
.. to_doc

-------------------------------
15.07
-------------------------------

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


.. enhancements

* Interactive environment (IE) framework updates including a new IE for RStudio.
  (Thanks to a team effort spearheaded by `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 229`_, `Pull Request 230`_
* Rework workflow editor to use newer tool form components and allow construction
  of workflows with tools explicitly producing output collections.
  `Pull Request 286`_, `Pull Request 328`_, `Pull Request 311`_,
  `Pull Request 397`_, `Pull Request 233`_, `Pull Request 625`_,
  `Pull Request 602`_
* Implement policies for committers and pull requests.
  `Pull Request 295`_, `Pull Request 314`_
* Allow exporting a library folder to a history. (Thanks to `@ericenns
  <https://github.com/ericenns>`__.) `Pull Request 426`_
* Fix and update documentation available on the ReadTheDocs with particular
  focus on the API documentation. (Thanks to `@nsoranzo
  <https://github.com/nsoranzo>`__.)
  `Pull Request 399`_, `Pull Request 405`_
* Add EDAM IDs to Galaxy datatypes. (Thanks to a team effort initiated by `@hexylena
  <https://github.com/hexylena>`__.)
  `Pull Request 80`_, `Pull Request 342`_
* Improved reports app sorting and bug fixes thanks to
  Daniel Bouchard (`@Airistotal <https://github.com/Airistotal>`__). Even more
  reports enhancements will be included in the next release of Galaxy including
  new landing page, pagination, and sparkline graphs.
  `Pull Request 303`_, `Pull Request 330`_, `Pull Request 338`_
* Significant speedup of tool panel/homepage loading. (Thanks to `@abretaud
  <https://github.com/abretaud>`__.) `Pull Request 159`_
* Allow parameterization of tool XML macros. `Pull Request 362`_
* Allow use of tool-style XML macros in ``job_conf.xml``. `Pull Request 362`_
* Update and clarify admin menu. `Pull Request 302`_
* Add usage information to python cleanup scripts. (Thanks to `@dpryan79
  <https://github.com/dpryan79>`__.) `Pull Request 274`_
* Added default indexing for bcf files. `Pull Request 163`_
* Implement merging of BAM files for the parallelism framework. (Thanks to
  `@roalva1 <https://github.com/roalva1>`__.) `Pull Request 149`_
* Send signal to reload data tables when adding an entry (Thanks to `@abretaud
  <https://github.com/abretaud>`__.) `Pull Request 250`_
* Add display for Interval files at IGV via bedstrict. `Pull Request 259`_
* Include more information in default ``welcome.html`` file. `Pull Request 190`_
* Implement a command line script for collecting stats on job runtimes. 
  `Pull Request 151`_
* Implement an authentication provider for PAM (Pluggable Authentication Modules)
  (Thanks to `@pvanheus <https://github.com/pvanheus>`__.) `Pull Request 458`_
* Re-implement library data and FTP file parameters for new tool form.
  `Pull Request 132`_, `Pull Request 546`_
* Adding tool error tracking. (Thanks to `@kellrott
  <https://github.com/kellrott>`__.) `Pull Request 322`_
* Implement ``<filter>`` tag for output collections. `Pull Request 455`_
* Allow environment variable definitions in tool XML. `Pull Request 395`_
* Add new ``exclude_min`` and ``exclude_max`` attributes to ``InRangeValidator``
  for numeric tool parameters. (Thanks to `@gregvonkuster
  <https://github.com/gregvonkuster>`__.) `Pull Request 339`_
* Added unlinked Tool Shed dependency resolver. (Thanks to `@Christian-B
  <https://github.com/Christian-B>`__.) `Pull Request 441`_
* Add emboss datatypes (previously migrated to Tool Shed). (Thanks to `@bgruening
  <https://github.com/bgruening>`__.) `Pull Request 148`_
* Add new Hmmer & Stockholm datatypes. (Thanks to `@hexylena
  <https://github.com/hexylena>`__.) `Pull Request 218`_
