.. to_doc

16.10
===============================

.. announce_start

Highlighted Enhancements
------------------------

.. major_feature

* Overhaul of charts visualization - more visualizations, more options, and better user interface.
  `Pull Request 2875`_, `Pull Request 2820`_
* Paginate contents of large histories.
  `Pull Request 2588`_
* Implement a collection operation tool for merging collections
  (thanks to `@Takadonet <https://github.com/Takadonet>`__).
  `Pull Request 2771`_
* Replace :doc:`reference documentation <../dev/schema>`
  for tool XML files with automatically generated
  documentation from a now official Galaxy XSD documentation (with help from many).
  `Pull Request 2923`_, `Pull Request 2936`_, `Pull Request 3086`_,
  `Pull Request 2932`_, `Pull Request 2903`_, `Pull Request 3020`_,
  `Pull Request 3072`_
* Add a password strength evaluation bar
  (thanks to `@benfulton <https://github.com/benfulton>`__).
  `Pull Request 2687`_
* Implement a GoDocker job runner
  (thanks to `@varunshankar <https://github.com/varunshankar>`__).
  `Pull Request 2791`_, `Pull Request 2653`_
* Support for API batch requests.
  `Pull Request 1768`_
* Allow JSONP to be returned from API endpoints.
  `Pull Request 2937`_
* Add "Save as" as an option in the workflow editor
  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
  `Pull Request 3035`_
* Allow naming input datasets and collections during workflow extraction.
  `Pull Request 2943`_
* Various enhancements for API driven installation of tool shed repositories.

Security
-------------------------------

.. security

* Fix an ACE vulnerability with gff filter tools (thanks to David Wyde).
  `Commit c1e3087`_
* Escape filename in upload dialog, default and composite (thanks to David Wyde).
  `Pull Request 3278`_

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

* Add "Save as" as an option in the workflow editor
  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
  `Pull Request 3035`_
* Allow '.' and '_' for public names
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2947`_
* Allow naming input datasets and collections during workflow extraction.
  `Pull Request 2943`_
* Various enhancements for API driven installation of Tool Shed repositories.
  `Pull Request 2769`_
* Implement beta support for discovering biocontainer Docker containers automatically for tool dependencies.
  `Pull Request 2986`_
* Improved API support for downloading datasets and relevant files.
  `Pull Request 2741`_, `Pull Request 2885`_
* Make tool search field stay at top of window when tool list scrolls.
  (thanks to `@sszakony <https://github.com/sszakony>`__).
  `Pull Request 2730`_, `Issue 2375`_
* Scratchbook enhancement to include info and view details links for datasets.
  `Pull Request 2733`_
* Add implicit conversions target extension to HDA name when listed as
  selection option in the tool form.
  `Pull Request 2734`_
* Add column names to BED datatype so that column names are displayed in
  the dataset viewer.
  `Pull Request 2784`_
* Add "All" and "None" buttons to copy dataset view.
  `Pull Request 2957`_
* Lazy load workflow invocation steps to vastly improve scheduling performance of large
  collection workflows
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2978`_
* Add CEL datatype
  (thanks to `@nturaga <https://github.com/nturaga>`__).
  `Pull Request 3073`_
* Add a netcdf datatype for metabolomics spectre data
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 2706`_
* Returning Blast datatypes to Galaxy core
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 2696`_
* Add HDT format (with turtle format sniffer improvements)
  (thanks to `@jjkoehorst <https://github.com/jjkoehorst>`__).
  `Pull Request 2787`_
* Allow more configurability for containerized jobs.
  `Pull Request 2790`_
* Functionality to allow admins to switch on/off the line endings conversion
  on library dataset import
  (thanks to `@SANBI-SA <https://github.com/SANBI-SA>`__).
  `Pull Request 2819`_
* Add a tutorial on building job runners to the documentation
  (thanks to `@varunshankar <https://github.com/varunshankar>`__).
  `Pull Request 2700`_
* Allow viewing tool help from history datasets
  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
  `Pull Request 3051`_
* Prevent TS from creating sessions for repository status checks.
  `Pull Request 2732`_
* Shorten Conda environment names
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 2794`_
* Various release process improvements (including an enhancement from
  `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2857`_, `Pull Request 2858`_, `Pull Request 2689`_,
  `Pull Request 2865`_, `Pull Request 2952`_, `Pull Request 2695`_,
  `Pull Request 2991`_, `Pull Request 3232`_
* Improve samtools usage with ``--version-only`` check
  (thanks to `@remimarenco <https://github.com/remimarenco>`__).
