
.. to_doc

17.05
===============================

.. announce_start

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

.. major_feature


.. feature

* Recalculate user disk usage on logout.
  `Pull Request 3600`_
* Overlay search for tools, workflows, libraries and histories
  (thanks to `@anuprulez <https://github.com/anuprulez>`__ and `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3460`_
* Webhook plugin: tool_list
  (thanks to `@blankclemens <https://github.com/blankclemens>`__).
  `Pull Request 3753`_
* Add Cytoscape as the Galaxy charts plugin
  (thanks to `@anuprulez <https://github.com/anuprulez>`__ and `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3817`_
* Ethercalc Interactive Environment
  (thanks to `@shiltemann <https://github.com/shiltemann>`__).
  `Pull Request 3699`_
* Add a simple UI to manage tool dependencies
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3479`_
* Add nrrd image datatype
  (thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__).
  `Pull Request 3385`_
* NGL Viewer for molecule representation
  (thanks to `@anuprulez <https://github.com/anuprulez>`__ and `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3601`_
* Add script to encode or decode the IDs that Galaxy exposes to users and admins
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3622`_
* Support Docker Engine swarm mode for Interactive Environments.
  `Pull Request 3666`_
* Interactive Environment container waiting and swarm management.
  `Pull Request 3740`_
* Phylocanvas as a BioJS component for the Galaxy charts
  (thanks to `@anuprulez <https://github.com/anuprulez>`__ `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3850`_
* Container interface abstraction.
  `Pull Request 3863`_
* Graphite support
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3964`_
* Normalize the handling of steps and missing tools for the workflow editor.
  `Pull Request 3181`_
* Add possibility to load collection into data library
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3559`_
* Prefer versioned Conda dependencies to unversioned Galaxy ones.
  `Pull Request 3708`_
* Speedup startup and toolbox operations
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3909`_

