.. to_doc

-------------------------------
16.01
-------------------------------

.. announce_start

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

.. major_feature

* Interactive tours (with significant help from
  `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1422`_, `Pull Request 1464`_
* Replace Galaxy eggs dependency management with wheels.
  `Pull Request 428`_, `Pull Request 989`_, `Pull Request 988`_,
  `Pull Request 1389`_, `Pull Request 1485`_, `Pull Request 995`_,
  `Pull Request 996`_, `Pull Request 1006`_, `Pull Request 1017`_,
  `Pull Request 1037`_, `Pull Request 1495`_
* Implement nested workflows.
  `Pull Request 1306`_

.. feature

* Use Webpack to greatly optimize JavaScript and other assets served by Galaxy.
  `Pull Request 1144`_
* Overhaul Galaxy analysis view toward a more modular JavaScript architecture.
  `Pull Request 706`_, `Pull Request 1184`_
* Add BAM iobio_ visualization as a Galaxy Interactive Environment
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1131`_
* Add Jupyter Interactive Environment
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1400`_
* Procedures for bug and issue handling as well as roadmap management.
  `Pull Request 902`_, `Pull Request 1020`_
* Implement a conda dependency resolver (with significant help from
  `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1345`_, `Pull Request 1527`_, `Pull Request 1421`_,
  `Pull Request 1409`_
* Many ToolBox improvements including allowing specifying labels on individual
  tools, monitoring and automatic reloading of ``tool_conf.xml`` files, and 
  allowing specification of such files in JSON/YAML.
  `Pull Request 1012`_, `Pull Request 1398`_
* Configurable client side logging.
  `Pull Request 1011`_
* Allow input collections to specify multiple ``collection_type``\ s.
  `Pull Request 1308`_
* Allow multiple collections to be supplied to a multiple data parameter.
  `Pull Request 805`_
* Implement ``type_source`` on output collections.
  `Pull Request 1153`_
* Allow tools to request a special configuration file containing tool parameters 
  dumped to json.
  `Pull Request 1405`_
* Add search on username/any for API calls to user and use Select2 for sharing
  workflows/pages/histories
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1111`_
* Improve masthead and scratchbook UI and architecture.
  `Pull Request 1407`_, `Pull Request 1424`_
* Add support for constructive solid geometry datatypes ``ply`` and ``vtk``.
  (Thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__.)
  `Pull Request 905`_, `Pull Request 1211`_
* Add searchgui datatype
  (thanks to `@jj-umn <https://github.com/jj-umn>`__.)
  `Pull Request 914`_
* Add BIOM v1 datatype
  (thanks to `@fescudie <https://github.com/fescudie>`__.)
  `Pull Request 950`_, `Pull Request 1198`_
* Add CRAM datatype 
  (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
  `Pull Request 1108`_, `Pull Request 1182`_
* Add UniProtXML datatype
  (thanks to `@jj-umn <https://github.com/jj-umn>`__.)
  `Pull Request 1004`_
* Avoid confusion by adding the PDF datatype to the list of uploadable file
  types.
  `Pull Request 901`_
* Add idpDB and HDF5 sniffers and fix MzSQlite sniffer
  (thanks to `@chambm <https://github.com/chambm>`__.)
  `Pull Request 1209`_
* Improve tool shed installation API for installation of repositories if they
  are already installed
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1095`_
* Prevent GIEs from being closed without user confirmation
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1178`_
* Add the constructive solid geometery (CSG) viewer visualization plugin
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__.)
  `Pull Request 1254`_
* Add Google analytics tracking to new data libraries.
  `Pull Request 959`_
* Extend users API with delete action
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1063`_
* Finish swapping unencoded ids with order_index in workflows API.
  `Pull Request 1137`_