  `Pull Request 2705`_
* All-around improvements to toolbox loading/reloading
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 2901`_
* Refactor shed tool lineage registration
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 2909`_
* Log the resolved dependency type
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 2917`_, `Pull Request 3036`_
* Fixes for Python 3 and new import linting for dozens of packages
  (largely thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2731`_, `Pull Request 3177`_, `Pull Request 2983`_,
  `Pull Request 2889`_, `Pull Request 3031`_, `Pull Request 3170`_,
  `Pull Request 3154`_
* Change every occurrence in the code of ``__all__`` from list to a tuple
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3041`_, `Pull Request 3071`_
* Docstring linting and fixes.
  `Pull Request 3003`_, `Pull Request 3004`_
* Update python-ldap module
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 2738`_
* Update sqlalchemy to 1.0.15 (from 1.0.8).
  `Pull Request 2979`_
* Slightly revise auto configuration of loggers.
  `Pull Request 2735`_
* Various ``Makefile`` improvements and fixes.
  `Pull Request 2757`_, `Pull Request 2688`_, `Pull Request 3167`_
* Improve startup scripts
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2765`_
* Remove ``enable_beta_tool_command_isolation`` config option
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2830`_
* Regularize comments configuration samples.
  `Pull Request 2824`_, `Pull Request 2841`_, `Pull Request 2814`_
* Skip whoami check for LDAP servers not supporting it
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2832`_
* Filter disposable mail blacklist on the first domain level only.
  `Pull Request 2839`_
* Refactor duplicated back-end code to create a new ``trans`` method for
  getting the most recently touched history.
  `Pull Request 2870`_
* Document setting column names in Galaxy tool XSD.
  `Pull Request 2965`_
* Functional test case for testing column names as meta-data
  (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__).
  `Pull Request 2970`_
* Improve ``version_command`` tag.
  `Pull Request 2961`_
* Add ``rgb`` option for color picker tool parameter.
  `Pull Request 3006`_
* Improved docs and testing for color parameters.
  `Pull Request 3016`_
* Add documentation on optional ``multiple="true"`` data parameters.
  `Pull Request 3024`_
* In Trackster, read numerical data directly from bigWig files.
  `Pull Request 2880`_
* Improve wording of tool installation forms
  (thanks to `@nturaga <https://github.com/nturaga>`__).
  `Pull Request 2893`_
* Add `database/dependencies` to  `.gitignore`
  (thanks to `@nturaga <https://github.com/nturaga>`__).
  `Pull Request 2904`_
* Allow admin to serialize/deserialize dataset permissions via the API.
  `Pull Request 2912`_
* Allow API access to genome fasta index and sequence
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 2939`_
* Extend ``PUT /api/workflows/{id}`` with additional workflow properties
  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
  `Pull Request 3080`_
* Remove unnecessary use of binascii
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2946`_
* Change wording to be more clear about how workflow output cleanup works.
  `Pull Request 2966`_
* Optimized workflow invocation step update.
  `Pull Request 2973`_
* Update issues.rst to bring inline with actual usage on Github.
  `Pull Request 2976`_
* Improve Conda FAQ documentation.
  `Pull Request 2998`_, `Pull Request 2891`_, `Pull Request 2871`_
* Add documentation for ``conda_copy_dependencies`` option
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 3105`_
* Slight clarification of run.sh messaging when using Conda.
  `Pull Request 3188`_
* Display tool requirements for conda-only tools
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3262`_
* Pass dependency shell command errors to log
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3129`_
* Increase min number of columns for pileup sniffing to 5
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3033`_
* Remove outdated warning on ID_SECRET
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 3046`_
* Add Galaxy architecture slides documentation to project.
  `Pull Request 3060`_, `Pull Request 3091`_
* Add tool XML reload to tool run page - for admins only
  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
  `Pull Request 3070`_, `Issue 943 <https://github.com/galaxyproject/galaxy/issues/943>`__
* Move thumbnail list view to shared UI elements, revise tabs, add test cases
  `Pull Request 3079`_
* Include filenames in .loc file DEBUG lines
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 3095`_
* Log loading of resources from .loc files
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 3099`_
* Eager load tags and annotations in history display.
  `Pull Request 3110`_
* Display an error message when toolbox filtering fails.
  `Pull Request 3123`_
* Bring in various updates from galaxy-lib.
  `Pull Request 3169`_, `Pull Request 2888`_
* Add links to local tours to sample welcome.
  `Pull Request 3176`_
* Fix dataset selector update when deleting history items.
  `Pull Request 2677`_
* Refactor upload dialog to use local CSS classes and avoid model listeners.
  `Pull Request 2711`_
* Rework Tool Shed middleware
  `Pull Request 2782`_, `Pull Request 2753`_
* Refactor - move filelock.py to galaxy.util.
  `Pull Request 2879`_
* Use requests in driver_util for better proxy handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3013`_
* Add ``download_to_file`` function to ``galaxy.util``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3100`_
* Quote all paths in converter tool XML files
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3165`_
* Add routes to get genomes indexes and sequences
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 3109`_
* Admin installation UX wording fixes.
