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.. to_doc
16.07
===============================
.. announce_start
Highlighted Enhancements
-------------------------------
* Implement an Azure backend for the Galaxy objectstore
(thanks to `@zfrenchee <https://github.com/zfrenchee>`__.)
`Pull Request 2621`_
* HTCondor Docker Integration
(thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2278`_
* Implement a Kubernetes job runner
(thanks to `@pcm32 <https://github.com/pcm32>`__.)
`Pull Request 2314`_, `Pull Request 2498`_, `Pull Request 2559`_,
`Pull Request 2578`_, `Pull Request 2616`_, `Pull Request 2528`_
* Implement collection operations - tool-like entities allowing users
to zip, unzip, flatten, and filter failed datasets out of collections.
(You may need to sync your ``tool_conf.xml`` against sample.)
`Pull Request 2434`_
* Allow history panel to display list of lists dataset collections.
`Pull Request 2613`_
* Add a Tool Shed API endpoint method to check the current user.
`Pull Request 2243`_
* Add a Galaxy API endpoint to update a user object.
`Pull Request 2595`_
* Improvements to toolbox search.
`Pull Request 2273`_
* New pages and general improvements to the Reports application
(thanks to `@BalthazarPavot <https://github.com/BalthazarPavot>`__.)
`Pull Request 2664`_
* Nicer bug report emails
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2143`_
* Tools with auto_format='true' now connectable in workflow editor
(thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
`Pull Request 2144`_
* Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip
>= 8.1).
`Pull Request 2383`_
* Allow tool form to listen to history
(thanks to `@nturaga <https://github.com/nturaga>`__.)
`Pull Request 2476`_
* Add `EDAM <http://edamontology.org/page>`__ operations to tools and expose in API
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__, `@nsoranzo <https://github.com/nsoranzo>`__ and `@odoppelt <https://github.com/odoppelt>`__.)
`Pull Request 2379`_
* Add support to PDBQT molecule datatype
(thanks to `@leobiscassi <https://github.com/leobiscassi>`__.)
`Pull Request 2452`_
* Add the trackhub composite datatype
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
`Pull Request 2348`_, `Pull Request 2646`_, `Pull Request 2701`_
* Add the Mothur datatypes
(thanks to `@shiltemann <https://github.com/shiltemann>`__.)
`Pull Request 2038`_, `Pull Request 2429`_
* Add the dynamic tool destination tool to Galaxy for defining finer grained
tool destination rules.
(thanks to `@ericenns <https://github.com/ericenns>`__.)
`Pull Request 2579`_
* Galaxy can now install Conda dependencies in addition to tool shed
dependencies during repository installations
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__
and `@bwlang <https://github.com/bwlang>`__.)
`Pull Request 2554`_
* Implement the Galaxy Communication Server (a simple in-Galaxy chat server)
(thanks to `@anuprulez <https://github.com/anuprulez>`__
and `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2515`_
Enhancements
-------------------------------
* Install Conda at startup; enable conda_auto_init in sample conf
`Pull Request 2759`_
* Add ``filter_failed_datasets_from_collection.py`` script to ``scripts/``
(thanks to `@chambm <https://github.com/chambm>`__.)
`Pull Request 2358`_
* Enhanced workflow run form using newer client forms architecture.
`Pull Request 2077`_
* Tweaks to various library functions for galaxy-lib.
`Pull Request 2110`_, `Pull Request 2494`_, `Pull Request 2354`_,
`Pull Request 2414`_, `Pull Request 2436`_
* Automate and clarify more of the release process.
`Pull Request 2117`_, `Pull Request 2366`_, `Pull Request 2372`_,
`Pull Request 2388`_
* Update template to include the release of the Docker container
(thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2378`_
* Add ``server_starttime`` to configuration API.
`Pull Request 2124`_
* Show line breaks in commit log in the Tool Shed
(thanks to `@nturaga <https://github.com/nturaga>`__.)
`Pull Request 2142`_
* Replacing the ``_getIndex`` method by UnderscoreJS method ``_.findIndex()``
(thanks to `@anuprulez <https://github.com/anuprulez>`__.)
`Pull Request 2157`_
* Small enhancements to user activation process.
`Pull Request 2158`_
* Implement ``single_user = <email>`` config option.
`Pull Request 2165`_
* More documentation and flexibility for FTP imports.
`Pull Request 2168`_
* Make stats prefix configurable and add a conditional wheel requirement.
`Pull Request 2171`_
* Fix running tool tests if remote user middleware is enabled.
`Pull Request 2173`_
* Improve handling of a missing R environment during Tool Shed dependency
installations.
`Pull Request 2215`_
* Quote some parameters in the trim tool command
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2248`_
* Remove overly chatty tool dependency resolution logging statement.
`Pull Request 2254`_
* Update the list of contributors.
`Pull Request 2256`_, `Pull Request 2257`_, `Pull Request 2258`_
* Add grunt watcher on .less files
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
`Pull Request 2274`_
* Remove dependency on custom Whoosh (requirements update).
`Pull Request 2276`_
* Various enhancements for library functions related to tools.
`Pull Request 2279`_
* Shift ``asbool`` handling in datatypes API so that an appropriate error message is now returned.
`Pull Request 2286`_
* More small fixes from downstream projects.