.. enhancement

* Add documentation and extra options to Environment Modules resolver
  (thanks to `@pvanheus <https://github.com/pvanheus>`__.)
  `Pull Request 1221`_
* Documentation for dependency resolvers
  (thanks to `@pvanheus <https://github.com/pvanheus>`__.)
  `Pull Request 1296`_
* Populate env.sh files created via tool shed installations with ``X_ROOT_DIR``
  environment variables.
  `Pull Request 564`_, `Pull Request 889`_
* Reorganize history menu
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 985`_
* Look up installed tools from different toolshed(s)
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 818`_, `Pull Request 1286`_
* Documentation updates for ObjectStore
  (thanks to `@mr-c <https://github.com/mr-c>`__.)
  `Pull Request 853`_
* Update JavaScript dependency Dynatree.
  `Pull Request 856`_
* Eliminate LWR from Galaxy (you will need to upgrade to Pulsar).
  `Pull Request 857`_
* Isolate tool commands by default.
  `Pull Request 1412`_, `Pull Request 1494`_
* Allow override of job shell (for conda resolver).
  `Pull Request 1473`_
* Slight tweak to sidebar section naming from 'security' to 'user management'.
  `Pull Request 877`_
* Fix the issue where too many datasets are linked to a certain role
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__.)
  `Pull Request 881`_
* Fix R dependency installation to be more portable
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 893`_
* Reorder workflow inputs to top
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__.)
  `Pull Request 912`_
* Add an API script to upload directory as a data library
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 918`_
* Enable dockerized toolshed tests.
  `Pull Request 942`_
* Improvements and fixes for abstract tool interface.
  `Pull Request 955`_
* Remove remaining references to galaxy.eggs and flake8 some tools
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 990`_
* Apply stricter flake8 rules for the directories shared with Pulsar
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1010`_
* Updates to default welcome page.
  `Pull Request 1013`_
* Revise deferred queue, use jQuery promises.
  `Pull Request 1018`_
* Keep select field open in tool form multi select fields to ease selecting many
  options quickly.
  `Pull Request 1019`_
* Allow resizing of regular multi-select boxes.
  `Pull Request 1025`_
* Add error message for wrongly formatted data in wig_to_bigwig
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__.)
  `Pull Request 1033`_
* Verify len files during download from UCSC
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1066`_
* Add biocrusoe to contributors
  `Pull Request 1067`_
* Outline "Format 2" workflow definitions.
  `Pull Request 1096`_
* Improve the API attributes display on parameters page.
  `Pull Request 1098`_
* Update run_tests.sh help for recent changes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1101`_
* Show welcome page with required login.
  `Pull Request 1105`_
* Allow accessing collection elements in format_source.
  (with significant help from `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1113`_, `Pull Request 1155`_
* Add nginx config for GIE proxy to documentation.
  `Pull Request 1123`_
* Enforce client build deps are up-to-date.
  `Pull Request 1130`_
* Menu onclick addition.
  `Pull Request 1142`_
* Ensure confirmation when leaving GIE windows.
  `Pull Request 1157`_
* Add local grunt-cli dependency for qunit tests.
  `Pull Request 1159`_
* Tighten up GG sniffing
  `Pull Request 864`_
* Use common exceptions in tools.
  `Pull Request 874`_
* Refactor the remote user middleware for complexity
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 875`_
* Allowed for capitalized package names such as R in unlinked tool shed
  dependency resolver
  (thanks to `@Christian-B <https://github.com/Christian-B>`__.)
  `Pull Request 1160`_
* A slew of tool execution performance optimizations including a huge
  fix from `@ericenns <https://github.com/ericenns>`__.
  `Pull Request 1166`_, `Pull Request 1163`_, `Pull Request 1199`_,
  `Pull Request 1212`_
* Do not check for tool migrations when running tests.
  `Pull Request 1176`_
* Lazy load HDA/LDDA metadata to speed up history loading
  (thanks to `@abretaud <https://github.com/abretaud>`__.)
  `Pull Request 1179`_
* Add debug statement in output checker for why job is failing.
  `Pull Request 1213`_
* Small enhancements in workflow inputs and outputs.
  `Pull Request 1214`_
* More small workflow tweaks.
  `Pull Request 1216`_
* Add Workflow editor UI for step labels.
  `Pull Request 1251`_
* Ease the grunt uglify process
  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1238`_
* Add beta run workflow form based on the newer tool form code.
  `Pull Request 1249`_
* During tool migrations, do not mess with galaxy_config_file if provided
  (thanks to `@openlangrid <https://github.com/openlangrid>`__ and `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1230`_, `Pull Request 1253`_
* In the users API, properly return a boolean from has_requests
  `Pull Request 1262`_
* Extend the logging of tool dependency status changes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1263`_
* Remove history_options and options.mako (history options as a page).
  `Pull Request 1271`_
* Minor mail config cleanup
  `Pull Request 1299`_
* Replace uses of history.imp and history.copy web methods for API create
  `Pull Request 1303`_
* More tightening up of parameter validation during workflow stuff.
  `Pull Request 1319`_
* Show a more user-friendly error when the webserver port is blocked
  (thanks to `@shano <https://github.com/shano>`__.)
  `Pull Request 1320`_
* Upgrade Paste to 2.0.2.
  `Pull Request 1344`_
* A series of small refactoring enabling use of certain Galaxy modules
  a stand-alone Python library with minimal dependencies and Python 3
  compatibility.
  `Pull Request 1350`_, `Pull Request 1351`_, `Pull Request 1352`_,
  `Pull Request 1359`_, `Pull Request 1362`_, `Pull Request 1376`_,
  `Pull Request 1413`_, `Pull Request 1427`_, `Pull Request 1363`_,
  `Pull Request 1367`_, `Pull Request 1377`_, `Pull Request 1388`_,
  `Pull Request 1448`_
* Adding UUID support to directory_hash_id
  (thanks to `@kellrott <https://github.com/kellrott>`__.)
  `Pull Request 1397`_
* Unify and abstract code for checking if file looks like a tool definition.
  `Pull Request 1368`_
* Added hashes to pip requirements file
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1393`_
* Interactive environment updates
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1399`_
* Change scratchbook close icon.
  `Pull Request 1425`_
* Rename reports_wsgi.ini to reports.ini
  (thanks to `@souravsingh <https://github.com/souravsingh>`__.)
  `Pull Request 1181`_