  `Pull Request 3226`_

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

* Fix for bioconda recipes depending on conda-forge.
  `Pull Request 3023`_
* Fix history deletion bug when using impersonation.
  `Pull Request 2654`_
* Fix workflow extraction API tests on PostgreSQL
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3039`_
* Fix link target in admin view of tool lineages.
  `Pull Request 2862`_
* Avoid pointless lambda function
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 3097`_
* Remove unnecessary ``set_output_history`` parameter
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3155`_
* Fix BLAST database ``*.loc`` files inconsistency
  (thanks to `@peterjc <https://github.com/peterjc>`__).
  `Pull Request 3098`_
* Log invalid XML filename
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3124`_
* Various code fixes for object store and docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 3119`_
* Use default job history on ``build_for_rerun`` if current history is unavailable.
  `Pull Request 2668`_
* Always display text
  `Pull Request 3052`_
* Fixing button width on composite upload dialog
  (thanks to `@sszakony <https://github.com/sszakony>`__).
  `Pull Request 2703`_, `Issue 2591 <https://github.com/galaxyproject/galaxy/issues/2591>`__
* Fix for splitting dataset collections
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 2708`_
* Various datatypes fixes and enhancements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2690`_
* Various fixes and improvements for galaxy.json.
  `Pull Request 2697`_
* Fix tours pasting content into text area.
  `Pull Request 2715`_
* Slight styling tweak to prevent overflow on the right edge in composite upload dialog.
  `Pull Request 2716`_
* Workflow toolbox style updates.
  `Pull Request 2740`_
* Fix docker command_list
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 2748`_
* Fix ``list:list`` history display in the GUI.
  `Pull Request 2758`_
* Parse internal parameters such as job resource selections when data
  converter tools are executed implicitly.
  `Pull Request 2761`_
* Fix broken check when creating Docker volumes default for jobs
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 2763`_
* Fix to prevent login form from appearing in scratchbook window
  (thanks to `@sszakony <https://github.com/sszakony>`__).
  `Pull Request 2808`_
* Allow NodeJS proxy to do reverse proxying
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 2817`_
* Fixes for the RStudio interactive environment
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 2818`_
* Acquire lock before attempting to install conda
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 2826`_
* Fix Galaxy for if pyuwsgi is install in Galaxy's virtual environment.
  `Pull Request 2836`_
* Fix tabular renderer display when ``total_cols > line_cols > 1``.
  `Pull Request 2845`_
* Remove empty file in toolbox module.
  `Pull Request 2877`_
* Fix for workflow execution when using collections.
  `Pull Request 2898`_, `Issue 2806 <https://github.com/galaxyproject/galaxy/issues/2806>`__
* Implement ``split`` on a validator.
  `Pull Request 2921`_
* Catch failure to import grp in util (for Pulsar on Windows)
  `Pull Request 2928`_
* Bump pysam, remove ``already_compressed`` usage due to new wheel.
  `Pull Request 2953`_
* Re-build DOM on render for modal in the front-end.
  `Pull Request 2955`_
* Fix optional column form values when editing dataset properties.
  `Pull Request 2960`_
* Fix optional flag for library datasets in legacy library UI.
  `Pull Request 2962`_
* Reload metadata and lib tools on toolbox reload
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 2992`_
* Update some old information in API guideline docs.
  `Pull Request 3011`_
* Fix for rerunning tool with workflow resume that is part of a collection.
  `Pull Request 3019`_
* Missing double quotation in tool XSD example
  (thanks to `@ramezrawas <https://github.com/ramezrawas>`__).
  `Pull Request 3027`_
* Include base classes when searching datatypes by name.
  `Pull Request 3028`_
* Image detection fixes.
  `Pull Request 3042`_
* Fix tabular filtering tool broken in `#2983
  <https://github.com/galaxyproject/galaxy/issues/2983>`__
  `Pull Request 3043`_
* Fix GFF attribute filtering tool broken in `#2983
  <https://github.com/galaxyproject/galaxy/issues/2983>`__
  `Pull Request 3044`_
* Fix for displaying parameters to the user that have a ``False`` value.
  `Pull Request 3045`_
* Fix downloading tool tarball with boolean test input values.
  `Pull Request 3047`_
* Sort bedtools output in ``bam_to_bigwig`` conversion
  (thanks to `@lparsons <https://github.com/lparsons>`__).
  `Pull Request 3049`_
* Remove incorrect communication server check.
  `Pull Request 3053`_
* Fix tool XSD to accept a help attribute for ``section``\ s
  (thanks to `@joachimwolff <https://github.com/joachimwolff>`__).
  `Pull Request 3131`_
* Fix import orders for updates to flake8_import_order.