* Add an RData datatype. (Thanks to `@hexylena
  <https://github.com/hexylena>`__.) `Pull Request 239`_
* Add mauve XMFA datatype (Thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 270`_
* Add ConnectivityTable (\*.ct) (RNA 2D structure format) datatype.
  (Thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
  `Pull Request 439`_
* Add Illumina methylation datatype (IDAT). `Pull Request 335`_
* Add Dot-Bracket notation (dbn) datatype. (Thanks to `@yhoogstrate
  <https://github.com/yhoogstrate>`__.) `Pull Request 366`_
* Add proteomics datatypes. (Thanks to `@iracooke
  <https://github.com/iracooke>`__.) `Pull Request 389`_
* Add new MzSQlite datatype for aggregating MS-based protein identification
  information. (Thanks to `@jj-umn <https://github.com/jj-umn>`__.)
  `Pull Request 427`_
* Allow ``display_in_upload`` by default for h5 files. `Pull Request 470`_
* Accept history id in tool state construction API. `Pull Request 268`_
* Adding dataset uuid information to job and workflow invocation calls.
  (Thanks to `@kellrott <https://github.com/kellrott>`__.) `Pull Request 181`_
* Allow workflows executed via the API to optionally run with tool upgrades.
  `Pull Request 402`_
* Various PEP-8 fixes, more to come next release. (Thanks to efforts lead by
  `@nsoranzo <https://github.com/nsoranzo>`__,
  `@remimarenco <https://github.com/remimarenco>`__, and
  `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 421`_, `Pull Request 422`_, `Pull Request 424`_,
  `Pull Request 433`_, `Pull Request 449`_, `Pull Request 350`_,
  `Pull Request 453`_, `Pull Request 394`_, `Pull Request 204`_
* Nose update with ``--debug`` option added to ``run_tests.sh``. `Pull Request 172`_
* Mention ``-installed`` option in ``run_tests.sh`` help. `Pull Request 323`_
* Allow config of shed tool configuration file used with ``run_tests.sh
  -installed``. `Pull Request 267`_
* Allow running tests from outer directories (Thanks to `@yhoogstrate
  <https://github.com/yhoogstrate>`__.) `Pull Request 137`_
* Enhancement allowing use of DRMAA when Galaxy instance isn't on a shared
  volume with compute nodes. (Thanks to `@vavrusa <https://github.com/vavrusa>`__.) 
  `Pull Request 160`_
* Enhancements for Condor. 
  (Thanks to `@dpryan79 <https://github.com/dpryan79>`__.)
  `Pull Request 289`_
* Update ``gsummary`` dependencies. (Thanks to `@bgruening
  <https://github.com/bgruening>`__.) `Pull Request 182`_
* Refactor visualization plugins to promote implementation to a class.
  `Pull Request 186`_
* Switch visualizations registry to entry_point config definition for 
  built-in visualizations. `Pull Request 243`_
* Set default value for IE sig proxy (Thanks to `@hexylena
  <https://github.com/hexylena>`__.) `Pull Request 197`_
* Other smaller interactive environment updates. (Thanks to
  `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 412`_
* Refuse to load interactive debugging middleware under uwsgi.
  `Pull Request 200`_
* Move stylesheet source files from ``static/style/src`` to
  ``client/galaxy/style``. `Pull Request 208`_
* Fix sprite paths by using hardcoded path in task. `Pull Request
  279`_
* Improve various focus handling behavior in the UI. `Pull Request 280`_
* Fixes and updates to various JavaScript-based unit tests. `Pull Request 219`_
* Update various client libs (e.g. jQuery, Raven, d3, requirejs).
  `Pull Request 221`_, `Pull Request 241`_
* Ignore sample files from toolshed installed tools. (Thanks to `@Unode
  <https://github.com/Unode>`__.) `Pull Request 248`_
* Add test option for disabling truncation of test diffs.
  `Pull Request 249`_
* Various documentation and wording improvements for various files.
  (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 277`_