.. small_enhancement

* Attempt to fix more transiently failing API tests.
  `Pull Request 859`_, `Pull Request 865`_  
* Fix data library test case.
  `Pull Request 898`_
* Remove ``test_map_over_two_collections_legacy`` test case as it is obsolete.
  `Pull Request 924`_
* Version the testing-base docker image.
  `Pull Request 938`_
* Update casperjs functional tests.
  `Pull Request 944`_
* Fix the docker db client_encoding to not be ascii (default).
  `Pull Request 952`_
* Use the database temp directory to store the Mako template cache when
  running framework tests.
  `Pull Request 956`_
* Rename ``lib/galaxy/main.py`` to scripts/galaxy-main
  `Pull Request 994`_
* Fix deferred dom removal.
  `Pull Request 997`_
* Options to more easily test esoteric tooling options.
  `Pull Request 1014`_
* Fix log statements and link to logger.
  `Pull Request 1040`_
* Add more data libraries API tests.
  `Pull Request 1074`_
* Remove upload unused function parameter
  (thanks to `@einon <https://github.com/einon>`__.)
  `Pull Request 1078`_
* Update testing docker image.
  `Pull Request 1083`_
* Small tool and workflow refactorings.
  `Pull Request 1097`_
* Revise and fix waiting for tool tests.
  `Pull Request 1119`_
* Small Tool and Workflow Refactoring and Fixes
  `Pull Request 1202`_
* Wait on jobs and history in certain API test cases.
  `Pull Request 1226`_
* Fix qunit shim to match base_panels.mako shim.
  `Pull Request 1233`_
* Improved logging related tool test timeouts.
  `Pull Request 1243`_
* Refactor generic side workflow editor panel toward backbone.
  `Pull Request 1247`_
* Attempt to fix transiently failing tool test on Jenkins.
  `Pull Request 1248`_
* Set client_encoding for TS dockerized test db
  `Pull Request 1276`_
* Check for sessionStorage using a more cross-browser way.
  `Pull Request 1279`_
* Small API test improvements.
  `Pull Request 1285`_
* Enforce metrics related to moving toward modern client infrastructure.
  `Pull Request 1292`_
* Refactor tool stuff for generic model actions.
  `Pull Request 1307`_
* Remove workflow casperjs API test duplicating test coverage of API tests.
  `Pull Request 1316`_
* Refactor tool parsing handling toward reuse outside Galaxy.
  `Pull Request 1349`_, `Pull Request 1353`_
* Lint with Python 3 several modules.
  `Pull Request 1354`_
* Fix and potential fix for transiently failing tests.
  `Pull Request 1401`_
* Fix CasperJS tests.
  `Pull Request 1438`_, `Pull Request 1439`_
* Add a log.warn() if extracted file does not exist when changing permissions.
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 939`_
* Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory.
  `Commit f540a16`_

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

.. security

* Security fixes for history imports.
  `Commit bf1c77d`_
* Security fixes for object store paths.
  `Commit 5da91bd`_
* Remove sample tracking manual external service transfer due to security concerns.
  `Commit cd8b965`_
* Security fixes for tool shed repository browsing.
  `Commit e4a1d57`_
* Security fixes for tool shed hg push and capsule/tarball uploads.
  `Commit e845d64`_