  `Pull Request 3059`_
* Dataset metadata should not be cached when building chart visualizations.
  `Pull Request 3062`_
* Fix libraries prefix.
  `Pull Request 3074`_
* Fix qunit local testing install -- now runs on modern node (v6.9.1).
  `Pull Request 3089`_
* Escape section name when writing to XML
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3122`_
* Fix tools placed outside of panel section
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3125`_
* Fix XSD for ``exclude_min`` and ``exclude_max``
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 3108`_
* Update galaxy.xsd
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 3132`_
* Fix to treat the value of ``message_box_visible`` in ``galaxy.ini`` as a boolean.
  `Pull Request 3139`_
* Ensure a From: address is set for user activation emails.
  `Pull Request 3140`_
* Explicitly specify attributes which should be copied to converted datasets.
  `Pull Request 3149`_
* Prefer existing .venv over conda, when both are available.
  `Pull Request 3180`_
* Validate cycles and step size before building model for workflow execution.
  `Pull Request 3183`_
* Fix a typo in the intro tour.
  `Pull Request 3184`_
* Make SAM to bam converter tool compatible with samtools >= 1.3
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3187`_
* Remove unused (and unintended) config override.
  `Pull Request 3198`_
* Fixes for deleting histories.
  `Pull Request 3203`_
* Change 'History Actions' to 'Current History' in history options menu.
  `Pull Request 3205`_
* Preserve custom event handler for form inputs.
  `Pull Request 3210`_
* Admin installation UX wording fixes.
  `Pull Request 3226`_
* Backport `#3106 <https://github.com/galaxyproject/galaxy/issues/3106>`__ and
  `#3222 <https://github.com/galaxyproject/galaxy/issues/3222>`__: Cached
  conda environments and API to manage them
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 3227`_
* Update the copyright year in the LICENSE.txt.
  `Pull Request 2926`_
* Fix for ToolShed install when copied sample data target exists, but is broken symlink.
  `Pull Request 3279`_

.. github_links
.. _Issue 2375: https://github.com/galaxyproject/galaxy/issues/2375
.. _Pull Request 1768: https://github.com/galaxyproject/galaxy/pull/1768
.. _Pull Request 2588: https://github.com/galaxyproject/galaxy/pull/2588
.. _Pull Request 2653: https://github.com/galaxyproject/galaxy/pull/2653
.. _Pull Request 2654: https://github.com/galaxyproject/galaxy/pull/2654
.. _Pull Request 2668: https://github.com/galaxyproject/galaxy/pull/2668
.. _Pull Request 2669: https://github.com/galaxyproject/galaxy/pull/2669
.. _Pull Request 2672: https://github.com/galaxyproject/galaxy/pull/2672
.. _Pull Request 2674: https://github.com/galaxyproject/galaxy/pull/2674
.. _Pull Request 2677: https://github.com/galaxyproject/galaxy/pull/2677
.. _Pull Request 2686: https://github.com/galaxyproject/galaxy/pull/2686
.. _Pull Request 2687: https://github.com/galaxyproject/galaxy/pull/2687
.. _Pull Request 2688: https://github.com/galaxyproject/galaxy/pull/2688
.. _Pull Request 2689: https://github.com/galaxyproject/galaxy/pull/2689
.. _Pull Request 2690: https://github.com/galaxyproject/galaxy/pull/2690
.. _Pull Request 2695: https://github.com/galaxyproject/galaxy/pull/2695
.. _Pull Request 2696: https://github.com/galaxyproject/galaxy/pull/2696
.. _Pull Request 2697: https://github.com/galaxyproject/galaxy/pull/2697
.. _Pull Request 2700: https://github.com/galaxyproject/galaxy/pull/2700
.. _Pull Request 2703: https://github.com/galaxyproject/galaxy/pull/2703
.. _Pull Request 2705: https://github.com/galaxyproject/galaxy/pull/2705
.. _Pull Request 2706: https://github.com/galaxyproject/galaxy/pull/2706
.. _Pull Request 2708: https://github.com/galaxyproject/galaxy/pull/2708
.. _Pull Request 2711: https://github.com/galaxyproject/galaxy/pull/2711
.. _Pull Request 2715: https://github.com/galaxyproject/galaxy/pull/2715
.. _Pull Request 2716: https://github.com/galaxyproject/galaxy/pull/2716