.. enhancement

* Add missing imports for documentation builds
  (thanks to `@athos-ribeiro <https://github.com/athos-ribeiro>`__).
  `Pull Request 3104`_
* Workflow editor UI touch up.
  `Pull Request 3407`_
* Add an example group filter for displaying tool panel sections
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 3484`_
* Python3: use @six.add_metaclass() decorator
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3491`_
* Improvements to build sites configuration.
  `Pull Request 3503`_
* Add peek and preview for compressed FASTQ datatype
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3512`_
* Add ``refresh_on_change`` to tool XSD.
  `Pull Request 3515`_
* Store module step states as nested dictionaries, fix export for backward
  compatibility.
  `Pull Request 3522`_
* Add Jenkins documentation tasks to the release issue.
  `Pull Request 3523`_
* Allow decompressing tool test outputs.
  `Pull Request 3550`_
* Add a task to protect the release branch in GitHub.
  `Pull Request 3562`_
* Remove duplicated/unused display_migration_details() functions
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3564`_
* Display the genbank datatype in upload.
  `Pull Request 3569`_
* Database migrations: improvements and fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3570`_
* Add d3_hierarchy subclass
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 3580`_
* Clean up docker-compose resources better for Selenium tests.
  `Pull Request 3583`_
* Add option to send API key in header
  (thanks to `@jvolkening <https://github.com/jvolkening>`__).
  `Pull Request 3584`_
* Increase patience of Galaxy tests throughout.
  `Pull Request 3589`_
* Introduce label and annotation attributes to subworkflows, fix annotation
  display, unify module form update handler.
  `Pull Request 3593`_
* Align architecture slides with training-material remarkjs template.
  `Pull Request 3594`_
* Revision of tool XML reloading feature.
  `Pull Request 3596`_
* Implement collection operation to relabel list identifiers from contents of a
  file.
  `Pull Request 3603`_
* Slow query logging.
  `Pull Request 3616`_
* Remove un-needed check in histories manager code.
  `Pull Request 3618`_
* Improve interaction between job state and purged datasets.
  `Pull Request 3619`_
* Usable slow query logging.
  `Pull Request 3625`_
* Allow composite datatypes of type auto_primary_file to automatically
  generate dataset.
  `Pull Request 3643`_
* Introduce labels for all workflow modules, remove name handling field for data
  inputs.
  `Pull Request 3644`_
* When using the new slow query logger, include parameters.
  `Pull Request 3649`_
* Allow nested parameters in the dynamic_tool rule -> argument
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 3657`_
* By default, do not allow workflow invocations to schedule indefinitely.
  `Pull Request 3659`_
* Add the mzData datatype
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 3661`_
* Display an error message when GIE loading raises an exception.
  `Pull Request 3662`_
* Set LDAP options only once
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3663`_
* Bump Jupyter container version to 16.01.1 .
  `Pull Request 3665`_
* Improve wording of getgalaxy in bootstrapping script for release notes.
  `Pull Request 3671`_
* Filter hda tags for tool parameters.
  `Pull Request 3688`_
* Add datatypes for soon coming PlantTribes Galaxy tools
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 3698`_
* Touch up Galaxy testing documentation.
  `Pull Request 3715`_
* Add API and UI to remove requirements installed by Conda
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3725`_
* Quota recalculation logic consolidation.
  `Pull Request 3734`_
* Percolator out datatypes
  (thanks to `@glormph <https://github.com/glormph>`__).
  `Pull Request 3737`_
* Modify our docs in preparation for restructuring.
  `Pull Request 3738`_
* Update codefile documentation in tool XSD with info from old Wiki.
  `Pull Request 3739`_
* Mirror latest galaxy-lib changes for Conda and CWL improvements.
  `Pull Request 3742`_
* Add the possibility to uninstall Conda environments that are not in use by
  Galaxy
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3750`_
* New Authentication section of the docs.
  `Pull Request 3751`_
* Bump routes requirement to 2.4.1 .
  `Pull Request 3752`_
* Abstract uWSGI handling into new galaxy.web.stack package.
  `Pull Request 3759`_
* i18n improvements and French localization.
  `Pull Request 3762`_
* Should exit immediately to avoid index error
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3770`_
* Made collection operations help sections slightly more readable.
  `Pull Request 3784`_
* Avoid potential inconsistencies between differently stored labels.
  `Pull Request 3793`_
* Remove custom builds mako.
  `Pull Request 3794`_
* Small enhancements for collection builders.
  `Pull Request 3806`_
* Small improvements for driving Qunit tests.
  `Pull Request 3810`_
* Implement more upload testing in Selenium.
  `Pull Request 3811`_
* API & reports documentation improvements.
  `Pull Request 3812`_
* Make ToolConfWatcher watch ToolCache
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3814`_
* Disable tool shed test function that fails frequently on Jenkins.
  `Pull Request 3819`_
* Restrict workflow scheduling within a history to a fixed, random handler.
  `Pull Request 3820`_
* Order processing evaluation of workflow invocations when scheduling.
  `Pull Request 3830`_
* Stricter checks for GFF/GFF3/GTF datatypes sniffing
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3832`_
* Add root redirect for backbone router.
  `Pull Request 3837`_
* Allow explicit configuration of handlers for workflow scheduling.
  `Pull Request 3844`_
* Log reason when workflow scheduling of a step is delayed.
  `Pull Request 3849`_
* Update datatypes_conf.xml.sample
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 3852`_
* Clean up old TODO into history tests.
  `Pull Request 3855`_
* Small changes to links and add Gitter
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3861`_
* Use detect_errors="exit_code" in Trim tool
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3869`_
* Synchronise against latest UCSC versions
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3874`_
* Hardklor and kronik datatypes for proteomics
  (thanks to `@glormph <https://github.com/glormph>`__).
  `Pull Request 3884`_
* History drag-and-drop feature with iframe support for run workflow form.
  `Pull Request 3886`_
* Update to a new Docker test image to fix dependency bugs.
  `Pull Request 3890`_
* Python3: Use shlex_quote() from six.moves instead of pipes.quote()
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3891`_
* Add a validator that ensures a dataset's extra_files_path
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 3918`_
* Update text.py  Add interaction annotations to SnpEffDb metadata
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 3938`_
* Collection operation: Filtering from a file.
  `Pull Request 3940`_
* Remove Google from OpenID providers in the sample.
  `Pull Request 3953`_
* Change 'User' menu to 'Login or Register' for anonymous users.
  `Pull Request 3955`_
* Stats docs
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3968`_
* Enhance filenames with collection context when downloading datasets from
  GUI.
  `Pull Request 3985`_
* Displaying a message instead of just redirecting.
  `Pull Request 4000`_
* Implicitly set use_volumes = False if using Docker swarm.
  `Pull Request 4006`_
* Update Jupyter image to 17.05 .
  `Pull Request 4007`_
* Inline CSS in error report email
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3445`_
* Improve routing for user preference views.
  `Pull Request 3446`_
* Tool documentation and testing improvements.
  `Pull Request 3457`_
* Update readme badges.
  `Pull Request 3465`_
* Lint some tools
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3468`_
* Improve release issue docs.
  `Pull Request 3496`_
* Watch tool data table ``*.loc`` files, and reload if modified
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3533`_

.. small_enhancement

* Attempt work around for race-y sort of condition in Selenium sizzle
  checkers.
  `Pull Request 3451`_
* Webhooks: add tests
  (thanks to `@anatskiy <https://github.com/anatskiy>`__).
  `Pull Request 3469`_
* Disable transiently failing tour test.
  `Pull Request 3599`_
* Selenium testing improvements.
  `Pull Request 3716`_
* Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox()
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3732`_
* Abstraction for re-use between collection creators.
  `Pull Request 3781`_
* Merge ToolConfWatchers and separate from Toolbox
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3821`_
* Attempt to improve the robustness and verboseness of the test_sharing_valid
  Selenium test.
  `Pull Request 3841`_
* Routes cleanup.
  `Pull Request 3895`_
* Standardize usage of log.exception .
  `Pull Request 3933`_
* Followup to exception refactoring.
  `Pull Request 3959`_
* Use container-based infrastructure (sudo: false) in TravisCI
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3977`_
* Improve implicit workflow connection test case.
  `Pull Request 3991`_