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

.. major_bug

.. bug

* Add check for ``HTTP_GX_SECRET``
  (thanks to `@golharam <https://github.com/golharam>`__.)
  `Pull Request 827`_
* Test if parameter present in value to avoid index error in
  tool state handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 863`_
* Bump version of sqlite3 in nodejs proxy
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 866`_
* Expose API keys to admins under ``REMOTE_USER``
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 872`_
* Bug fix for tool shed repository API
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 891`_
* Add a workaround to return a proper error code during R
  package installation
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 892`_
* Various Quota bug fixes.
  `Pull Request 907`_
* Always set 'tests' for a visualization plugin to avoid an attribute
  error.
  `Pull Request 908`_
* Bug fix for condor runner changes made this release cycle
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 909`_
* Change user preference datatype to text.
  `Pull Request 916`_
* Fix syntax of error parameter of ``tryCatch`` in ``setup_r_environment action``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 929`_
* Revise tool URL building.
  `Pull Request 947`_
* Fix for code checking if a file seems to a tool definition file
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 949`_
* Fix base panels to include scripts as the last element of the body.
  `Pull Request 969`_
* Grid batch operation fixes.
  `Pull Request 971`_
* Fix extra files path URL problem.
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 991`_
* Fixes broken env-var declarations for tools with weird chars in their names
  (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
  `Pull Request 1028`_
* Added gitignore rules to ignore custom tool-data
  (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
  `Pull Request 1048`_
* Fix import of history datasets into library.
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1049`_
* Fix for reloading tools that have non-standard tool_ids/versions.
  `Pull Request 1050`_
* Improved encoding handling for Jobs.
  `Pull Request 1052`_
* Fix lped report output from converter.
  `Pull Request 1069`_, `Pull Request 1070`_, `Pull Request 1072`_
* Trivial: Replace unnecessary duplicated var check with 'else if'
  (thanks to `@einon <https://github.com/einon>`__.)
  `Pull Request 1073`_
* Fix a bug in IEs when proxying the proxy.
  `Pull Request 1076`_
* Fix 500 error when attempting to update installed repository.
  `Pull Request 1082`_
* Resolve conflicting label CSS class for trackster.
  `Pull Request 1086`_
* Fix bug with referrer attribute type change in WebOb.
  `Pull Request 1091`_
* Fix API TS installation
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1094`_
* Better error when tool shed repository directory is missing
  (thanks to `@lparsons <https://github.com/lparsons>`__.)
  `Pull Request 1107`_
* Don't let ``$input`` hang cheetah evaluation.
  `Pull Request 1117`_
* Fix for re-installing an uninstalled TS repository with a dependency
  (Thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__.)
  `Pull Request 1154`_
* Fix interface and usage of ``WorkflowModule.get_runtime_inputs``.
  `Pull Request 1174`_
* Add enhancements to the Galaxy repository install process
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1193`_
* Tool shed fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1200`_
* Fix for updating tool parameter dicts when a new parameter has been added to
  a section.
  `Pull Request 1215`_
* Replace the defunct readthedocs badge.
  `Pull Request 1229`_
* Export ``GALAXY_TEST_DBURI`` as ``GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION``
  before installing wheels.
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1231`_
* Fix passing of nginx_upload_path and ftp_upload_site.
  `Pull Request 1250`_
* Fixed indentation errors for reports app
  (thanks to `@markiskander <https://github.com/markiskander>`__.)
  `Pull Request 1259`_
* Open select2 drop down on caret click.
  `Pull Request 1298`_
* Improved validation of tools during workflow execution.
  `Pull Request 1302`_
* Properly remove datasets from the filtered lists when pairing datasets
  for the paired dataset list creator.
  `Pull Request 1310`_
* Update Kombu and AMQP wheels to fix problems with El Capitan's System
  Integrity Protection.
  `Pull Request 1327`_
* Fix for creating workflow outputs on initial workflow upload.
  `Pull Request 1330`_
* Don't query on unencoded IDs for error form
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1340`_
* If ``GALAXY_SLOTS`` is defined in the environment, use it for the local runner.
  `Pull Request 1346`_
* Use both ``SLURM_NTASKS`` and ``SLURM_CPUS_PER_TASK`` to set ``GALAXY_SLOTS``
  (thanks to `@lparsons <https://github.com/lparsons>`__.)
  `Pull Request 1347`_
* Fix for loading workflows that have tool version / step upgrade messages.
  `Pull Request 1348`_
* Allow installation of different repositories with the same name in a single
  request
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1366`_
* Copy workflow objects when importing them.
  `Pull Request 1474`_
* Undo user icon in masthead.
  `Pull Request 1493`_
* Fix mime type when previewing certain tabular data.
  `Pull Request 1498`_
* Fix disabled CSS.
  `Pull Request 1501`_
* catch Exception and properly log errors
  `Pull Request 1511`_
* Fix for workflow validation problem introduced in 15.10.
  `Pull Request 1536`_,
  `Issue #1514 <https://github.com/galaxyproject/galaxy/issues/1514>`__
* Keep track of hidden datasets.
  `Pull Request 1551`_
* Force ``--skip-venv`` if we can detect that Python is Conda Python.
  `Pull Request 1554`_
* Fix installation of Tool Shed repositories containing non-ASCII characters
  in the description.
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1759`_
* Fix pretty_print_time_interval for MySQL.
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1761`_