.. _Pull Request 2720: https://github.com/galaxyproject/galaxy/pull/2720
.. _Pull Request 2730: https://github.com/galaxyproject/galaxy/pull/2730
.. _Pull Request 2731: https://github.com/galaxyproject/galaxy/pull/2731
.. _Pull Request 2732: https://github.com/galaxyproject/galaxy/pull/2732
.. _Pull Request 2733: https://github.com/galaxyproject/galaxy/pull/2733
.. _Pull Request 2734: https://github.com/galaxyproject/galaxy/pull/2734
.. _Pull Request 2735: https://github.com/galaxyproject/galaxy/pull/2735
.. _Pull Request 2738: https://github.com/galaxyproject/galaxy/pull/2738
.. _Pull Request 2740: https://github.com/galaxyproject/galaxy/pull/2740
.. _Pull Request 2741: https://github.com/galaxyproject/galaxy/pull/2741
.. _Pull Request 2748: https://github.com/galaxyproject/galaxy/pull/2748
.. _Pull Request 2753: https://github.com/galaxyproject/galaxy/pull/2753
.. _Pull Request 2757: https://github.com/galaxyproject/galaxy/pull/2757
.. _Pull Request 2758: https://github.com/galaxyproject/galaxy/pull/2758
.. _Pull Request 2761: https://github.com/galaxyproject/galaxy/pull/2761
.. _Pull Request 2762: https://github.com/galaxyproject/galaxy/pull/2762
.. _Pull Request 2763: https://github.com/galaxyproject/galaxy/pull/2763
.. _Pull Request 2765: https://github.com/galaxyproject/galaxy/pull/2765
.. _Pull Request 2766: https://github.com/galaxyproject/galaxy/pull/2766
.. _Pull Request 2769: https://github.com/galaxyproject/galaxy/pull/2769
.. _Pull Request 2770: https://github.com/galaxyproject/galaxy/pull/2770
.. _Pull Request 2771: https://github.com/galaxyproject/galaxy/pull/2771
.. _Pull Request 2776: https://github.com/galaxyproject/galaxy/pull/2776
.. _Pull Request 2777: https://github.com/galaxyproject/galaxy/pull/2777
.. _Pull Request 2782: https://github.com/galaxyproject/galaxy/pull/2782
.. _Pull Request 2784: https://github.com/galaxyproject/galaxy/pull/2784
.. _Pull Request 2787: https://github.com/galaxyproject/galaxy/pull/2787
.. _Pull Request 2790: https://github.com/galaxyproject/galaxy/pull/2790
.. _Pull Request 2791: https://github.com/galaxyproject/galaxy/pull/2791
.. _Pull Request 2794: https://github.com/galaxyproject/galaxy/pull/2794
.. _Pull Request 2799: https://github.com/galaxyproject/galaxy/pull/2799
.. _Pull Request 2808: https://github.com/galaxyproject/galaxy/pull/2808
.. _Pull Request 2814: https://github.com/galaxyproject/galaxy/pull/2814
.. _Pull Request 2816: https://github.com/galaxyproject/galaxy/pull/2816
.. _Pull Request 2817: https://github.com/galaxyproject/galaxy/pull/2817
.. _Pull Request 2818: https://github.com/galaxyproject/galaxy/pull/2818
.. _Pull Request 2819: https://github.com/galaxyproject/galaxy/pull/2819
.. _Pull Request 2820: https://github.com/galaxyproject/galaxy/pull/2820
.. _Pull Request 2824: https://github.com/galaxyproject/galaxy/pull/2824
.. _Pull Request 2826: https://github.com/galaxyproject/galaxy/pull/2826
.. _Pull Request 2830: https://github.com/galaxyproject/galaxy/pull/2830
.. _Pull Request 2832: https://github.com/galaxyproject/galaxy/pull/2832
.. _Pull Request 2836: https://github.com/galaxyproject/galaxy/pull/2836
.. _Pull Request 2839: https://github.com/galaxyproject/galaxy/pull/2839
.. _Pull Request 2840: https://github.com/galaxyproject/galaxy/pull/2840
.. _Pull Request 2841: https://github.com/galaxyproject/galaxy/pull/2841
.. _Pull Request 2845: https://github.com/galaxyproject/galaxy/pull/2845
.. _Pull Request 2848: https://github.com/galaxyproject/galaxy/pull/2848
.. _Pull Request 2857: https://github.com/galaxyproject/galaxy/pull/2857
.. _Pull Request 2858: https://github.com/galaxyproject/galaxy/pull/2858
.. _Pull Request 2862: https://github.com/galaxyproject/galaxy/pull/2862
.. _Pull Request 2865: https://github.com/galaxyproject/galaxy/pull/2865
.. _Pull Request 2870: https://github.com/galaxyproject/galaxy/pull/2870
.. _Pull Request 2871: https://github.com/galaxyproject/galaxy/pull/2871