`Pull Request 2292`_
* For published workflow display, provide a better error when the workflow or user cannot be found
`Pull Request 2302`_
* Bump sqlite3 version
(thanks to `@matthdsm <https://github.com/matthdsm>`__.)
`Pull Request 2307`_
* Show collection counts in collection and history collection views.
`Pull Request 2326`_
* Various client library updates.
`Pull Request 2328`_
* Revise form data visitor.
`Pull Request 2330`_
* Update using xhr date header.
`Pull Request 2335`_
* Implement an API for managing history/sharable model user sharing.
`Pull Request 2340`_
* Revise portlet view, integrate collapsible option.
`Pull Request 2360`_
* Fix issue with lowercasing in datatypes/registry.py
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
`Pull Request 2361`_
* Improve composite output tool test.
`Pull Request 2363`_
* Upgrade shared ui libraries, add test cases
`Pull Request 2368`_
* Throughout backend use open() instead of file() for Python 3
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2370`_
* Remove backported importlib and ordereddict.
`Pull Request 2380`_
* Note on updating tool testing
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2381`_
* Docker swarm support for Galaxy Interactive Environments (GIEs)
`Pull Request 2386`_, `Pull Request 2392`_
* Add support for EDAM data annotations to datatypes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__, `@bgruening <https://github.com/bgruening>`__, `@hmenager <https://github.com/hmenager>`__ and `@mvdbeek <https://github.com/mvdbeek>`__.)
`Pull Request 2387`_
* Add a new workflow building mode variation which does access the history
`Pull Request 2390`_
* Add conda search function to ``conda_util`` library function
(thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2395`_
* Add history navigation options for dataset frames to scratch book
`Pull Request 2396`_
* Add EDAM topics to tools and expose in API
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2397`_
* Update SLURM runner so when scontrol fails, Galaxy attempts to get job
state with sacct
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2403`_
* Enhancements to tool test output verification.
`Pull Request 2409`_
* Show history dataset id (hid) in dataset 'view details' page.
`Pull Request 2411`_
* Updates and fixes for the run workflow UI elements.
`Pull Request 2416`_
* Raise ``Exception`` if ``watch_tools`` has an unrecognized value
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2418`_
* Use ``log.warning()`` instead of deprecated ``log.warn()`` (for Python 3)
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2420`_
* Minor updates to documentation.
`Pull Request 2427`_
* Correct various EDAM data/format annotations in datatypes
(thanks to `@hmenager <https://github.com/hmenager>`__.)
`Pull Request 2428`_
* Fix ``$defaults`` according to `#2430
<https://github.com/galaxyproject/galaxy/issues/2430>`__
(thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__.)
`Pull Request 2438`_
* Properly list subworkflows in run workflow form.
`Pull Request 2440`_
* Make some files compatible with Python3
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2453`_
* Add parameter expansion caller and test cases as preparation for workflow
API extension.
`Pull Request 2464`_
* Set a default for ``tool_dependencies_dir``.
`Pull Request 2480`_
* Add a password expiration config option (resolves `#2485
<https://github.com/galaxyproject/galaxy/issues/2485>`__)
(thanks to `@benfulton <https://github.com/benfulton>`__.)
`Pull Request 2486`_
* Display TIFF format in upload
(thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2516`_
* Use ``self.decode_id`` instead of ``trans.security.decode_id``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2529`_
* Charts revision.
`Pull Request 2531`_
* Add ``Makefile`` target for fetching updated bower dependencies.
`Pull Request 2534`_
* Make conda autoinstall of packages safer:
(thanks to `@pvanheus <https://github.com/pvanheus>`__.)
`Pull Request 2538`_
* Updates to Interactive Environment docs
(thanks to `@pvanheus <https://github.com/pvanheus>`__.)
`Pull Request 2543`_
* Allow displaying bigWig files in IGV
(thanks to `@dpryan79 <https://github.com/dpryan79>`__.)
`Pull Request 2545`_
* Allow users to purge datasets by default.
`Pull Request 2553`_
* Add Jupyter IE to the allowed visualizations for BAM datasets
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2572`_
* Python3: port 215 files
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__, `@tshtatland <https://github.com/tshtatland>`__, `@xiaoqian1984 <https://github.com/xiaoqian1984>`__, `@alanryanwang <https://github.com/alanryanwang>`__ and `@ericenns <https://github.com/ericenns>`__.)
`Pull Request 2574`_
* Add python-ldap module to conditional requirements
(thanks to `@abretaud <https://github.com/abretaud>`__.)
`Pull Request 2576`_
* Update gsummary.xml
(thanks to `@lecorguille <https://github.com/lecorguille>`__.)
`Pull Request 2590`_
* Add Warning when Conda is installed
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
`Pull Request 2596`_
* Added the neostore (neo4j db) for noe4jdb dataset
(thanks to `@zipho <https://github.com/zipho>`__.)
`Pull Request 2605`_
* Fix smart_str for Python 3. Add doctests
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2608`_
* Added Neo4j IE
(thanks to `@thobalose <https://github.com/thobalose>`__.)
`Pull Request 2610`_
* Committing format changes to the user impersonation dropdown.
(thanks to `@sszakony <https://github.com/sszakony>`__.)