.. _iobio: http://iobio.io/

.. github_links

.. _Pull Request 428: https://github.com/galaxyproject/galaxy/pull/428
.. _Pull Request 564: https://github.com/galaxyproject/galaxy/pull/564
.. _Pull Request 706: https://github.com/galaxyproject/galaxy/pull/706
.. _Pull Request 805: https://github.com/galaxyproject/galaxy/pull/805
.. _Pull Request 818: https://github.com/galaxyproject/galaxy/pull/818
.. _Pull Request 827: https://github.com/galaxyproject/galaxy/pull/827
.. _Pull Request 853: https://github.com/galaxyproject/galaxy/pull/853
.. _Pull Request 856: https://github.com/galaxyproject/galaxy/pull/856
.. _Pull Request 857: https://github.com/galaxyproject/galaxy/pull/857
.. _Pull Request 859: https://github.com/galaxyproject/galaxy/pull/859
.. _Pull Request 863: https://github.com/galaxyproject/galaxy/pull/863
.. _Pull Request 864: https://github.com/galaxyproject/galaxy/pull/864
.. _Pull Request 865: https://github.com/galaxyproject/galaxy/pull/865
.. _Pull Request 866: https://github.com/galaxyproject/galaxy/pull/866
.. _Pull Request 872: https://github.com/galaxyproject/galaxy/pull/872
.. _Pull Request 874: https://github.com/galaxyproject/galaxy/pull/874
.. _Pull Request 875: https://github.com/galaxyproject/galaxy/pull/875
.. _Pull Request 876: https://github.com/galaxyproject/galaxy/pull/876
.. _Pull Request 877: https://github.com/galaxyproject/galaxy/pull/877
.. _Pull Request 881: https://github.com/galaxyproject/galaxy/pull/881
.. _Pull Request 889: https://github.com/galaxyproject/galaxy/pull/889
.. _Pull Request 891: https://github.com/galaxyproject/galaxy/pull/891
.. _Pull Request 892: https://github.com/galaxyproject/galaxy/pull/892
.. _Pull Request 893: https://github.com/galaxyproject/galaxy/pull/893
.. _Pull Request 898: https://github.com/galaxyproject/galaxy/pull/898
.. _Pull Request 901: https://github.com/galaxyproject/galaxy/pull/901
.. _Pull Request 902: https://github.com/galaxyproject/galaxy/pull/902
.. _Pull Request 905: https://github.com/galaxyproject/galaxy/pull/905
.. _Pull Request 907: https://github.com/galaxyproject/galaxy/pull/907
.. _Pull Request 908: https://github.com/galaxyproject/galaxy/pull/908
.. _Pull Request 909: https://github.com/galaxyproject/galaxy/pull/909
.. _Pull Request 912: https://github.com/galaxyproject/galaxy/pull/912
.. _Pull Request 914: https://github.com/galaxyproject/galaxy/pull/914
.. _Pull Request 916: https://github.com/galaxyproject/galaxy/pull/916
.. _Pull Request 918: https://github.com/galaxyproject/galaxy/pull/918
.. _Pull Request 924: https://github.com/galaxyproject/galaxy/pull/924
.. _Pull Request 929: https://github.com/galaxyproject/galaxy/pull/929
.. _Pull Request 938: https://github.com/galaxyproject/galaxy/pull/938
.. _Pull Request 939: https://github.com/galaxyproject/galaxy/pull/939
.. _Pull Request 942: https://github.com/galaxyproject/galaxy/pull/942
.. _Pull Request 944: https://github.com/galaxyproject/galaxy/pull/944
.. _Pull Request 947: https://github.com/galaxyproject/galaxy/pull/947
.. _Pull Request 949: https://github.com/galaxyproject/galaxy/pull/949
.. _Pull Request 950: https://github.com/galaxyproject/galaxy/pull/950
.. _Pull Request 952: https://github.com/galaxyproject/galaxy/pull/952
.. _Pull Request 955: https://github.com/galaxyproject/galaxy/pull/955
.. _Pull Request 956: https://github.com/galaxyproject/galaxy/pull/956
.. _Pull Request 959: https://github.com/galaxyproject/galaxy/pull/959
.. _Pull Request 960: https://github.com/galaxyproject/galaxy/pull/960
.. _Pull Request 969: https://github.com/galaxyproject/galaxy/pull/969
.. _Pull Request 971: https://github.com/galaxyproject/galaxy/pull/971
.. _Pull Request 985: https://github.com/galaxyproject/galaxy/pull/985
.. _Pull Request 988: https://github.com/galaxyproject/galaxy/pull/988
.. _Pull Request 989: https://github.com/galaxyproject/galaxy/pull/989
.. _Pull Request 990: https://github.com/galaxyproject/galaxy/pull/990
.. _Pull Request 991: https://github.com/galaxyproject/galaxy/pull/991
.. _Pull Request 994: https://github.com/galaxyproject/galaxy/pull/994
.. _Pull Request 995: https://github.com/galaxyproject/galaxy/pull/995
.. _Pull Request 996: https://github.com/galaxyproject/galaxy/pull/996
.. _Pull Request 997: https://github.com/galaxyproject/galaxy/pull/997
.. _Pull Request 1004: https://github.com/galaxyproject/galaxy/pull/1004
.. _Pull Request 1006: https://github.com/galaxyproject/galaxy/pull/1006
.. _Pull Request 1010: https://github.com/galaxyproject/galaxy/pull/1010
.. _Pull Request 1011: https://github.com/galaxyproject/galaxy/pull/1011