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

.. major_bug


.. bug

* Fix tag escaping.
  `Pull Request 3720`_
* Fix kombu documentation link in galaxy.ini.sample .
  `Pull Request 3629`_
* Fix for EtherCalc IE image specification.
  `Pull Request 3825`_
* Fix margin style values for color picker element.
  `Pull Request 3965`_
* 17.05 rstudio fixes / one small GIE fix
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3975`_
* Fix transiently failing Selenium upload test.
  `Pull Request 3587`_
* Fix webhook search overlay interfering with masthead load.
  `Pull Request 3731`_
* Fix collection operations in workflows.
  `Pull Request 3848`_
* Remove old, unused search controller.
  `Pull Request 3894`_
* Deduplicate obsolete API readme.
  `Pull Request 3777`_
* Assorted fixes for dockerized test setup.
  `Pull Request 3755`_
* Another fix for Selenium testing on Jenkins.
  `Pull Request 3422`_
* Fix most broken Selenium tests.
  `Pull Request 3440`_
* Fix for transiently failing workflow test.
  `Pull Request 3668`_
* Fix selenium workflow tests broken with `#3181
  <https://github.com/galaxyproject/galaxy/issues/3181>`__.
  `Pull Request 3504`_
* Fix integration test for default Conda mapping.
  `Pull Request 3508`_
* Various fixes for test image Docker user switching.
  `Pull Request 3443`_
* Fix Travix builds which use flake8-docstrings
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3981`_
* Azure - Leasing container sometimes breaks things in Docker Galaxy
  (thanks to `@zfrenchee <https://github.com/zfrenchee>`__).
  `Pull Request 3263`_
* run_tests.sh: a small typo
  (thanks to `@anatskiy <https://github.com/anatskiy>`__).
  `Pull Request 3322`_
* Fix cycle detection for single node workflows.
  `Pull Request 3374`_
* Small selenium hack to fix occasionally failing collection upload tests.
  `Pull Request 3967`_
* Bug fix in mulled.py
  (thanks to `@abdulrahmanazab <https://github.com/abdulrahmanazab>`__).
  `Pull Request 3434`_
* Do not select first value as default if select value is optional.
  `Pull Request 3472`_
* jsonify initial value when returned through to_dict caller.
  `Pull Request 3513`_
* Fix <is_valid_xml> output test assert check
  (thanks to `@jvolkening <https://github.com/jvolkening>`__).
  `Pull Request 3530`_
* Fix output tests for checksum example tools.
  `Pull Request 3545`_
* Update Nagios check.
  `Pull Request 3568`_
* Set 'deleted' to True when purging a history dataset association
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3572`_
* Update tool XSD for (hopefully deprecated) change_format syntax.
  `Pull Request 3579`_
* Remove broken tour step.
  `Pull Request 3582`_
* Avoid step duplication when ordering steps on the fly.
  `Pull Request 3590`_
* Minor fix of core.galaxy-ui tour.
  `Pull Request 3608`_
* Fix RELEASE_ISSUE_TEMPLATE in bootstrap_history.py
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3653`_
* Update dynamic_tool_destination.py
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 3655`_
* Ignore Node modules installed for the GIE proxy when linting.
  `Pull Request 3664`_
* Logout recalc improvements.
  `Pull Request 3669`_
* Strip broken autocomplete feature, webbrowsers console error is an artifact.
  `Pull Request 3676`_
* Generate primary composite file after extra files collection.
  `Pull Request 3678`_
* Fix tool search index building for tools with slash in id and not from
  ToolShed.
  `Pull Request 3680`_
* Set $HOME to a temp directory rather than conda_prefix because conda_prefix
  may not be writable either.
  `Pull Request 3701`_
* Properly handle boolean values when parsed to a string-based/default tool
  parameter.
  `Pull Request 3702`_
* Mothur datatypes: fix metadata failure for large count tables
  (thanks to `@shiltemann <https://github.com/shiltemann>`__).
  `Pull Request 3706`_
* Filename handling for FTP upload.
  `Pull Request 3722`_
* Do not require stored workflow id for subworkflows.
  `Pull Request 3723`_
* Remove outdated items from tool cache when reloading the toolbox
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3729`_
* Change API path in docstrings to correct /api/dependency_resolvers/*
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3749`_
* Wiki to hub link update.
  `Pull Request 3754`_
* Fix KeyError when getting request and response content-type headers
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3757`_
* Fix for uploading rdata datasets when explicitly declaring datatype.