* Allow external display applications optional access to files within a
  dataset's ``extra_files_path``. `Pull Request 284`_
* Improve the data manager JSON datatype's class to be more specific.
  `Pull Request 285`_
* Allow setting connection options for LDAP authentication. (Thanks to `@Unode
  <https://github.com/Unode>`__.) `Pull Request 287`_
* Fix for gzip being imported twice. (Thanks to `@bgruening
  <https://github.com/bgruening>`__.) `Pull Request 296`_
* Export environment variables from all dependent repositories.
  (Thanks to `@bgruening <https://github.com/bgruening>`__.) `Pull Request 297`_
* Improve ``auth_conf.xml.sample`` documentation. (Thanks to `@nsoranzo
  <https://github.com/nsoranzo>`__.) `Pull Request 299`_
* Preserve unix permissions, if any, when extracting .zip files during tool shed
  installations. `Pull Request 308`_
* Update mailing lists to use lists.galaxyproject.org addresses.
  `Pull Request 316`_
* Add new argument to inject volumes in ``docker_cmd()`` and ``launch()``.
  (Thanks to `@bgruening <https://github.com/bgruening>`__.) `Pull Request 318`_
* Create a separate application entry point to be used by uWSGI without ``--ini-
  paste`` and PasteDeploy. `Pull Request 325`_
* Implement groups in Tool Shed models and UI. `Pull Request 326`_,
  `Pull Request 374`_
* Improved datatype registry debugging. `Pull Request 329`_
* Add app option to client process to allow building Tool Shed scripts. 
  `Pull Request 332`_
* Add grunt command ``grunt decompress`` to copy decompressed artifacts.
  `Pull Request 173`_
* Improvements to Tool Shed search API.
  `Pull Request 334`_, `Pull Request 376`_, `Pull Request 420`_, `Pull Request 563`_
* Restore link to mercurial browsing of repositories. `Pull Request 340`_
* Enhance tool testing to only cleanup successful jobs. `Pull Request 341`_
* Implement metadata size limiting. `Pull Request 345`_, `Pull Request 416`_
* Add tool parameter argument to parameter help.
  `Pull Request 346`_, `Pull Request 351`_
* Refactor Tool Shed JavaScript files to be separated from Galaxy Java Script
  `Pull Request 347`_
* Fixed object store path - ``job_work``. (Thanks to `@charz
  <https://github.com/charz>`__.) `Pull Request 354`_
* Make debugging output nicer for IE's (Thanks to `@bgruening
  <https://github.com/bgruening>`__.) `Pull Request 355`_
* Add configurable Docker hostname (Thanks to `@bgruening
  <https://github.com/bgruening>`__.) `Pull Request 356`_
* Improve XML styling of display applications. 
  (Thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 364`_
* README improvements including - adding shields for Biostar, IRC, and Travis.
  `Pull Request 368`_, `Pull Request 369`_
* Use passed in URL for getbuilds method of parse_builds.py (Thanks to
  `@dctrud <https://github.com/dctrud>`__.) `Pull Request 384`_
* Add error message for bad dependency declaration (Thanks to `@kaktus42
  <https://github.com/kaktus42>`__.) `Pull Request 419`_
* Refactor JavaScript set up code for tagging toward reuse. `Pull Request 429`_
* Improved md5sum/sha256 in Tool Shed actions. (Thanks to `@yhoogstrate
  <https://github.com/yhoogstrate>`__.) `Pull Request 444`_
* Include owner annotations of HDAs in published history display.
  `Pull Request 490`_
* Added log error for config file not found. (Thanks to `@Christian-B
  <https://github.com/Christian-B>`__.) `Pull Request 443`_
* Fix for installing dependencies from source when download of precompiled
  binaries has failed. `Pull Request 531`_
* Use a password field for deprecated cloudlaunch's secret key field.
  `Pull Request 551`_
* Normalize ``datatypes_by_ext`` upon entry. `Pull Request 567`_
* Stop creating unneeded ``database/message.mako.py``. `Pull Request 575`_