.. _Pull Request 1012: https://github.com/galaxyproject/galaxy/pull/1012
.. _Pull Request 1013: https://github.com/galaxyproject/galaxy/pull/1013
.. _Pull Request 1014: https://github.com/galaxyproject/galaxy/pull/1014
.. _Pull Request 1017: https://github.com/galaxyproject/galaxy/pull/1017
.. _Pull Request 1018: https://github.com/galaxyproject/galaxy/pull/1018
.. _Pull Request 1019: https://github.com/galaxyproject/galaxy/pull/1019
.. _Pull Request 1020: https://github.com/galaxyproject/galaxy/pull/1020
.. _Pull Request 1025: https://github.com/galaxyproject/galaxy/pull/1025
.. _Pull Request 1028: https://github.com/galaxyproject/galaxy/pull/1028
.. _Pull Request 1033: https://github.com/galaxyproject/galaxy/pull/1033
.. _Pull Request 1037: https://github.com/galaxyproject/galaxy/pull/1037
.. _Pull Request 1040: https://github.com/galaxyproject/galaxy/pull/1040
.. _Pull Request 1048: https://github.com/galaxyproject/galaxy/pull/1048
.. _Pull Request 1049: https://github.com/galaxyproject/galaxy/pull/1049
.. _Pull Request 1050: https://github.com/galaxyproject/galaxy/pull/1050
.. _Pull Request 1052: https://github.com/galaxyproject/galaxy/pull/1052
.. _Pull Request 1063: https://github.com/galaxyproject/galaxy/pull/1063
.. _Pull Request 1066: https://github.com/galaxyproject/galaxy/pull/1066
.. _Pull Request 1067: https://github.com/galaxyproject/galaxy/pull/1067
.. _Pull Request 1069: https://github.com/galaxyproject/galaxy/pull/1069
.. _Pull Request 1070: https://github.com/galaxyproject/galaxy/pull/1070
.. _Pull Request 1072: https://github.com/galaxyproject/galaxy/pull/1072
.. _Pull Request 1073: https://github.com/galaxyproject/galaxy/pull/1073
.. _Pull Request 1074: https://github.com/galaxyproject/galaxy/pull/1074
.. _Pull Request 1076: https://github.com/galaxyproject/galaxy/pull/1076
.. _Pull Request 1078: https://github.com/galaxyproject/galaxy/pull/1078
.. _Pull Request 1082: https://github.com/galaxyproject/galaxy/pull/1082
.. _Pull Request 1083: https://github.com/galaxyproject/galaxy/pull/1083
.. _Pull Request 1086: https://github.com/galaxyproject/galaxy/pull/1086
.. _Pull Request 1091: https://github.com/galaxyproject/galaxy/pull/1091
.. _Pull Request 1094: https://github.com/galaxyproject/galaxy/pull/1094
.. _Pull Request 1095: https://github.com/galaxyproject/galaxy/pull/1095
.. _Pull Request 1096: https://github.com/galaxyproject/galaxy/pull/1096
.. _Pull Request 1097: https://github.com/galaxyproject/galaxy/pull/1097
.. _Pull Request 1098: https://github.com/galaxyproject/galaxy/pull/1098
.. _Pull Request 1101: https://github.com/galaxyproject/galaxy/pull/1101
.. _Pull Request 1105: https://github.com/galaxyproject/galaxy/pull/1105
.. _Pull Request 1107: https://github.com/galaxyproject/galaxy/pull/1107
.. _Pull Request 1108: https://github.com/galaxyproject/galaxy/pull/1108
.. _Pull Request 1111: https://github.com/galaxyproject/galaxy/pull/1111
.. _Pull Request 1113: https://github.com/galaxyproject/galaxy/pull/1113
.. _Pull Request 1117: https://github.com/galaxyproject/galaxy/pull/1117
.. _Pull Request 1119: https://github.com/galaxyproject/galaxy/pull/1119
.. _Pull Request 1123: https://github.com/galaxyproject/galaxy/pull/1123
.. _Pull Request 1126: https://github.com/galaxyproject/galaxy/pull/1126
.. _Pull Request 1130: https://github.com/galaxyproject/galaxy/pull/1130
.. _Pull Request 1131: https://github.com/galaxyproject/galaxy/pull/1131
.. _Pull Request 1137: https://github.com/galaxyproject/galaxy/pull/1137
.. _Pull Request 1142: https://github.com/galaxyproject/galaxy/pull/1142
.. _Pull Request 1144: https://github.com/galaxyproject/galaxy/pull/1144
.. _Pull Request 1153: https://github.com/galaxyproject/galaxy/pull/1153
.. _Pull Request 1154: https://github.com/galaxyproject/galaxy/pull/1154
.. _Pull Request 1155: https://github.com/galaxyproject/galaxy/pull/1155
.. _Pull Request 1157: https://github.com/galaxyproject/galaxy/pull/1157
.. _Pull Request 1159: https://github.com/galaxyproject/galaxy/pull/1159
.. _Pull Request 1160: https://github.com/galaxyproject/galaxy/pull/1160
.. _Pull Request 1163: https://github.com/galaxyproject/galaxy/pull/1163
.. _Pull Request 1166: https://github.com/galaxyproject/galaxy/pull/1166
.. _Pull Request 1174: https://github.com/galaxyproject/galaxy/pull/1174
.. _Pull Request 1176: https://github.com/galaxyproject/galaxy/pull/1176
.. _Pull Request 1178: https://github.com/galaxyproject/galaxy/pull/1178
.. _Pull Request 1179: https://github.com/galaxyproject/galaxy/pull/1179
.. _Pull Request 1181: https://github.com/galaxyproject/galaxy/pull/1181
.. _Pull Request 1182: https://github.com/galaxyproject/galaxy/pull/1182
