy/pull/4455
.. _Pull Request 4456: https://github.com/galaxyproject/galaxy/pull/4456
.. _Pull Request 4457: https://github.com/galaxyproject/galaxy/pull/4457
.. _Pull Request 4458: https://github.com/galaxyproject/galaxy/pull/4458
.. _Pull Request 4465: https://github.com/galaxyproject/galaxy/pull/4465
.. _Pull Request 4466: https://github.com/galaxyproject/galaxy/pull/4466
.. _Pull Request 4467: https://github.com/galaxyproject/galaxy/pull/4467
.. _Pull Request 4469: https://github.com/galaxyproject/galaxy/pull/4469
.. _Pull Request 4470: https://github.com/galaxyproject/galaxy/pull/4470
.. _Pull Request 4471: https://github.com/galaxyproject/galaxy/pull/4471
.. _Pull Request 4476: https://github.com/galaxyproject/galaxy/pull/4476
.. _Pull Request 4477: https://github.com/galaxyproject/galaxy/pull/4477
.. _Pull Request 4479: https://github.com/galaxyproject/galaxy/pull/4479
.. _Pull Request 4483: https://github.com/galaxyproject/galaxy/pull/4483
.. _Pull Request 4485: https://github.com/galaxyproject/galaxy/pull/4485
.. _Pull Request 4486: https://github.com/galaxyproject/galaxy/pull/4486
.. _Pull Request 4489: https://github.com/galaxyproject/galaxy/pull/4489
.. _Pull Request 4492: https://github.com/galaxyproject/galaxy/pull/4492
.. _Pull Request 4494: https://github.com/galaxyproject/galaxy/pull/4494
.. _Pull Request 4495: https://github.com/galaxyproject/galaxy/pull/4495
.. _Pull Request 4496: https://github.com/galaxyproject/galaxy/pull/4496
.. _Pull Request 4500: https://github.com/galaxyproject/galaxy/pull/4500
.. _Pull Request 4501: https://github.com/galaxyproject/galaxy/pull/4501
.. _Pull Request 4502: https://github.com/galaxyproject/galaxy/pull/4502
.. _Pull Request 4503: https://github.com/galaxyproject/galaxy/pull/4503
.. _Pull Request 4505: https://github.com/galaxyproject/galaxy/pull/4505
.. _Pull Request 4508: https://github.com/galaxyproject/galaxy/pull/4508
.. _Pull Request 4510: https://github.com/galaxyproject/galaxy/pull/4510
.. _Pull Request 4511: https://github.com/galaxyproject/galaxy/pull/4511
.. _Pull Request 4512: https://github.com/galaxyproject/galaxy/pull/4512
.. _Pull Request 4514: https://github.com/galaxyproject/galaxy/pull/4514
.. _Pull Request 4515: https://github.com/galaxyproject/galaxy/pull/4515
.. _Pull Request 4519: https://github.com/galaxyproject/galaxy/pull/4519
.. _Pull Request 4522: https://github.com/galaxyproject/galaxy/pull/4522
.. _Pull Request 4523: https://github.com/galaxyproject/galaxy/pull/4523
.. _Pull Request 4524: https://github.com/galaxyproject/galaxy/pull/4524
.. _Pull Request 4530: https://github.com/galaxyproject/galaxy/pull/4530
.. _Pull Request 4531: https://github.com/galaxyproject/galaxy/pull/4531
.. _Pull Request 4533: https://github.com/galaxyproject/galaxy/pull/4533
.. _Pull Request 4534: https://github.com/galaxyproject/galaxy/pull/4534
.. _Pull Request 4535: https://github.com/galaxyproject/galaxy/pull/4535
.. _Pull Request 4536: https://github.com/galaxyproject/galaxy/pull/4536
.. _Pull Request 4539: https://github.com/galaxyproject/galaxy/pull/4539
.. _Pull Request 4541: https://github.com/galaxyproject/galaxy/pull/4541
.. _Pull Request 4542: https://github.com/galaxyproject/galaxy/pull/4542
.. _Pull Request 4546: https://github.com/galaxyproject/galaxy/pull/4546
.. _Pull Request 4547: https://github.com/galaxyproject/galaxy/pull/4547
.. _Pull Request 4549: https://github.com/galaxyproject/galaxy/pull/4549
.. _Pull Request 4552: https://github.com/galaxyproject/galaxy/pull/4552
.. _Pull Request 4553: https://github.com/galaxyproject/galaxy/pull/4553
.. _Pull Request 4555: https://github.com/galaxyproject/galaxy/pull/4555
.. _Pull Request 4556: https://github.com/galaxyproject/galaxy/pull/4556
.. _Pull Request 4557: https://github.com/galaxyproject/galaxy/pull/4557
.. _Pull Request 4559: https://github.com/galaxyproject/galaxy/pull/4559
.. _Pull Request 4560: https://github.com/galaxyproject/galaxy/pull/4560
.. _Pull Request 4561: https://github.com/galaxyproject/galaxy/pull/4561
.. _Pull Request 4562: https://github.com/galaxyproject/galaxy/pull/4562
.. _Pull Request 4564: https://github.com/galaxyproject/galaxy/pull/4564
.. _Pull Request 4565: https://github.com/galaxyproject/galaxy/pull/4565
.. _Pull Request 4567: https://github.com/galaxyproject/galaxy/pull/4567
.. _Pull Request 4568: https://github.com/galaxyproject/galaxy/pull/4568
.. _Pull Request 4570: https://github.com/galaxyproject/galaxy/pull/4570
.. _Pull Request 4574: https://github.com/galaxyproject/galaxy/pull/4574
.. _Pull Request 4576: https://github.com/galaxyproject/galaxy/pull/4576