`Pull Request 2612`_
* Use pagination and filtering for select2 fields
`Pull Request 2615`_
* Update workflow share dropdown width
(thanks to `@sszakony <https://github.com/sszakony>`__.)
`Pull Request 2617`_
* Graph visualization: add parsers, change datatypes
`Pull Request 2620`_
* Fix certain combos of dynamic deeply nested collections in workflows.
`Pull Request 2634`_
* add tar to datatypes_conf.xml
(thanks to `@mariabernard <https://github.com/mariabernard>`__.)
`Pull Request 2636`_
* Optimize get_file_peek()
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2637`_
* Move workflow run and history options to top, add loading indicator
`Pull Request 2643`_
* Enhance workflow run button to indicate workflow loading progress, keep
header fixed
`Pull Request 2647`_
* Allow uploading strict BED datatypes.
`Pull Request 2648`_
* Reduce server sided refresh requests to changes in data associated input
fields
`Pull Request 2652`_
* Add import order linting using tox and flake8-import-order.
`Pull Request 2661`_
* Add hg38 to main for ucsc_build_sites.txt.sample
`Pull Request 2670`_
* Extend the list of files tested with flake8-import-order to all files
already passing
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2682`_
* List resolver Tool Shed packages
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
`Pull Request 2750`_
.. small_enhancement
* Remove buildbot remnants
`Pull Request 2125`_
* Try pushing again when we get unexpected exception (test fix)
`Pull Request 2130`_
* Refactor checking tool files toward reuse with workflows in Planemo.
`Pull Request 2183`_
* Rename/refactor Utils.validate() to Utils.isEmpty()
`Pull Request 2239`_
* Cleanup of the install and test framework.
`Pull Request 2249`_
* cleanup TS and Reports configs
`Pull Request 2267`_
* Move specific methods from shed_util_common.py to specific_util.py
`Pull Request 2269`_
* Revise selection, options and drilldown wrappers, add tests
`Pull Request 2305`_
* Visualizations: remove graphview
`Pull Request 2329`_
* Update qunit and sinon
`Pull Request 2338`_
* Build job success messages within tool form view
`Pull Request 2355`_
* Cleanup of E203 primarily, and some other misc formatting
`Pull Request 2364`_
* Isolate the data libraries css to affect only the libraries app
`Pull Request 2444`_
* Re-add get_updated_changeset_revisions_from_tool_shed() method
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2472`_
* Workaround for circular import. Refactor.
`Pull Request 2477`_
* run_tests.sh: Clarify when/where the report file is created.
(thanks to `@NickSto <https://github.com/NickSto>`__.)
`Pull Request 2564`_
* Reroute consistent workflow endpoint to internal API
`Pull Request 2622`_
* Add tool test for what happens when output filter throws exception.
`Pull Request 2631`_
* Ignore .tox and eggs directories for flake8
`Pull Request 2650`_
* Reorder base templates meta tags
`Pull Request 2651`_
* Import pyparsing in testing so twill's older version doesn't get loaded.
`Pull Request 2656`_
* Change default refresh mode for form views
`Pull Request 2667`_
* Fix unit tests
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2691`_
* Create a uWSGI postfork function registry and start the tool conf watcher
thread post-fork
`Pull Request 2774`_
Fixes
-------------------------------
.. major_bug
* Do not encode dict items that start with ``metadata\_`` in return value of
api/tools/create.
`Pull Request 2459`_
* Generate metadata in separate conda environment
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
`Pull Request 2253`_
* Fix to use "$NCPUS" if defined to set GALAXY_SLOTS
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
`Pull Request 2145`_
.. bug
* fix blocking issue check
`Pull Request 2113`_
* Correctly check set_environment declarations when updating repository.
`Pull Request 2116`_
* Hide hidden data parameters in workflow editor
`Pull Request 2120`_
* Place $headers before integrity_check
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
`Pull Request 2146`_
* Fix bug when determining locale
(thanks to `@xiaojay <https://github.com/xiaojay>`__.)
`Pull Request 2213`_
* Add pyparsing dependency of svgwrite. Unpin mercurial.
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2223`_
* Sanitize poorly escaped input value in run workflow form
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2231`_
* Multi-data collection reductions in repeat blocks are broken.
`Pull Request 2233`_
* Encode collection reduce in serializable fashion
`Pull Request 2241`_
* Cast everything to a string
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2252`_
* Use standard model.orm.now for toolshed's password reset token datetime math
`Pull Request 2261`_
* fixed ui bugs in tours
(thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__.)
`Pull Request 2262`_
* Preliminary fix for displaying raw text/html
`Pull Request 2263`_
* Correctly use defaults specified in galaxy.ini.sample for statsd.
`Pull Request 2268`_
* Fix encoding issues in test/unit/test_objectstore.py.
`Pull Request 2280`_
* Workflow sharing slug edit fix.
`Pull Request 2293`_
* Always remove the working directory after creating the capsule archive.
`Pull Request 2294`_
* update check for Conda env.
(thanks to `@matthdsm <https://github.com/matthdsm>`__.)