.. _Pull Request 2872: https://github.com/galaxyproject/galaxy/pull/2872
.. _Pull Request 2875: https://github.com/galaxyproject/galaxy/pull/2875
.. _Pull Request 2877: https://github.com/galaxyproject/galaxy/pull/2877
.. _Pull Request 2879: https://github.com/galaxyproject/galaxy/pull/2879
.. _Pull Request 2880: https://github.com/galaxyproject/galaxy/pull/2880
.. _Pull Request 2885: https://github.com/galaxyproject/galaxy/pull/2885
.. _Pull Request 2887: https://github.com/galaxyproject/galaxy/pull/2887
.. _Pull Request 2888: https://github.com/galaxyproject/galaxy/pull/2888
.. _Pull Request 2889: https://github.com/galaxyproject/galaxy/pull/2889
.. _Pull Request 2891: https://github.com/galaxyproject/galaxy/pull/2891
.. _Pull Request 2893: https://github.com/galaxyproject/galaxy/pull/2893
.. _Pull Request 2894: https://github.com/galaxyproject/galaxy/pull/2894
.. _Pull Request 2895: https://github.com/galaxyproject/galaxy/pull/2895
.. _Pull Request 2898: https://github.com/galaxyproject/galaxy/pull/2898
.. _Pull Request 2901: https://github.com/galaxyproject/galaxy/pull/2901
.. _Pull Request 2902: https://github.com/galaxyproject/galaxy/pull/2902
.. _Pull Request 2903: https://github.com/galaxyproject/galaxy/pull/2903
.. _Pull Request 2904: https://github.com/galaxyproject/galaxy/pull/2904
.. _Pull Request 2905: https://github.com/galaxyproject/galaxy/pull/2905
.. _Pull Request 2909: https://github.com/galaxyproject/galaxy/pull/2909
.. _Pull Request 2912: https://github.com/galaxyproject/galaxy/pull/2912
.. _Pull Request 2917: https://github.com/galaxyproject/galaxy/pull/2917
.. _Pull Request 2920: https://github.com/galaxyproject/galaxy/pull/2920
.. _Pull Request 2921: https://github.com/galaxyproject/galaxy/pull/2921
.. _Pull Request 2923: https://github.com/galaxyproject/galaxy/pull/2923
.. _Pull Request 2926: https://github.com/galaxyproject/galaxy/pull/2926
.. _Pull Request 2928: https://github.com/galaxyproject/galaxy/pull/2928
.. _Pull Request 2932: https://github.com/galaxyproject/galaxy/pull/2932
.. _Pull Request 2935: https://github.com/galaxyproject/galaxy/pull/2935
.. _Pull Request 2936: https://github.com/galaxyproject/galaxy/pull/2936
.. _Pull Request 2937: https://github.com/galaxyproject/galaxy/pull/2937
.. _Pull Request 2939: https://github.com/galaxyproject/galaxy/pull/2939
.. _Pull Request 2943: https://github.com/galaxyproject/galaxy/pull/2943
.. _Pull Request 2946: https://github.com/galaxyproject/galaxy/pull/2946
.. _Pull Request 2947: https://github.com/galaxyproject/galaxy/pull/2947
.. _Pull Request 2952: https://github.com/galaxyproject/galaxy/pull/2952
.. _Pull Request 2953: https://github.com/galaxyproject/galaxy/pull/2953
.. _Pull Request 2955: https://github.com/galaxyproject/galaxy/pull/2955
.. _Pull Request 2957: https://github.com/galaxyproject/galaxy/pull/2957
.. _Pull Request 2960: https://github.com/galaxyproject/galaxy/pull/2960
.. _Pull Request 2961: https://github.com/galaxyproject/galaxy/pull/2961
.. _Pull Request 2962: https://github.com/galaxyproject/galaxy/pull/2962
.. _Pull Request 2965: https://github.com/galaxyproject/galaxy/pull/2965
.. _Pull Request 2966: https://github.com/galaxyproject/galaxy/pull/2966
.. _Pull Request 2969: https://github.com/galaxyproject/galaxy/pull/2969
.. _Pull Request 2970: https://github.com/galaxyproject/galaxy/pull/2970
.. _Pull Request 2971: https://github.com/galaxyproject/galaxy/pull/2971
.. _Pull Request 2972: https://github.com/galaxyproject/galaxy/pull/2972
.. _Pull Request 2973: https://github.com/galaxyproject/galaxy/pull/2973
.. _Pull Request 2974: https://github.com/galaxyproject/galaxy/pull/2974
.. _Pull Request 2975: https://github.com/galaxyproject/galaxy/pull/2975
.. _Pull Request 2976: https://github.com/galaxyproject/galaxy/pull/2976
.. _Pull Request 2978: https://github.com/galaxyproject/galaxy/pull/2978
.. _Pull Request 2979: https://github.com/galaxyproject/galaxy/pull/2979
.. _Pull Request 2983: https://github.com/galaxyproject/galaxy/pull/2983