.. _Pull Request 1184: https://github.com/galaxyproject/galaxy/pull/1184
.. _Pull Request 1193: https://github.com/galaxyproject/galaxy/pull/1193
.. _Pull Request 1198: https://github.com/galaxyproject/galaxy/pull/1198
.. _Pull Request 1199: https://github.com/galaxyproject/galaxy/pull/1199
.. _Pull Request 1200: https://github.com/galaxyproject/galaxy/pull/1200
.. _Pull Request 1202: https://github.com/galaxyproject/galaxy/pull/1202
.. _Pull Request 1209: https://github.com/galaxyproject/galaxy/pull/1209
.. _Pull Request 1211: https://github.com/galaxyproject/galaxy/pull/1211
.. _Pull Request 1212: https://github.com/galaxyproject/galaxy/pull/1212
.. _Pull Request 1213: https://github.com/galaxyproject/galaxy/pull/1213
.. _Pull Request 1214: https://github.com/galaxyproject/galaxy/pull/1214
.. _Pull Request 1215: https://github.com/galaxyproject/galaxy/pull/1215
.. _Pull Request 1216: https://github.com/galaxyproject/galaxy/pull/1216
.. _Pull Request 1217: https://github.com/galaxyproject/galaxy/pull/1217
.. _Pull Request 1221: https://github.com/galaxyproject/galaxy/pull/1221
.. _Pull Request 1226: https://github.com/galaxyproject/galaxy/pull/1226
.. _Pull Request 1229: https://github.com/galaxyproject/galaxy/pull/1229
.. _Pull Request 1230: https://github.com/galaxyproject/galaxy/pull/1230
.. _Pull Request 1231: https://github.com/galaxyproject/galaxy/pull/1231
.. _Pull Request 1233: https://github.com/galaxyproject/galaxy/pull/1233
.. _Pull Request 1238: https://github.com/galaxyproject/galaxy/pull/1238
.. _Pull Request 1243: https://github.com/galaxyproject/galaxy/pull/1243
.. _Pull Request 1247: https://github.com/galaxyproject/galaxy/pull/1247
.. _Pull Request 1248: https://github.com/galaxyproject/galaxy/pull/1248
.. _Pull Request 1249: https://github.com/galaxyproject/galaxy/pull/1249
.. _Pull Request 1250: https://github.com/galaxyproject/galaxy/pull/1250
.. _Pull Request 1251: https://github.com/galaxyproject/galaxy/pull/1251
.. _Pull Request 1253: https://github.com/galaxyproject/galaxy/pull/1253
.. _Pull Request 1254: https://github.com/galaxyproject/galaxy/pull/1254
.. _Pull Request 1259: https://github.com/galaxyproject/galaxy/pull/1259
.. _Pull Request 1261: https://github.com/galaxyproject/galaxy/pull/1261
.. _Pull Request 1262: https://github.com/galaxyproject/galaxy/pull/1262
.. _Pull Request 1263: https://github.com/galaxyproject/galaxy/pull/1263
.. _Pull Request 1271: https://github.com/galaxyproject/galaxy/pull/1271
.. _Pull Request 1276: https://github.com/galaxyproject/galaxy/pull/1276
.. _Pull Request 1277: https://github.com/galaxyproject/galaxy/pull/1277
.. _Pull Request 1279: https://github.com/galaxyproject/galaxy/pull/1279
.. _Pull Request 1285: https://github.com/galaxyproject/galaxy/pull/1285
.. _Pull Request 1286: https://github.com/galaxyproject/galaxy/pull/1286
.. _Pull Request 1292: https://github.com/galaxyproject/galaxy/pull/1292
.. _Pull Request 1296: https://github.com/galaxyproject/galaxy/pull/1296
.. _Pull Request 1298: https://github.com/galaxyproject/galaxy/pull/1298
.. _Pull Request 1299: https://github.com/galaxyproject/galaxy/pull/1299
.. _Pull Request 1302: https://github.com/galaxyproject/galaxy/pull/1302
.. _Pull Request 1303: https://github.com/galaxyproject/galaxy/pull/1303
.. _Pull Request 1306: https://github.com/galaxyproject/galaxy/pull/1306
.. _Pull Request 1307: https://github.com/galaxyproject/galaxy/pull/1307
.. _Pull Request 1308: https://github.com/galaxyproject/galaxy/pull/1308
.. _Pull Request 1310: https://github.com/galaxyproject/galaxy/pull/1310
.. _Pull Request 1316: https://github.com/galaxyproject/galaxy/pull/1316
.. _Pull Request 1319: https://github.com/galaxyproject/galaxy/pull/1319
.. _Pull Request 1320: https://github.com/galaxyproject/galaxy/pull/1320
.. _Pull Request 1327: https://github.com/galaxyproject/galaxy/pull/1327
.. _Pull Request 1330: https://github.com/galaxyproject/galaxy/pull/1330
.. _Pull Request 1340: https://github.com/galaxyproject/galaxy/pull/1340
.. _Pull Request 1343: https://github.com/galaxyproject/galaxy/pull/1343
.. _Pull Request 1344: https://github.com/galaxyproject/galaxy/pull/1344
.. _Pull Request 1345: https://github.com/galaxyproject/galaxy/pull/1345
.. _Pull Request 1346: https://github.com/galaxyproject/galaxy/pull/1346
.. _Pull Request 1347: https://github.com/galaxyproject/galaxy/pull/1347
.. _Pull Request 1348: https://github.com/galaxyproject/galaxy/pull/1348
.. _Pull Request 1349: https://github.com/galaxyproject/galaxy/pull/1349
.. _Pull Request 1350: https://github.com/galaxyproject/galaxy/pull/1350