`Pull Request 2295`_
* Make grunt watch (for scripts) work again, settings were being overwritten by the new watch-style command
`Pull Request 2296`_
* Monkeypatch Whoosh to use mkdtemp rather than a fixed temporary directory
`Pull Request 2310`_
* Build: remove redundant webpack step in makefile
`Pull Request 2327`_
* Unicodify has different semantics to str, causing bug reporter bug
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2336`_
* Wrap statsd timing middleware more closely around the core application
`Pull Request 2342`_
* UI & API: fix display of inaccessible datasets
`Pull Request 2351`_
* Update README to remove 2.6
(thanks to `@remimarenco <https://github.com/remimarenco>`__.)
`Pull Request 2367`_
* Revise asserts triggering false exceptions for dynamic parameters
`Pull Request 2374`_
* Fix the installed conda version to 3.19.3.
(thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2394`_
* Check variable's presence before calling str methods
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2408`_
* UI, history: correctly handle index API defaults
`Pull Request 2413`_
* Fix to 4a61a4c: add hids for dataset inputs
`Pull Request 2415`_
* wrap bare str raises with generic Exception()
`Pull Request 2421`_
* Fix raven.js import order in galaxy.panels.mako
`Pull Request 2445`_
* Fix usage of super() in the mothur datatypes.
(thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2457`_
* Make pykube an optional dependency since we don't have wheels for it.
`Pull Request 2468`_
* fix markup for button links on sharing template
`Pull Request 2481`_
* fix image generation for workflows with missing tools
`Pull Request 2488`_
* mothur datatypes: don't generate error for pairwise distance matrices
(thanks to `@shiltemann <https://github.com/shiltemann>`__.)
`Pull Request 2489`_
* Toolbox filter fixes
`Pull Request 2499`_
* Fix Post Job Action problem
`Pull Request 2505`_
* Copy PJAs when importing a workflow.
`Pull Request 2508`_
* Fix two errors in sff_extract.py detected by flake8
`Pull Request 2509`_
* Fix HTML errors on 2 templates
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2524`_
* Fix tabular display chunking
`Pull Request 2527`_
* Fix dataset matcher when no tool available.
(thanks to `@zipho <https://github.com/zipho>`__.)
`Pull Request 2540`_
* Initialize objectstore for fix_set_dataset_sizes script
`Pull Request 2544`_
* Fix old bug in non-allowed_images.yml GIEs
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2548`_
* More defensive GIE Proxying
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2552`_
* Fixes for showing min/max labels in Trackster.
`Pull Request 2555`_
* Fix tag_autocomplete issue in workflow editor.
`Pull Request 2569`_
* Fix element_identifier unavailable with data_collection input param
(thanks to `@abretaud <https://github.com/abretaud>`__.)
`Pull Request 2570`_
* Ignore W503 (line break before binary operator) as PEP 8 has reversed its
position on this.
`Pull Request 2594`_
* Fix hex vs float parsing in request body
`Pull Request 2597`_
* Fixes for workflow extraction of mapping collection jobs.
`Pull Request 2625`_
* Workflow SVG generation fix
`Pull Request 2628`_
* Properly initialize datasets when workflow is loaded for execution
`Pull Request 2632`_
* typo in summary statistics tool
(thanks to `@nturaga <https://github.com/nturaga>`__.)
`Pull Request 2639`_
* Set allow_duplicate_entries="False" for built-in Tool Data Tables.
`Pull Request 2644`_
* Ensure Galaxy's python binary is used for metadata generation.
`Pull Request 2660`_
* Fix an error with getting the size of an object from Azure
`Pull Request 2678`_
* Limit creation of multitudes of default, empty histories.
`Pull Request 2684`_
* Fix the sanitization of ``None`` values in utils
`Pull Request 2693`_
* Fix metadata collection on workdir outputs for Pulsar.
`Pull Request 2721`_
* Allow link buttons to trigger regular click events
`Pull Request 2743`_
* Fix unused href parameter when adding scratchbook frames
`Pull Request 2744`_
* Update common_startup.sh to require python2.7 in .venv
(thanks to `@BenjaminHCCarr <https://github.com/BenjaminHCCarr>`__.)