  `Pull Request 3766`_
* Fixes for users API.
  `Pull Request 3771`_
* Fix XSS vulnerability in grids.
  `Pull Request 3776`_
* Layered routing fix for when controller route fails and client route does
  not exist.
  `Pull Request 3783`_
* Fix collection operations not having a history.
  `Pull Request 3786`_
* Fix problem with cleaning up jobs in local runner.
  `Pull Request 3803`_
* Have tool-search listen to change as well as keyup.
  `Pull Request 3808`_
* Fix BED dataset display in Trackster
  (thanks to `@hrhotz <https://github.com/hrhotz>`__).
  `Pull Request 3822`_
* More CONVERTER fixes for restricting tools' Python environment.
  `Pull Request 3824`_
* Have IGV bigWig display application make use of build_sites/ site_type config
  instead of direct filename.
  `Pull Request 3828`_
* Properly handle multiple hidden datasets when populating data select options.
  `Pull Request 3842`_
* Fix for direct message routing using a 'real' exchange like RabbitMQ.
  `Pull Request 3846`_
* Fix setting UUID on steps when copying steps from another workflow.
  `Pull Request 3856`_
* Fix certain aspects of collection reductions in conditionals/repeats.
  `Pull Request 3864`_
* Fix multiple collection reductions on multiple data parameters.
  `Pull Request 3875`_
* Fix inability for viz to raise loading with non-ascii messages
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3881`_
* Fix new history endpoint providing custom builds metadata.
  `Pull Request 3887`_
* Remove unused model import from users API.
  `Pull Request 3888`_
* Cytoscape bugfix for SIF files
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 3896`_
* Add missing trigger event to drop handler in content selector.
  `Pull Request 3897`_
* Fix Instance is not bound to a Session
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3904`_
* Fix library parameter style width to avoid second line.
  `Pull Request 3926`_
* More careful inspection of fixes for MAF tools requiring Galaxy.
  `Pull Request 3935`_
* Containers interface and GIE bugfixes.
  `Pull Request 3941`_
* Show default value for runtime values.
  `Pull Request 3943`_
* Fix JJ's column_join tool depending on Galaxy at runtime.
  `Pull Request 3961`_
* Fix edge case for workflow mapping handling when tools not available.
  `Pull Request 3962`_
* Tour fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3970`_
* Fix some typos in config/galaxy.ini.sample
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3971`_
* Add two tools from str_fm repository to galaxy module whitelist.
  `Pull Request 3973`_
* Remote user logout fixes, rework header handling a bit.
  `Pull Request 3976`_
* Fixes to get GIEs working on Mac OS X.
  `Pull Request 3978`_
* Rework Jupyter IE for additional_ids handling.
  `Pull Request 3980`_
* Update Babel to a version compat. with sphinx.
  `Pull Request 3986`_
* Use the configured tool_path when loading data managers.
  `Pull Request 3989`_
* Typo in remote user / user preferences exception
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4015`_
* Fix setting up explicit container resolution from a container resolution
  config file.
  `Pull Request 4020`_
* Fix spelling error in error message
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 4026`_
* Fixes for containerized job executions.
  `Pull Request 4033`_
* Try activating Conda environment again if previous activation failed
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4035`_
* HTCondor fix for running containers
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4038`_
* Fix destructive tag rerender to be a simpler, more precise html replacement.
  `Pull Request 4052`_
* Fix for S3ObjectStore _clean_cache method.
  `Pull Request 4055`_
* Correct webhooks to use Galaxy.root and be compatible with proxy_prefix
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 4065`_
* Fix global grid action event handler.
  `Pull Request 4068`_
* Fix various transiently failing Selenium tests.
  `Pull Request 3450`_
* Do not modify self.app.config.tool_data_path and
  self.app.config.tool_data_table_config_path during metadata setting
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 4089`_
* Open Babel update for datatype converters
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 4094`_
* Change to only inheriting 'name' tags.
  `Pull Request 4104`_
* Fixes repeat handling in workflow editor, store values as passed from UI.
  `Pull Request 4107`_