.. _Pull Request 4577: https://github.com/galaxyproject/galaxy/pull/4577
.. _Pull Request 4578: https://github.com/galaxyproject/galaxy/pull/4578
.. _Pull Request 4579: https://github.com/galaxyproject/galaxy/pull/4579
.. _Pull Request 4580: https://github.com/galaxyproject/galaxy/pull/4580
.. _Pull Request 4581: https://github.com/galaxyproject/galaxy/pull/4581
.. _Pull Request 4582: https://github.com/galaxyproject/galaxy/pull/4582
.. _Pull Request 4586: https://github.com/galaxyproject/galaxy/pull/4586
.. _Pull Request 4587: https://github.com/galaxyproject/galaxy/pull/4587
.. _Pull Request 4588: https://github.com/galaxyproject/galaxy/pull/4588
.. _Pull Request 4589: https://github.com/galaxyproject/galaxy/pull/4589
.. _Pull Request 4592: https://github.com/galaxyproject/galaxy/pull/4592
.. _Pull Request 4594: https://github.com/galaxyproject/galaxy/pull/4594
.. _Pull Request 4595: https://github.com/galaxyproject/galaxy/pull/4595
.. _Pull Request 4598: https://github.com/galaxyproject/galaxy/pull/4598
.. _Pull Request 4599: https://github.com/galaxyproject/galaxy/pull/4599
.. _Pull Request 4600: https://github.com/galaxyproject/galaxy/pull/4600
.. _Pull Request 4603: https://github.com/galaxyproject/galaxy/pull/4603
.. _Pull Request 4607: https://github.com/galaxyproject/galaxy/pull/4607
.. _Pull Request 4610: https://github.com/galaxyproject/galaxy/pull/4610
.. _Pull Request 4611: https://github.com/galaxyproject/galaxy/pull/4611
.. _Pull Request 4616: https://github.com/galaxyproject/galaxy/pull/4616
.. _Pull Request 4617: https://github.com/galaxyproject/galaxy/pull/4617
.. _Pull Request 4619: https://github.com/galaxyproject/galaxy/pull/4619
.. _Pull Request 4621: https://github.com/galaxyproject/galaxy/pull/4621
.. _Pull Request 4622: https://github.com/galaxyproject/galaxy/pull/4622
.. _Pull Request 4625: https://github.com/galaxyproject/galaxy/pull/4625
.. _Pull Request 4626: https://github.com/galaxyproject/galaxy/pull/4626
.. _Pull Request 4628: https://github.com/galaxyproject/galaxy/pull/4628
.. _Pull Request 4629: https://github.com/galaxyproject/galaxy/pull/4629
.. _Pull Request 4630: https://github.com/galaxyproject/galaxy/pull/4630
.. _Pull Request 4631: https://github.com/galaxyproject/galaxy/pull/4631
.. _Pull Request 4632: https://github.com/galaxyproject/galaxy/pull/4632
.. _Pull Request 4634: https://github.com/galaxyproject/galaxy/pull/4634
.. _Pull Request 4636: https://github.com/galaxyproject/galaxy/pull/4636
.. _Pull Request 4639: https://github.com/galaxyproject/galaxy/pull/4639
.. _Pull Request 4640: https://github.com/galaxyproject/galaxy/pull/4640
.. _Pull Request 4641: https://github.com/galaxyproject/galaxy/pull/4641
.. _Pull Request 4644: https://github.com/galaxyproject/galaxy/pull/4644
.. _Pull Request 4647: https://github.com/galaxyproject/galaxy/pull/4647
.. _Pull Request 4648: https://github.com/galaxyproject/galaxy/pull/4648
.. _Pull Request 4650: https://github.com/galaxyproject/galaxy/pull/4650
.. _Pull Request 4652: https://github.com/galaxyproject/galaxy/pull/4652
.. _Pull Request 4656: https://github.com/galaxyproject/galaxy/pull/4656
.. _Pull Request 4663: https://github.com/galaxyproject/galaxy/pull/4663
.. _Pull Request 4671: https://github.com/galaxyproject/galaxy/pull/4671
.. _Pull Request 4674: https://github.com/galaxyproject/galaxy/pull/4674
.. _Pull Request 4680: https://github.com/galaxyproject/galaxy/pull/4680
.. _Pull Request 4701: https://github.com/galaxyproject/galaxy/pull/4701
.. _Pull Request 4705: https://github.com/galaxyproject/galaxy/pull/4705
.. _Pull Request 4710: https://github.com/galaxyproject/galaxy/pull/4710
.. _Pull Request 4713: https://github.com/galaxyproject/galaxy/pull/4713
.. _Pull Request 4714: https://github.com/galaxyproject/galaxy/pull/4714
.. _Pull Request 4715: https://github.com/galaxyproject/galaxy/pull/4715
.. _Pull Request 4716: https://github.com/galaxyproject/galaxy/pull/4716
.. _Pull Request 4726: https://github.com/galaxyproject/galaxy/pull/4726
.. _Pull Request 4740: https://github.com/galaxyproject/galaxy/pull/4740
.. _Pull Request 4742: https://github.com/galaxyproject/galaxy/pull/4742
.. _Pull Request 4743: https://github.com/galaxyproject/galaxy/pull/4743
.. _Pull Request 4745: https://github.com/galaxyproject/galaxy/pull/4745
.. _Pull Request 4748: https://github.com/galaxyproject/galaxy/pull/4748
.. _Pull Request 4750: https://github.com/galaxyproject/galaxy/pull/4750
.. _Pull Request 4752: https://github.com/galaxyproject/galaxy/pull/4752
.. _Pull Request 4760: https://github.com/galaxyproject/galaxy/pull/4760