`Pull Request 2756`_
* Separate styles of new and old libraries fixing various ui bugs
`Pull Request 2780`_
* Make conda install and resolver status more robust
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
`Pull Request 2789`_
* Smart string handling on the wsgi response -- this fixes uWSGI blanking out when handling endpoints that return Unicode
`Pull Request 2630`_
* Do not instantiate the raven (sentry) client or tool conf watchdog threads
until uWSGI postfork
`Pull Request 2792`_
* API, history contents: allow ``source`` in payload
`Pull Request 2809`_
.. github_links
.. _Pull Request 2038: https://github.com/galaxyproject/galaxy/pull/2038
.. _Pull Request 2077: https://github.com/galaxyproject/galaxy/pull/2077
.. _Pull Request 2079: https://github.com/galaxyproject/galaxy/pull/2079
.. _Pull Request 2110: https://github.com/galaxyproject/galaxy/pull/2110
.. _Pull Request 2113: https://github.com/galaxyproject/galaxy/pull/2113
.. _Pull Request 2116: https://github.com/galaxyproject/galaxy/pull/2116
.. _Pull Request 2117: https://github.com/galaxyproject/galaxy/pull/2117
.. _Pull Request 2119: https://github.com/galaxyproject/galaxy/pull/2119
.. _Pull Request 2120: https://github.com/galaxyproject/galaxy/pull/2120
.. _Pull Request 2121: https://github.com/galaxyproject/galaxy/pull/2121
.. _Pull Request 2124: https://github.com/galaxyproject/galaxy/pull/2124
.. _Pull Request 2125: https://github.com/galaxyproject/galaxy/pull/2125
.. _Pull Request 2130: https://github.com/galaxyproject/galaxy/pull/2130
.. _Pull Request 2142: https://github.com/galaxyproject/galaxy/pull/2142
.. _Pull Request 2143: https://github.com/galaxyproject/galaxy/pull/2143
.. _Pull Request 2144: https://github.com/galaxyproject/galaxy/pull/2144
.. _Pull Request 2145: https://github.com/galaxyproject/galaxy/pull/2145
.. _Pull Request 2146: https://github.com/galaxyproject/galaxy/pull/2146
.. _Pull Request 2157: https://github.com/galaxyproject/galaxy/pull/2157
.. _Pull Request 2158: https://github.com/galaxyproject/galaxy/pull/2158
.. _Pull Request 2165: https://github.com/galaxyproject/galaxy/pull/2165
.. _Pull Request 2168: https://github.com/galaxyproject/galaxy/pull/2168
.. _Pull Request 2171: https://github.com/galaxyproject/galaxy/pull/2171
.. _Pull Request 2173: https://github.com/galaxyproject/galaxy/pull/2173
.. _Pull Request 2183: https://github.com/galaxyproject/galaxy/pull/2183
.. _Pull Request 2213: https://github.com/galaxyproject/galaxy/pull/2213
.. _Pull Request 2215: https://github.com/galaxyproject/galaxy/pull/2215
.. _Pull Request 2223: https://github.com/galaxyproject/galaxy/pull/2223
.. _Pull Request 2231: https://github.com/galaxyproject/galaxy/pull/2231
.. _Pull Request 2233: https://github.com/galaxyproject/galaxy/pull/2233
.. _Pull Request 2239: https://github.com/galaxyproject/galaxy/pull/2239
.. _Pull Request 2241: https://github.com/galaxyproject/galaxy/pull/2241
.. _Pull Request 2243: https://github.com/galaxyproject/galaxy/pull/2243
.. _Pull Request 2248: https://github.com/galaxyproject/galaxy/pull/2248
.. _Pull Request 2249: https://github.com/galaxyproject/galaxy/pull/2249
.. _Pull Request 2252: https://github.com/galaxyproject/galaxy/pull/2252
.. _Pull Request 2253: https://github.com/galaxyproject/galaxy/pull/2253
.. _Pull Request 2254: https://github.com/galaxyproject/galaxy/pull/2254
.. _Pull Request 2256: https://github.com/galaxyproject/galaxy/pull/2256
.. _Pull Request 2257: https://github.com/galaxyproject/galaxy/pull/2257
.. _Pull Request 2258: https://github.com/galaxyproject/galaxy/pull/2258
.. _Pull Request 2261: https://github.com/galaxyproject/galaxy/pull/2261
.. _Pull Request 2262: https://github.com/galaxyproject/galaxy/pull/2262
.. _Pull Request 2263: https://github.com/galaxyproject/galaxy/pull/2263
.. _Pull Request 2267: https://github.com/galaxyproject/galaxy/pull/2267
.. _Pull Request 2268: https://github.com/galaxyproject/galaxy/pull/2268
.. _Pull Request 2269: https://github.com/galaxyproject/galaxy/pull/2269
.. _Pull Request 2271: https://github.com/galaxyproject/galaxy/pull/2271
.. _Pull Request 2273: https://github.com/galaxyproject/galaxy/pull/2273
.. _Pull Request 2274: https://github.com/galaxyproject/galaxy/pull/2274
.. _Pull Request 2276: https://github.com/galaxyproject/galaxy/pull/2276
.. _Pull Request 2278: https://github.com/galaxyproject/galaxy/pull/2278
.. _Pull Request 2279: https://github.com/galaxyproject/galaxy/pull/2279
.. _Pull Request 2280: https://github.com/galaxyproject/galaxy/pull/2280
.. _Pull Request 2286: https://github.com/galaxyproject/galaxy/pull/2286