.. _Pull Request 2986: https://github.com/galaxyproject/galaxy/pull/2986
.. _Pull Request 2990: https://github.com/galaxyproject/galaxy/pull/2990
.. _Pull Request 2991: https://github.com/galaxyproject/galaxy/pull/2991
.. _Pull Request 2992: https://github.com/galaxyproject/galaxy/pull/2992
.. _Pull Request 2998: https://github.com/galaxyproject/galaxy/pull/2998
.. _Pull Request 3003: https://github.com/galaxyproject/galaxy/pull/3003
.. _Pull Request 3004: https://github.com/galaxyproject/galaxy/pull/3004
.. _Pull Request 3005: https://github.com/galaxyproject/galaxy/pull/3005
.. _Pull Request 3006: https://github.com/galaxyproject/galaxy/pull/3006
.. _Pull Request 3007: https://github.com/galaxyproject/galaxy/pull/3007
.. _Pull Request 3010: https://github.com/galaxyproject/galaxy/pull/3010
.. _Pull Request 3011: https://github.com/galaxyproject/galaxy/pull/3011
.. _Pull Request 3013: https://github.com/galaxyproject/galaxy/pull/3013
.. _Pull Request 3016: https://github.com/galaxyproject/galaxy/pull/3016
.. _Pull Request 3019: https://github.com/galaxyproject/galaxy/pull/3019
.. _Pull Request 3020: https://github.com/galaxyproject/galaxy/pull/3020
.. _Pull Request 3023: https://github.com/galaxyproject/galaxy/pull/3023
.. _Pull Request 3024: https://github.com/galaxyproject/galaxy/pull/3024
.. _Pull Request 3025: https://github.com/galaxyproject/galaxy/pull/3025
.. _Pull Request 3027: https://github.com/galaxyproject/galaxy/pull/3027
.. _Pull Request 3028: https://github.com/galaxyproject/galaxy/pull/3028
.. _Pull Request 3031: https://github.com/galaxyproject/galaxy/pull/3031
.. _Pull Request 3032: https://github.com/galaxyproject/galaxy/pull/3032
.. _Pull Request 3033: https://github.com/galaxyproject/galaxy/pull/3033
.. _Pull Request 3035: https://github.com/galaxyproject/galaxy/pull/3035
.. _Pull Request 3036: https://github.com/galaxyproject/galaxy/pull/3036
.. _Pull Request 3037: https://github.com/galaxyproject/galaxy/pull/3037
.. _Pull Request 3039: https://github.com/galaxyproject/galaxy/pull/3039
.. _Pull Request 3040: https://github.com/galaxyproject/galaxy/pull/3040
.. _Pull Request 3041: https://github.com/galaxyproject/galaxy/pull/3041
.. _Pull Request 3042: https://github.com/galaxyproject/galaxy/pull/3042
.. _Pull Request 3043: https://github.com/galaxyproject/galaxy/pull/3043
.. _Pull Request 3044: https://github.com/galaxyproject/galaxy/pull/3044
.. _Pull Request 3045: https://github.com/galaxyproject/galaxy/pull/3045
.. _Pull Request 3046: https://github.com/galaxyproject/galaxy/pull/3046
.. _Pull Request 3047: https://github.com/galaxyproject/galaxy/pull/3047
.. _Pull Request 3049: https://github.com/galaxyproject/galaxy/pull/3049
.. _Pull Request 3051: https://github.com/galaxyproject/galaxy/pull/3051
.. _Pull Request 3052: https://github.com/galaxyproject/galaxy/pull/3052
.. _Pull Request 3053: https://github.com/galaxyproject/galaxy/pull/3053
.. _Pull Request 3056: https://github.com/galaxyproject/galaxy/pull/3056
.. _Pull Request 3059: https://github.com/galaxyproject/galaxy/pull/3059
.. _Pull Request 3060: https://github.com/galaxyproject/galaxy/pull/3060
.. _Pull Request 3062: https://github.com/galaxyproject/galaxy/pull/3062
.. _Pull Request 3070: https://github.com/galaxyproject/galaxy/pull/3070
.. _Pull Request 3071: https://github.com/galaxyproject/galaxy/pull/3071
.. _Pull Request 3072: https://github.com/galaxyproject/galaxy/pull/3072
.. _Pull Request 3073: https://github.com/galaxyproject/galaxy/pull/3073
.. _Pull Request 3074: https://github.com/galaxyproject/galaxy/pull/3074
.. _Pull Request 3077: https://github.com/galaxyproject/galaxy/pull/3077
.. _Pull Request 3079: https://github.com/galaxyproject/galaxy/pull/3079
.. _Pull Request 3080: https://github.com/galaxyproject/galaxy/pull/3080
.. _Pull Request 3082: https://github.com/galaxyproject/galaxy/pull/3082
.. _Pull Request 3086: https://github.com/galaxyproject/galaxy/pull/3086
.. _Pull Request 3087: https://github.com/galaxyproject/galaxy/pull/3087