.. github_links
.. _Pull Request 3104: https://github.com/galaxyproject/galaxy/pull/3104
.. _Pull Request 3181: https://github.com/galaxyproject/galaxy/pull/3181
.. _Pull Request 3263: https://github.com/galaxyproject/galaxy/pull/3263
.. _Pull Request 3322: https://github.com/galaxyproject/galaxy/pull/3322
.. _Pull Request 3374: https://github.com/galaxyproject/galaxy/pull/3374
.. _Pull Request 3385: https://github.com/galaxyproject/galaxy/pull/3385
.. _Pull Request 3407: https://github.com/galaxyproject/galaxy/pull/3407
.. _Pull Request 3420: https://github.com/galaxyproject/galaxy/pull/3420
.. _Pull Request 3422: https://github.com/galaxyproject/galaxy/pull/3422
.. _Pull Request 3434: https://github.com/galaxyproject/galaxy/pull/3434
.. _Pull Request 3440: https://github.com/galaxyproject/galaxy/pull/3440
.. _Pull Request 3443: https://github.com/galaxyproject/galaxy/pull/3443
.. _Pull Request 3445: https://github.com/galaxyproject/galaxy/pull/3445
.. _Pull Request 3446: https://github.com/galaxyproject/galaxy/pull/3446
.. _Pull Request 3450: https://github.com/galaxyproject/galaxy/pull/3450
.. _Pull Request 3451: https://github.com/galaxyproject/galaxy/pull/3451
.. _Pull Request 3457: https://github.com/galaxyproject/galaxy/pull/3457
.. _Pull Request 3460: https://github.com/galaxyproject/galaxy/pull/3460
.. _Pull Request 3465: https://github.com/galaxyproject/galaxy/pull/3465
.. _Pull Request 3468: https://github.com/galaxyproject/galaxy/pull/3468
.. _Pull Request 3469: https://github.com/galaxyproject/galaxy/pull/3469
.. _Pull Request 3472: https://github.com/galaxyproject/galaxy/pull/3472
.. _Pull Request 3478: https://github.com/galaxyproject/galaxy/pull/3478
.. _Pull Request 3479: https://github.com/galaxyproject/galaxy/pull/3479
.. _Pull Request 3484: https://github.com/galaxyproject/galaxy/pull/3484
.. _Pull Request 3491: https://github.com/galaxyproject/galaxy/pull/3491
.. _Pull Request 3496: https://github.com/galaxyproject/galaxy/pull/3496
.. _Pull Request 3503: https://github.com/galaxyproject/galaxy/pull/3503
.. _Pull Request 3504: https://github.com/galaxyproject/galaxy/pull/3504
.. _Pull Request 3508: https://github.com/galaxyproject/galaxy/pull/3508
.. _Pull Request 3512: https://github.com/galaxyproject/galaxy/pull/3512
.. _Pull Request 3513: https://github.com/galaxyproject/galaxy/pull/3513
.. _Pull Request 3515: https://github.com/galaxyproject/galaxy/pull/3515
.. _Pull Request 3522: https://github.com/galaxyproject/galaxy/pull/3522
.. _Pull Request 3523: https://github.com/galaxyproject/galaxy/pull/3523
.. _Pull Request 3530: https://github.com/galaxyproject/galaxy/pull/3530
.. _Pull Request 3531: https://github.com/galaxyproject/galaxy/pull/3531
.. _Pull Request 3533: https://github.com/galaxyproject/galaxy/pull/3533
.. _Pull Request 3545: https://github.com/galaxyproject/galaxy/pull/3545
.. _Pull Request 3550: https://github.com/galaxyproject/galaxy/pull/3550
.. _Pull Request 3553: https://github.com/galaxyproject/galaxy/pull/3553
.. _Pull Request 3559: https://github.com/galaxyproject/galaxy/pull/3559
.. _Pull Request 3562: https://github.com/galaxyproject/galaxy/pull/3562
.. _Pull Request 3564: https://github.com/galaxyproject/galaxy/pull/3564
.. _Pull Request 3565: https://github.com/galaxyproject/galaxy/pull/3565
.. _Pull Request 3568: https://github.com/galaxyproject/galaxy/pull/3568
.. _Pull Request 3569: https://github.com/galaxyproject/galaxy/pull/3569
.. _Pull Request 3570: https://github.com/galaxyproject/galaxy/pull/3570
.. _Pull Request 3572: https://github.com/galaxyproject/galaxy/pull/3572
.. _Pull Request 3576: https://github.com/galaxyproject/galaxy/pull/3576
.. _Pull Request 3579: https://github.com/galaxyproject/galaxy/pull/3579
.. _Pull Request 3580: https://github.com/galaxyproject/galaxy/pull/3580
.. _Pull Request 3582: https://github.com/galaxyproject/galaxy/pull/3582
.. _Pull Request 3583: https://github.com/galaxyproject/galaxy/pull/3583
.. _Pull Request 3584: https://github.com/galaxyproject/galaxy/pull/3584
.. _Pull Request 3587: https://github.com/galaxyproject/galaxy/pull/3587
.. _Pull Request 3589: https://github.com/galaxyproject/galaxy/pull/3589
.. _Pull Request 3590: https://github.com/galaxyproject/galaxy/pull/3590
.. _Pull Request 3593: https://github.com/galaxyproject/galaxy/pull/3593
.. _Pull Request 3594: https://github.com/galaxyproject/galaxy/pull/3594
.. _Pull Request 3596: https://github.com/galaxyproject/galaxy/pull/3596
.. _Pull Request 3599: https://github.com/galaxyproject/galaxy/pull/3599
.. _Pull Request 3600: https://github.com/galaxyproject/galaxy/pull/3600
.. _Pull Request 3601: https://github.com/galaxyproject/galaxy/pull/3601