.. _Pull Request 2289: https://github.com/galaxyproject/galaxy/pull/2289
.. _Pull Request 2292: https://github.com/galaxyproject/galaxy/pull/2292
.. _Pull Request 2293: https://github.com/galaxyproject/galaxy/pull/2293
.. _Pull Request 2294: https://github.com/galaxyproject/galaxy/pull/2294
.. _Pull Request 2295: https://github.com/galaxyproject/galaxy/pull/2295
.. _Pull Request 2296: https://github.com/galaxyproject/galaxy/pull/2296
.. _Pull Request 2302: https://github.com/galaxyproject/galaxy/pull/2302
.. _Pull Request 2305: https://github.com/galaxyproject/galaxy/pull/2305
.. _Pull Request 2307: https://github.com/galaxyproject/galaxy/pull/2307
.. _Pull Request 2308: https://github.com/galaxyproject/galaxy/pull/2308
.. _Pull Request 2310: https://github.com/galaxyproject/galaxy/pull/2310
.. _Pull Request 2314: https://github.com/galaxyproject/galaxy/pull/2314
.. _Pull Request 2326: https://github.com/galaxyproject/galaxy/pull/2326
.. _Pull Request 2327: https://github.com/galaxyproject/galaxy/pull/2327
.. _Pull Request 2328: https://github.com/galaxyproject/galaxy/pull/2328
.. _Pull Request 2329: https://github.com/galaxyproject/galaxy/pull/2329
.. _Pull Request 2330: https://github.com/galaxyproject/galaxy/pull/2330
.. _Pull Request 2335: https://github.com/galaxyproject/galaxy/pull/2335
.. _Pull Request 2336: https://github.com/galaxyproject/galaxy/pull/2336
.. _Pull Request 2338: https://github.com/galaxyproject/galaxy/pull/2338
.. _Pull Request 2340: https://github.com/galaxyproject/galaxy/pull/2340
.. _Pull Request 2342: https://github.com/galaxyproject/galaxy/pull/2342
.. _Pull Request 2348: https://github.com/galaxyproject/galaxy/pull/2348
.. _Pull Request 2351: https://github.com/galaxyproject/galaxy/pull/2351
.. _Pull Request 2354: https://github.com/galaxyproject/galaxy/pull/2354
.. _Pull Request 2355: https://github.com/galaxyproject/galaxy/pull/2355
.. _Pull Request 2358: https://github.com/galaxyproject/galaxy/pull/2358
.. _Pull Request 2360: https://github.com/galaxyproject/galaxy/pull/2360
.. _Pull Request 2361: https://github.com/galaxyproject/galaxy/pull/2361
.. _Pull Request 2363: https://github.com/galaxyproject/galaxy/pull/2363
.. _Pull Request 2364: https://github.com/galaxyproject/galaxy/pull/2364
.. _Pull Request 2366: https://github.com/galaxyproject/galaxy/pull/2366
.. _Pull Request 2367: https://github.com/galaxyproject/galaxy/pull/2367
.. _Pull Request 2368: https://github.com/galaxyproject/galaxy/pull/2368
.. _Pull Request 2370: https://github.com/galaxyproject/galaxy/pull/2370
.. _Pull Request 2372: https://github.com/galaxyproject/galaxy/pull/2372
.. _Pull Request 2374: https://github.com/galaxyproject/galaxy/pull/2374
.. _Pull Request 2378: https://github.com/galaxyproject/galaxy/pull/2378
.. _Pull Request 2379: https://github.com/galaxyproject/galaxy/pull/2379
.. _Pull Request 2380: https://github.com/galaxyproject/galaxy/pull/2380
.. _Pull Request 2381: https://github.com/galaxyproject/galaxy/pull/2381
.. _Pull Request 2383: https://github.com/galaxyproject/galaxy/pull/2383
.. _Pull Request 2386: https://github.com/galaxyproject/galaxy/pull/2386
.. _Pull Request 2387: https://github.com/galaxyproject/galaxy/pull/2387
.. _Pull Request 2388: https://github.com/galaxyproject/galaxy/pull/2388
.. _Pull Request 2390: https://github.com/galaxyproject/galaxy/pull/2390
.. _Pull Request 2391: https://github.com/galaxyproject/galaxy/pull/2391
.. _Pull Request 2392: https://github.com/galaxyproject/galaxy/pull/2392
.. _Pull Request 2394: https://github.com/galaxyproject/galaxy/pull/2394
.. _Pull Request 2395: https://github.com/galaxyproject/galaxy/pull/2395
.. _Pull Request 2396: https://github.com/galaxyproject/galaxy/pull/2396
.. _Pull Request 2397: https://github.com/galaxyproject/galaxy/pull/2397
.. _Pull Request 2403: https://github.com/galaxyproject/galaxy/pull/2403
.. _Pull Request 2408: https://github.com/galaxyproject/galaxy/pull/2408
.. _Pull Request 2409: https://github.com/galaxyproject/galaxy/pull/2409
.. _Pull Request 2410: https://github.com/galaxyproject/galaxy/pull/2410
.. _Pull Request 2411: https://github.com/galaxyproject/galaxy/pull/2411
.. _Pull Request 2412: https://github.com/galaxyproject/galaxy/pull/2412
.. _Pull Request 2413: https://github.com/galaxyproject/galaxy/pull/2413
.. _Pull Request 2414: https://github.com/galaxyproject/galaxy/pull/2414
.. _Pull Request 2415: https://github.com/galaxyproject/galaxy/pull/2415
.. _Pull Request 2416: https://github.com/galaxyproject/galaxy/pull/2416
.. _Pull Request 2418: https://github.com/galaxyproject/galaxy/pull/2418