.. _Pull Request 3089: https://github.com/galaxyproject/galaxy/pull/3089
.. _Pull Request 3091: https://github.com/galaxyproject/galaxy/pull/3091
.. _Pull Request 3095: https://github.com/galaxyproject/galaxy/pull/3095
.. _Pull Request 3097: https://github.com/galaxyproject/galaxy/pull/3097
.. _Pull Request 3098: https://github.com/galaxyproject/galaxy/pull/3098
.. _Pull Request 3099: https://github.com/galaxyproject/galaxy/pull/3099
.. _Pull Request 3100: https://github.com/galaxyproject/galaxy/pull/3100
.. _Pull Request 3102: https://github.com/galaxyproject/galaxy/pull/3102
.. _Pull Request 3103: https://github.com/galaxyproject/galaxy/pull/3103
.. _Pull Request 3105: https://github.com/galaxyproject/galaxy/pull/3105
.. _Pull Request 3108: https://github.com/galaxyproject/galaxy/pull/3108
.. _Pull Request 3109: https://github.com/galaxyproject/galaxy/pull/3109
.. _Pull Request 3110: https://github.com/galaxyproject/galaxy/pull/3110
.. _Pull Request 3113: https://github.com/galaxyproject/galaxy/pull/3113
.. _Pull Request 3116: https://github.com/galaxyproject/galaxy/pull/3116
.. _Pull Request 3119: https://github.com/galaxyproject/galaxy/pull/3119
.. _Pull Request 3122: https://github.com/galaxyproject/galaxy/pull/3122
.. _Pull Request 3123: https://github.com/galaxyproject/galaxy/pull/3123
.. _Pull Request 3124: https://github.com/galaxyproject/galaxy/pull/3124
.. _Pull Request 3125: https://github.com/galaxyproject/galaxy/pull/3125
.. _Pull Request 3129: https://github.com/galaxyproject/galaxy/pull/3129
.. _Pull Request 3130: https://github.com/galaxyproject/galaxy/pull/3130
.. _Pull Request 3131: https://github.com/galaxyproject/galaxy/pull/3131
.. _Pull Request 3132: https://github.com/galaxyproject/galaxy/pull/3132
.. _Pull Request 3135: https://github.com/galaxyproject/galaxy/pull/3135
.. _Pull Request 3139: https://github.com/galaxyproject/galaxy/pull/3139
.. _Pull Request 3140: https://github.com/galaxyproject/galaxy/pull/3140
.. _Pull Request 3141: https://github.com/galaxyproject/galaxy/pull/3141
.. _Pull Request 3149: https://github.com/galaxyproject/galaxy/pull/3149
.. _Pull Request 3154: https://github.com/galaxyproject/galaxy/pull/3154
.. _Pull Request 3155: https://github.com/galaxyproject/galaxy/pull/3155
.. _Pull Request 3165: https://github.com/galaxyproject/galaxy/pull/3165
.. _Pull Request 3167: https://github.com/galaxyproject/galaxy/pull/3167
.. _Pull Request 3169: https://github.com/galaxyproject/galaxy/pull/3169
.. _Pull Request 3170: https://github.com/galaxyproject/galaxy/pull/3170
.. _Pull Request 3176: https://github.com/galaxyproject/galaxy/pull/3176
.. _Pull Request 3177: https://github.com/galaxyproject/galaxy/pull/3177
.. _Pull Request 3180: https://github.com/galaxyproject/galaxy/pull/3180
.. _Pull Request 3183: https://github.com/galaxyproject/galaxy/pull/3183
.. _Pull Request 3184: https://github.com/galaxyproject/galaxy/pull/3184
.. _Pull Request 3187: https://github.com/galaxyproject/galaxy/pull/3187
.. _Pull Request 3188: https://github.com/galaxyproject/galaxy/pull/3188
.. _Pull Request 3191: https://github.com/galaxyproject/galaxy/pull/3191
.. _Pull Request 3198: https://github.com/galaxyproject/galaxy/pull/3198
.. _Pull Request 3203: https://github.com/galaxyproject/galaxy/pull/3203
.. _Pull Request 3205: https://github.com/galaxyproject/galaxy/pull/3205
.. _Pull Request 3210: https://github.com/galaxyproject/galaxy/pull/3210
.. _Pull Request 3226: https://github.com/galaxyproject/galaxy/pull/3226
.. _Pull Request 3227: https://github.com/galaxyproject/galaxy/pull/3227
.. _Pull Request 3232: https://github.com/galaxyproject/galaxy/pull/3232
.. _Pull Request 3262: https://github.com/galaxyproject/galaxy/pull/3262
.. _Pull Request 3279: https://github.com/galaxyproject/galaxy/pull/3279

.. _Commit c1e3087: https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe4769d666d3f934
.. _Pull Request 3278: https://github.com/galaxyproject/galaxy/pull/3278