.. _Pull Request 3603: https://github.com/galaxyproject/galaxy/pull/3603
.. _Pull Request 3608: https://github.com/galaxyproject/galaxy/pull/3608
.. _Pull Request 3616: https://github.com/galaxyproject/galaxy/pull/3616
.. _Pull Request 3618: https://github.com/galaxyproject/galaxy/pull/3618
.. _Pull Request 3619: https://github.com/galaxyproject/galaxy/pull/3619
.. _Pull Request 3622: https://github.com/galaxyproject/galaxy/pull/3622
.. _Pull Request 3625: https://github.com/galaxyproject/galaxy/pull/3625
.. _Pull Request 3629: https://github.com/galaxyproject/galaxy/pull/3629
.. _Pull Request 3641: https://github.com/galaxyproject/galaxy/pull/3641
.. _Pull Request 3643: https://github.com/galaxyproject/galaxy/pull/3643
.. _Pull Request 3644: https://github.com/galaxyproject/galaxy/pull/3644
.. _Pull Request 3649: https://github.com/galaxyproject/galaxy/pull/3649
.. _Pull Request 3652: https://github.com/galaxyproject/galaxy/pull/3652
.. _Pull Request 3653: https://github.com/galaxyproject/galaxy/pull/3653
.. _Pull Request 3654: https://github.com/galaxyproject/galaxy/pull/3654
.. _Pull Request 3655: https://github.com/galaxyproject/galaxy/pull/3655
.. _Pull Request 3657: https://github.com/galaxyproject/galaxy/pull/3657
.. _Pull Request 3659: https://github.com/galaxyproject/galaxy/pull/3659
.. _Pull Request 3661: https://github.com/galaxyproject/galaxy/pull/3661
.. _Pull Request 3662: https://github.com/galaxyproject/galaxy/pull/3662
.. _Pull Request 3663: https://github.com/galaxyproject/galaxy/pull/3663
.. _Pull Request 3664: https://github.com/galaxyproject/galaxy/pull/3664
.. _Pull Request 3665: https://github.com/galaxyproject/galaxy/pull/3665
.. _Pull Request 3666: https://github.com/galaxyproject/galaxy/pull/3666
.. _Pull Request 3668: https://github.com/galaxyproject/galaxy/pull/3668
.. _Pull Request 3669: https://github.com/galaxyproject/galaxy/pull/3669
.. _Pull Request 3671: https://github.com/galaxyproject/galaxy/pull/3671
.. _Pull Request 3674: https://github.com/galaxyproject/galaxy/pull/3674
.. _Pull Request 3676: https://github.com/galaxyproject/galaxy/pull/3676
.. _Pull Request 3678: https://github.com/galaxyproject/galaxy/pull/3678
.. _Pull Request 3680: https://github.com/galaxyproject/galaxy/pull/3680
.. _Pull Request 3688: https://github.com/galaxyproject/galaxy/pull/3688
.. _Pull Request 3696: https://github.com/galaxyproject/galaxy/pull/3696
.. _Pull Request 3698: https://github.com/galaxyproject/galaxy/pull/3698
.. _Pull Request 3699: https://github.com/galaxyproject/galaxy/pull/3699
.. _Pull Request 3701: https://github.com/galaxyproject/galaxy/pull/3701
.. _Pull Request 3702: https://github.com/galaxyproject/galaxy/pull/3702
.. _Pull Request 3704: https://github.com/galaxyproject/galaxy/pull/3704
.. _Pull Request 3706: https://github.com/galaxyproject/galaxy/pull/3706
.. _Pull Request 3708: https://github.com/galaxyproject/galaxy/pull/3708
.. _Pull Request 3715: https://github.com/galaxyproject/galaxy/pull/3715
.. _Pull Request 3716: https://github.com/galaxyproject/galaxy/pull/3716
.. _Pull Request 3718: https://github.com/galaxyproject/galaxy/pull/3718
.. _Pull Request 3719: https://github.com/galaxyproject/galaxy/pull/3719
.. _Pull Request 3720: https://github.com/galaxyproject/galaxy/pull/3720
.. _Pull Request 3722: https://github.com/galaxyproject/galaxy/pull/3722
.. _Pull Request 3723: https://github.com/galaxyproject/galaxy/pull/3723
.. _Pull Request 3725: https://github.com/galaxyproject/galaxy/pull/3725
.. _Pull Request 3729: https://github.com/galaxyproject/galaxy/pull/3729
.. _Pull Request 3731: https://github.com/galaxyproject/galaxy/pull/3731
.. _Pull Request 3732: https://github.com/galaxyproject/galaxy/pull/3732
.. _Pull Request 3734: https://github.com/galaxyproject/galaxy/pull/3734
.. _Pull Request 3737: https://github.com/galaxyproject/galaxy/pull/3737
.. _Pull Request 3738: https://github.com/galaxyproject/galaxy/pull/3738
.. _Pull Request 3739: https://github.com/galaxyproject/galaxy/pull/3739
.. _Pull Request 3740: https://github.com/galaxyproject/galaxy/pull/3740
.. _Pull Request 3742: https://github.com/galaxyproject/galaxy/pull/3742
.. _Pull Request 3746: https://github.com/galaxyproject/galaxy/pull/3746
.. _Pull Request 3749: https://github.com/galaxyproject/galaxy/pull/3749
.. _Pull Request 3750: https://github.com/galaxyproject/galaxy/pull/3750
.. _Pull Request 3751: https://github.com/galaxyproject/galaxy/pull/3751
.. _Pull Request 3752: https://github.com/galaxyproject/galaxy/pull/3752
.. _Pull Request 3753: https://github.com/galaxyproject/galaxy/pull/3753
.. _Pull Request 3754: https://github.com/galaxyproject/galaxy/pull/3754