.. _Pull Request 2420: https://github.com/galaxyproject/galaxy/pull/2420
.. _Pull Request 2421: https://github.com/galaxyproject/galaxy/pull/2421
.. _Pull Request 2427: https://github.com/galaxyproject/galaxy/pull/2427
.. _Pull Request 2428: https://github.com/galaxyproject/galaxy/pull/2428
.. _Pull Request 2429: https://github.com/galaxyproject/galaxy/pull/2429
.. _Pull Request 2434: https://github.com/galaxyproject/galaxy/pull/2434
.. _Pull Request 2436: https://github.com/galaxyproject/galaxy/pull/2436
.. _Pull Request 2438: https://github.com/galaxyproject/galaxy/pull/2438
.. _Pull Request 2440: https://github.com/galaxyproject/galaxy/pull/2440
.. _Pull Request 2444: https://github.com/galaxyproject/galaxy/pull/2444
.. _Pull Request 2445: https://github.com/galaxyproject/galaxy/pull/2445
.. _Pull Request 2452: https://github.com/galaxyproject/galaxy/pull/2452
.. _Pull Request 2453: https://github.com/galaxyproject/galaxy/pull/2453
.. _Pull Request 2455: https://github.com/galaxyproject/galaxy/pull/2455
.. _Pull Request 2457: https://github.com/galaxyproject/galaxy/pull/2457
.. _Pull Request 2459: https://github.com/galaxyproject/galaxy/pull/2459
.. _Pull Request 2464: https://github.com/galaxyproject/galaxy/pull/2464
.. _Pull Request 2468: https://github.com/galaxyproject/galaxy/pull/2468
.. _Pull Request 2469: https://github.com/galaxyproject/galaxy/pull/2469
.. _Pull Request 2472: https://github.com/galaxyproject/galaxy/pull/2472
.. _Pull Request 2476: https://github.com/galaxyproject/galaxy/pull/2476
.. _Pull Request 2477: https://github.com/galaxyproject/galaxy/pull/2477
.. _Pull Request 2480: https://github.com/galaxyproject/galaxy/pull/2480
.. _Pull Request 2481: https://github.com/galaxyproject/galaxy/pull/2481
.. _Pull Request 2486: https://github.com/galaxyproject/galaxy/pull/2486
.. _Pull Request 2488: https://github.com/galaxyproject/galaxy/pull/2488
.. _Pull Request 2489: https://github.com/galaxyproject/galaxy/pull/2489
.. _Pull Request 2494: https://github.com/galaxyproject/galaxy/pull/2494
.. _Pull Request 2498: https://github.com/galaxyproject/galaxy/pull/2498
.. _Pull Request 2499: https://github.com/galaxyproject/galaxy/pull/2499
.. _Pull Request 2505: https://github.com/galaxyproject/galaxy/pull/2505
.. _Pull Request 2508: https://github.com/galaxyproject/galaxy/pull/2508
.. _Pull Request 2509: https://github.com/galaxyproject/galaxy/pull/2509
.. _Pull Request 2515: https://github.com/galaxyproject/galaxy/pull/2515
.. _Pull Request 2516: https://github.com/galaxyproject/galaxy/pull/2516
.. _Pull Request 2524: https://github.com/galaxyproject/galaxy/pull/2524
.. _Pull Request 2527: https://github.com/galaxyproject/galaxy/pull/2527
.. _Pull Request 2528: https://github.com/galaxyproject/galaxy/pull/2528
.. _Pull Request 2529: https://github.com/galaxyproject/galaxy/pull/2529
.. _Pull Request 2531: https://github.com/galaxyproject/galaxy/pull/2531
.. _Pull Request 2534: https://github.com/galaxyproject/galaxy/pull/2534
.. _Pull Request 2538: https://github.com/galaxyproject/galaxy/pull/2538
.. _Pull Request 2540: https://github.com/galaxyproject/galaxy/pull/2540
.. _Pull Request 2543: https://github.com/galaxyproject/galaxy/pull/2543
.. _Pull Request 2544: https://github.com/galaxyproject/galaxy/pull/2544
.. _Pull Request 2545: https://github.com/galaxyproject/galaxy/pull/2545
.. _Pull Request 2548: https://github.com/galaxyproject/galaxy/pull/2548
.. _Pull Request 2552: https://github.com/galaxyproject/galaxy/pull/2552
.. _Pull Request 2553: https://github.com/galaxyproject/galaxy/pull/2553
.. _Pull Request 2554: https://github.com/galaxyproject/galaxy/pull/2554
.. _Pull Request 2555: https://github.com/galaxyproject/galaxy/pull/2555
.. _Pull Request 2559: https://github.com/galaxyproject/galaxy/pull/2559
.. _Pull Request 2564: https://github.com/galaxyproject/galaxy/pull/2564
.. _Pull Request 2569: https://github.com/galaxyproject/galaxy/pull/2569
.. _Pull Request 2570: https://github.com/galaxyproject/galaxy/pull/2570
.. _Pull Request 2572: https://github.com/galaxyproject/galaxy/pull/2572
.. _Pull Request 2574: https://github.com/galaxyproject/galaxy/pull/2574
.. _Pull Request 2576: https://github.com/galaxyproject/galaxy/pull/2576
.. _Pull Request 2578: https://github.com/galaxyproject/galaxy/pull/2578
.. _Pull Request 2579: https://github.com/galaxyproject/galaxy/pull/2579
.. _Pull Request 2590: https://github.com/galaxyproject/galaxy/pull/2590
.. _Pull Request 2594: https://github.com/galaxyproject/galaxy/pull/2594
.. _Pull Request 2595: https://github.com/galaxyproject/galaxy/pull/2595