.. _Pull Request 1351: https://github.com/galaxyproject/galaxy/pull/1351
.. _Pull Request 1352: https://github.com/galaxyproject/galaxy/pull/1352
.. _Pull Request 1353: https://github.com/galaxyproject/galaxy/pull/1353
.. _Pull Request 1354: https://github.com/galaxyproject/galaxy/pull/1354
.. _Pull Request 1359: https://github.com/galaxyproject/galaxy/pull/1359
.. _Pull Request 1362: https://github.com/galaxyproject/galaxy/pull/1362
.. _Pull Request 1363: https://github.com/galaxyproject/galaxy/pull/1363
.. _Pull Request 1366: https://github.com/galaxyproject/galaxy/pull/1366
.. _Pull Request 1367: https://github.com/galaxyproject/galaxy/pull/1367
.. _Pull Request 1368: https://github.com/galaxyproject/galaxy/pull/1368
.. _Pull Request 1376: https://github.com/galaxyproject/galaxy/pull/1376
.. _Pull Request 1377: https://github.com/galaxyproject/galaxy/pull/1377
.. _Pull Request 1385: https://github.com/galaxyproject/galaxy/pull/1385
.. _Pull Request 1388: https://github.com/galaxyproject/galaxy/pull/1388
.. _Pull Request 1389: https://github.com/galaxyproject/galaxy/pull/1389
.. _Pull Request 1393: https://github.com/galaxyproject/galaxy/pull/1393
.. _Pull Request 1397: https://github.com/galaxyproject/galaxy/pull/1397
.. _Pull Request 1398: https://github.com/galaxyproject/galaxy/pull/1398
.. _Pull Request 1399: https://github.com/galaxyproject/galaxy/pull/1399
.. _Pull Request 1400: https://github.com/galaxyproject/galaxy/pull/1400
.. _Pull Request 1401: https://github.com/galaxyproject/galaxy/pull/1401
.. _Pull Request 1405: https://github.com/galaxyproject/galaxy/pull/1405
.. _Pull Request 1407: https://github.com/galaxyproject/galaxy/pull/1407
.. _Pull Request 1409: https://github.com/galaxyproject/galaxy/pull/1409
.. _Pull Request 1412: https://github.com/galaxyproject/galaxy/pull/1412
.. _Pull Request 1413: https://github.com/galaxyproject/galaxy/pull/1413
.. _Pull Request 1414: https://github.com/galaxyproject/galaxy/pull/1414
.. _Pull Request 1415: https://github.com/galaxyproject/galaxy/pull/1415
.. _Pull Request 1421: https://github.com/galaxyproject/galaxy/pull/1421
.. _Pull Request 1422: https://github.com/galaxyproject/galaxy/pull/1422
.. _Pull Request 1424: https://github.com/galaxyproject/galaxy/pull/1424
.. _Pull Request 1425: https://github.com/galaxyproject/galaxy/pull/1425
.. _Pull Request 1427: https://github.com/galaxyproject/galaxy/pull/1427
.. _Pull Request 1430: https://github.com/galaxyproject/galaxy/pull/1430
.. _Pull Request 1438: https://github.com/galaxyproject/galaxy/pull/1438
.. _Pull Request 1439: https://github.com/galaxyproject/galaxy/pull/1439
.. _Pull Request 1448: https://github.com/galaxyproject/galaxy/pull/1448
.. _Pull Request 1464: https://github.com/galaxyproject/galaxy/pull/1464
.. _Pull Request 1473: https://github.com/galaxyproject/galaxy/pull/1473
.. _Pull Request 1474: https://github.com/galaxyproject/galaxy/pull/1474
.. _Pull Request 1485: https://github.com/galaxyproject/galaxy/pull/1485
.. _Pull Request 1487: https://github.com/galaxyproject/galaxy/pull/1487
.. _Pull Request 1493: https://github.com/galaxyproject/galaxy/pull/1493
.. _Pull Request 1494: https://github.com/galaxyproject/galaxy/pull/1494
.. _Pull Request 1495: https://github.com/galaxyproject/galaxy/pull/1495
.. _Pull Request 1498: https://github.com/galaxyproject/galaxy/pull/1498
.. _Pull Request 1501: https://github.com/galaxyproject/galaxy/pull/1501
.. _Pull Request 1511: https://github.com/galaxyproject/galaxy/pull/1511
.. _Pull Request 1527: https://github.com/galaxyproject/galaxy/pull/1527
.. _Pull Request 1536: https://github.com/galaxyproject/galaxy/pull/1536
.. _Pull Request 1551: https://github.com/galaxyproject/galaxy/pull/1551
.. _Pull Request 1554: https://github.com/galaxyproject/galaxy/pull/1554
.. _Pull Request 1558: https://github.com/galaxyproject/galaxy/pull/1558
.. _Pull Request 1759: https://github.com/galaxyproject/galaxy/pull/1759
.. _Pull Request 1761: https://github.com/galaxyproject/galaxy/pull/1761

.. _Commit f540a16: https://github.com/galaxyproject/galaxy/commit/f540a16768307995ea49c5d241948537ebbfa540
.. _Commit bf1c77d: https://github.com/galaxyproject/galaxy/commit/bf1c77d171f079f42d481ad465dbaef3bac8b4d4
.. _Commit 5da91bd: https://github.com/galaxyproject/galaxy/commit/5da91bddcda3ad3a4942e752d9b4bb3e7872046c
.. _Commit cd8b965: https://github.com/galaxyproject/galaxy/commit/cd8b96553f673145ee64a86d32960ba42643baed
.. _Commit e4a1d57: https://github.com/galaxyproject/galaxy/commit/e4a1d5727805168a9fd15aca1cdd21630ada2bbc
.. _Commit e845d64: https://github.com/galaxyproject/galaxy/commit/e845d649c672c51cc2336da0d880c9ff74ea6b5f