.. _Pull Request 3755: https://github.com/galaxyproject/galaxy/pull/3755
.. _Pull Request 3757: https://github.com/galaxyproject/galaxy/pull/3757
.. _Pull Request 3759: https://github.com/galaxyproject/galaxy/pull/3759
.. _Pull Request 3760: https://github.com/galaxyproject/galaxy/pull/3760
.. _Pull Request 3762: https://github.com/galaxyproject/galaxy/pull/3762
.. _Pull Request 3766: https://github.com/galaxyproject/galaxy/pull/3766
.. _Pull Request 3768: https://github.com/galaxyproject/galaxy/pull/3768
.. _Pull Request 3770: https://github.com/galaxyproject/galaxy/pull/3770
.. _Pull Request 3771: https://github.com/galaxyproject/galaxy/pull/3771
.. _Pull Request 3776: https://github.com/galaxyproject/galaxy/pull/3776
.. _Pull Request 3777: https://github.com/galaxyproject/galaxy/pull/3777
.. _Pull Request 3781: https://github.com/galaxyproject/galaxy/pull/3781
.. _Pull Request 3783: https://github.com/galaxyproject/galaxy/pull/3783
.. _Pull Request 3784: https://github.com/galaxyproject/galaxy/pull/3784
.. _Pull Request 3786: https://github.com/galaxyproject/galaxy/pull/3786
.. _Pull Request 3793: https://github.com/galaxyproject/galaxy/pull/3793
.. _Pull Request 3794: https://github.com/galaxyproject/galaxy/pull/3794
.. _Pull Request 3799: https://github.com/galaxyproject/galaxy/pull/3799
.. _Pull Request 3803: https://github.com/galaxyproject/galaxy/pull/3803
.. _Pull Request 3805: https://github.com/galaxyproject/galaxy/pull/3805
.. _Pull Request 3806: https://github.com/galaxyproject/galaxy/pull/3806
.. _Pull Request 3808: https://github.com/galaxyproject/galaxy/pull/3808
.. _Pull Request 3809: https://github.com/galaxyproject/galaxy/pull/3809
.. _Pull Request 3810: https://github.com/galaxyproject/galaxy/pull/3810
.. _Pull Request 3811: https://github.com/galaxyproject/galaxy/pull/3811
.. _Pull Request 3812: https://github.com/galaxyproject/galaxy/pull/3812
.. _Pull Request 3814: https://github.com/galaxyproject/galaxy/pull/3814
.. _Pull Request 3817: https://github.com/galaxyproject/galaxy/pull/3817
.. _Pull Request 3819: https://github.com/galaxyproject/galaxy/pull/3819
.. _Pull Request 3820: https://github.com/galaxyproject/galaxy/pull/3820
.. _Pull Request 3821: https://github.com/galaxyproject/galaxy/pull/3821
.. _Pull Request 3822: https://github.com/galaxyproject/galaxy/pull/3822
.. _Pull Request 3824: https://github.com/galaxyproject/galaxy/pull/3824
.. _Pull Request 3825: https://github.com/galaxyproject/galaxy/pull/3825
.. _Pull Request 3828: https://github.com/galaxyproject/galaxy/pull/3828
.. _Pull Request 3830: https://github.com/galaxyproject/galaxy/pull/3830
.. _Pull Request 3832: https://github.com/galaxyproject/galaxy/pull/3832
.. _Pull Request 3837: https://github.com/galaxyproject/galaxy/pull/3837
.. _Pull Request 3841: https://github.com/galaxyproject/galaxy/pull/3841
.. _Pull Request 3842: https://github.com/galaxyproject/galaxy/pull/3842
.. _Pull Request 3844: https://github.com/galaxyproject/galaxy/pull/3844
.. _Pull Request 3846: https://github.com/galaxyproject/galaxy/pull/3846
.. _Pull Request 3848: https://github.com/galaxyproject/galaxy/pull/3848
.. _Pull Request 3849: https://github.com/galaxyproject/galaxy/pull/3849
.. _Pull Request 3850: https://github.com/galaxyproject/galaxy/pull/3850
.. _Pull Request 3852: https://github.com/galaxyproject/galaxy/pull/3852
.. _Pull Request 3855: https://github.com/galaxyproject/galaxy/pull/3855
.. _Pull Request 3856: https://github.com/galaxyproject/galaxy/pull/3856
.. _Pull Request 3857: https://github.com/galaxyproject/galaxy/pull/3857
.. _Pull Request 3861: https://github.com/galaxyproject/galaxy/pull/3861
.. _Pull Request 3863: https://github.com/galaxyproject/galaxy/pull/3863
.. _Pull Request 3864: https://github.com/galaxyproject/galaxy/pull/3864
.. _Pull Request 3868: https://github.com/galaxyproject/galaxy/pull/3868
.. _Pull Request 3869: https://github.com/galaxyproject/galaxy/pull/3869
.. _Pull Request 3871: https://github.com/galaxyproject/galaxy/pull/3871
.. _Pull Request 3874: https://github.com/galaxyproject/galaxy/pull/3874
.. _Pull Request 3875: https://github.com/galaxyproject/galaxy/pull/3875
.. _Pull Request 3881: https://github.com/galaxyproject/galaxy/pull/3881
.. _Pull Request 3884: https://github.com/galaxyproject/galaxy/pull/3884
.. _Pull Request 3886: https://github.com/galaxyproject/galaxy/pull/3886
.. _Pull Request 3887: https://github.com/galaxyproject/galaxy/pull/3887
.. _Pull Request 3888: https://github.com/galaxyproject/galaxy/pull/3888
.. _Pull Request 3889: https://github.com/galaxyproject/galaxy/pull/3889
.. _Pull Request 3890: https://github.com/galaxyproject/galaxy/pull/3890
.. _Pull Request 3891: https://github.com/galaxyproject/galaxy/pull/3891