.. _Pull Request 2596: https://github.com/galaxyproject/galaxy/pull/2596
.. _Pull Request 2597: https://github.com/galaxyproject/galaxy/pull/2597
.. _Pull Request 2599: https://github.com/galaxyproject/galaxy/pull/2599
.. _Pull Request 2605: https://github.com/galaxyproject/galaxy/pull/2605
.. _Pull Request 2608: https://github.com/galaxyproject/galaxy/pull/2608
.. _Pull Request 2610: https://github.com/galaxyproject/galaxy/pull/2610
.. _Pull Request 2612: https://github.com/galaxyproject/galaxy/pull/2612
.. _Pull Request 2613: https://github.com/galaxyproject/galaxy/pull/2613
.. _Pull Request 2615: https://github.com/galaxyproject/galaxy/pull/2615
.. _Pull Request 2616: https://github.com/galaxyproject/galaxy/pull/2616
.. _Pull Request 2617: https://github.com/galaxyproject/galaxy/pull/2617
.. _Pull Request 2620: https://github.com/galaxyproject/galaxy/pull/2620
.. _Pull Request 2621: https://github.com/galaxyproject/galaxy/pull/2621
.. _Pull Request 2622: https://github.com/galaxyproject/galaxy/pull/2622
.. _Pull Request 2625: https://github.com/galaxyproject/galaxy/pull/2625
.. _Pull Request 2628: https://github.com/galaxyproject/galaxy/pull/2628
.. _Pull Request 2630: https://github.com/galaxyproject/galaxy/pull/2630
.. _Pull Request 2631: https://github.com/galaxyproject/galaxy/pull/2631
.. _Pull Request 2632: https://github.com/galaxyproject/galaxy/pull/2632
.. _Pull Request 2634: https://github.com/galaxyproject/galaxy/pull/2634
.. _Pull Request 2636: https://github.com/galaxyproject/galaxy/pull/2636
.. _Pull Request 2637: https://github.com/galaxyproject/galaxy/pull/2637
.. _Pull Request 2639: https://github.com/galaxyproject/galaxy/pull/2639
.. _Pull Request 2643: https://github.com/galaxyproject/galaxy/pull/2643
.. _Pull Request 2644: https://github.com/galaxyproject/galaxy/pull/2644
.. _Pull Request 2646: https://github.com/galaxyproject/galaxy/pull/2646
.. _Pull Request 2647: https://github.com/galaxyproject/galaxy/pull/2647
.. _Pull Request 2648: https://github.com/galaxyproject/galaxy/pull/2648
.. _Pull Request 2650: https://github.com/galaxyproject/galaxy/pull/2650
.. _Pull Request 2651: https://github.com/galaxyproject/galaxy/pull/2651
.. _Pull Request 2652: https://github.com/galaxyproject/galaxy/pull/2652
.. _Pull Request 2656: https://github.com/galaxyproject/galaxy/pull/2656
.. _Pull Request 2660: https://github.com/galaxyproject/galaxy/pull/2660
.. _Pull Request 2661: https://github.com/galaxyproject/galaxy/pull/2661
.. _Pull Request 2664: https://github.com/galaxyproject/galaxy/pull/2664
.. _Pull Request 2667: https://github.com/galaxyproject/galaxy/pull/2667
.. _Pull Request 2670: https://github.com/galaxyproject/galaxy/pull/2670
.. _Pull Request 2678: https://github.com/galaxyproject/galaxy/pull/2678
.. _Pull Request 2680: https://github.com/galaxyproject/galaxy/pull/2680
.. _Pull Request 2681: https://github.com/galaxyproject/galaxy/pull/2681
.. _Pull Request 2682: https://github.com/galaxyproject/galaxy/pull/2682
.. _Pull Request 2684: https://github.com/galaxyproject/galaxy/pull/2684
.. _Pull Request 2685: https://github.com/galaxyproject/galaxy/pull/2685
.. _Pull Request 2691: https://github.com/galaxyproject/galaxy/pull/2691
.. _Pull Request 2693: https://github.com/galaxyproject/galaxy/pull/2693
.. _Pull Request 2701: https://github.com/galaxyproject/galaxy/pull/2701
.. _Pull Request 2721: https://github.com/galaxyproject/galaxy/pull/2721
.. _Pull Request 2723: https://github.com/galaxyproject/galaxy/pull/2723
.. _Pull Request 2737: https://github.com/galaxyproject/galaxy/pull/2737
.. _Pull Request 2743: https://github.com/galaxyproject/galaxy/pull/2743
.. _Pull Request 2744: https://github.com/galaxyproject/galaxy/pull/2744
.. _Pull Request 2749: https://github.com/galaxyproject/galaxy/pull/2749
.. _Pull Request 2750: https://github.com/galaxyproject/galaxy/pull/2750
.. _Pull Request 2756: https://github.com/galaxyproject/galaxy/pull/2756
.. _Pull Request 2759: https://github.com/galaxyproject/galaxy/pull/2759
.. _Pull Request 2773: https://github.com/galaxyproject/galaxy/pull/2773
.. _Pull Request 2774: https://github.com/galaxyproject/galaxy/pull/2774
.. _Pull Request 2780: https://github.com/galaxyproject/galaxy/pull/2780
.. _Pull Request 2789: https://github.com/galaxyproject/galaxy/pull/2789
.. _Pull Request 2792: https://github.com/galaxyproject/galaxy/pull/2792
.. _Pull Request 2809: https://github.com/galaxyproject/galaxy/pull/2809
.. _Pull Request 2810: https://github.com/galaxyproject/galaxy/pull/2810
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