.. _Pull Request 3894: https://github.com/galaxyproject/galaxy/pull/3894
.. _Pull Request 3895: https://github.com/galaxyproject/galaxy/pull/3895
.. _Pull Request 3896: https://github.com/galaxyproject/galaxy/pull/3896
.. _Pull Request 3897: https://github.com/galaxyproject/galaxy/pull/3897
.. _Pull Request 3904: https://github.com/galaxyproject/galaxy/pull/3904
.. _Pull Request 3909: https://github.com/galaxyproject/galaxy/pull/3909
.. _Pull Request 3918: https://github.com/galaxyproject/galaxy/pull/3918
.. _Pull Request 3920: https://github.com/galaxyproject/galaxy/pull/3920
.. _Pull Request 3926: https://github.com/galaxyproject/galaxy/pull/3926
.. _Pull Request 3931: https://github.com/galaxyproject/galaxy/pull/3931
.. _Pull Request 3933: https://github.com/galaxyproject/galaxy/pull/3933
.. _Pull Request 3935: https://github.com/galaxyproject/galaxy/pull/3935
.. _Pull Request 3938: https://github.com/galaxyproject/galaxy/pull/3938
.. _Pull Request 3940: https://github.com/galaxyproject/galaxy/pull/3940
.. _Pull Request 3941: https://github.com/galaxyproject/galaxy/pull/3941
.. _Pull Request 3943: https://github.com/galaxyproject/galaxy/pull/3943
.. _Pull Request 3953: https://github.com/galaxyproject/galaxy/pull/3953
.. _Pull Request 3955: https://github.com/galaxyproject/galaxy/pull/3955
.. _Pull Request 3956: https://github.com/galaxyproject/galaxy/pull/3956
.. _Pull Request 3959: https://github.com/galaxyproject/galaxy/pull/3959
.. _Pull Request 3961: https://github.com/galaxyproject/galaxy/pull/3961
.. _Pull Request 3962: https://github.com/galaxyproject/galaxy/pull/3962
.. _Pull Request 3964: https://github.com/galaxyproject/galaxy/pull/3964
.. _Pull Request 3965: https://github.com/galaxyproject/galaxy/pull/3965
.. _Pull Request 3967: https://github.com/galaxyproject/galaxy/pull/3967
.. _Pull Request 3968: https://github.com/galaxyproject/galaxy/pull/3968
.. _Pull Request 3970: https://github.com/galaxyproject/galaxy/pull/3970
.. _Pull Request 3971: https://github.com/galaxyproject/galaxy/pull/3971
.. _Pull Request 3973: https://github.com/galaxyproject/galaxy/pull/3973
.. _Pull Request 3975: https://github.com/galaxyproject/galaxy/pull/3975
.. _Pull Request 3976: https://github.com/galaxyproject/galaxy/pull/3976
.. _Pull Request 3977: https://github.com/galaxyproject/galaxy/pull/3977
.. _Pull Request 3978: https://github.com/galaxyproject/galaxy/pull/3978
.. _Pull Request 3979: https://github.com/galaxyproject/galaxy/pull/3979
.. _Pull Request 3980: https://github.com/galaxyproject/galaxy/pull/3980
.. _Pull Request 3981: https://github.com/galaxyproject/galaxy/pull/3981
.. _Pull Request 3985: https://github.com/galaxyproject/galaxy/pull/3985
.. _Pull Request 3986: https://github.com/galaxyproject/galaxy/pull/3986
.. _Pull Request 3988: https://github.com/galaxyproject/galaxy/pull/3988
.. _Pull Request 3989: https://github.com/galaxyproject/galaxy/pull/3989
.. _Pull Request 3991: https://github.com/galaxyproject/galaxy/pull/3991
.. _Pull Request 3996: https://github.com/galaxyproject/galaxy/pull/3996
.. _Pull Request 4000: https://github.com/galaxyproject/galaxy/pull/4000
.. _Pull Request 4004: https://github.com/galaxyproject/galaxy/pull/4004
.. _Pull Request 4006: https://github.com/galaxyproject/galaxy/pull/4006
.. _Pull Request 4007: https://github.com/galaxyproject/galaxy/pull/4007
.. _Pull Request 4009: https://github.com/galaxyproject/galaxy/pull/4009
.. _Pull Request 4012: https://github.com/galaxyproject/galaxy/pull/4012
.. _Pull Request 4015: https://github.com/galaxyproject/galaxy/pull/4015
.. _Pull Request 4017: https://github.com/galaxyproject/galaxy/pull/4017
.. _Pull Request 4020: https://github.com/galaxyproject/galaxy/pull/4020
.. _Pull Request 4026: https://github.com/galaxyproject/galaxy/pull/4026
.. _Pull Request 4033: https://github.com/galaxyproject/galaxy/pull/4033
.. _Pull Request 4035: https://github.com/galaxyproject/galaxy/pull/4035
.. _Pull Request 4038: https://github.com/galaxyproject/galaxy/pull/4038
.. _Pull Request 4052: https://github.com/galaxyproject/galaxy/pull/4052
.. _Pull Request 4055: https://github.com/galaxyproject/galaxy/pull/4055
.. _Pull Request 4058: https://github.com/galaxyproject/galaxy/pull/4058
.. _Pull Request 4065: https://github.com/galaxyproject/galaxy/pull/4065
.. _Pull Request 4068: https://github.com/galaxyproject/galaxy/pull/4068
.. _Pull Request 4089: https://github.com/galaxyproject/galaxy/pull/4089
.. _Pull Request 4094: https://github.com/galaxyproject/galaxy/pull/4094
.. _Pull Request 4104: https://github.com/galaxyproject/galaxy/pull/4104
.. _Pull Request 4107: https://github.com/galaxyproject/galaxy/pull/4107