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

.. fixes

* During the 15.07 development cycle dozens of fixes were pushed to the
  ``release_15.05`` branch of Galaxy. These are all included in 15.07 and
  summarized `here
  <https://github.com/galaxyproject/galaxy/compare/v15.05...release_15.05>`__
  (with special thanks to `@bgruening <https://github.com/bgruening>`__,
  `@mvdbeek <https://github.com/mvdbeek>`__,
  `@nsoranzo <https://github.com/nsoranzo>`__,
  and `@abretaud <https://github.com/abretaud>`__).
* Stop Trackster location wrapping in Chrome. (Thanks to `@dctrud
  <https://github.com/dctrud>`__.) `Pull Request 440`_
* Fix return integer values when 'round to nearest integer' is selected in
  Group tool. `Pull Request 452`_
* Fix external set_meta under sqlalchemy 1.0.0. `Pull Request 150`_
* Fix ``base.util`` to get the changeset from git. `Pull Request 161`_
* Remove ``biomart_test`` tool, http://test.biomart.org/ is down. (Thanks to
  `@nsoranzo <https://github.com/nsoranzo>`__.) `Pull Request 183`_
* Fix broken browser tests. `Pull Request 202`_
* Fix assertions in ``test_VisualizationsRegistry.py``. `Pull Request 223`_
* Fix ``run_tests.sh`` exit code. `Pull Request 225`_
* Use ``unittest2`` to allow Python 2.7 assertions under Python 2.6.
  `Pull Request 246`_
* Have ``trans.user_ftp_dir`` return ``None`` instead of error if upload dir unset.
  `Pull Request 257`_
* Allow IGV external displays to use a name with a comma in it. `Pull Request 261`_
* Fix bug in history sharing. (Thanks to `@bgruening
  <https://github.com/bgruening>`__.) `Pull Request 263`_
* Convert tools directory to only use unix newline characters.
  (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.) `Pull Request 264`_
* Remove spurious numpy requirement on ``maf_stats.xml`` tool.
  (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.) `Pull Request 264`_
* Use more actionable ``package`` requirement type on some tools.
  (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.) `Pull Request 264`_
* Small doc fix for ``config/plugins/visualizations/README.txt``.
  (Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.) `Pull Request 264`_
* Fix function names for dynamic tool test functions. `Pull Request 266`_
* Fixes to dataset chooser. `Pull Request 272`_
* Fix Trackster load order of require and d3. `Pull Request 291`_
* Remove bad HTML tags from login template. (Thanks to `@Unode
  <https://github.com/Unode>`__.) `Pull Request 294`_
* Exclude curly braces from API-key to fix toolshed bootstrapping. (Thanks to
  `@mvdbeek <https://github.com/mvdbeek>`__.) `Pull Request 301`_
* Fix repeated error messages with identical text. `Pull Request 306`_
* Fix shared mako templates that would not work properly with the Tool Shed.
  `Pull Request 307`_
* Fix json sniffer for large files. `Pull Request 309`_
* Fix a typo error in ``visualization/plugins/resource_parser.py``. (Thanks to
  `@remimarenco <https://github.com/remimarenco>`__.) `Pull Request 312`_
* Fix for generating metadata on toolshed tools tests, under certain
  conditions. `Pull Request 319`_
* Fix Tool Shed metadata generation bug. (Thanks to `@bgruening
  <https://github.com/bgruening>`__.) `Pull Request 333`_
* Fixing string appending error in library dictification. (Thanks to `@kellrott
  <https://github.com/kellrott>`__.) `Pull Request 336`_
* Hide constantly broken Tool Shed test results. `Pull Request 337`_
* Fix for fix for handling of unix permissions in .zip files. `Pull Request
  344`_
* Fix common API scripts so they don't fail when response has no URL param.
  `Pull Request 352`_
* Fix for dynamic test data fetching. `Pull Request 371`_
* Fix bug in ``Text.split()`` method. (Thanks to `@nsoranzo
  <https://github.com/nsoranzo>`__.) `Pull Request 373`_
* Fix and update serializer call to non-``trans`` form for histories.
  `Pull Request 390`_
* Fix getting admin key when bootstrapping toolshed. (Thanks to
  `@galaxyproject <https://github.com/galaxyproject>`__.) `Pull Request 392`_
* Fix error when displaying job params for tools containing a section.
  (Thanks to `@abretaud <https://github.com/abretaud>`__.) `Pull Request 398`_
* Fix for setting environment variable paths for installed tools. (Thanks to
  `@gregvonkuster <https://github.com/gregvonkuster>`__.) `Pull Request 403`_
* Quota calculation fixes for managers. `Pull Request 406`_
* Fix paging issue with whoosh due to missing ``str`` to ``int`` conversion.
  `Pull Request 407`_
* Use ``web.url_for( '/', qualified=True )`` instead of ``'/'`` to generate
  URLs (for correctness). (Thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 414`_
* Fix for async datasources. `Pull Request 423`_
* Fix UI bug related to ID collisions for display of certain collections.
  `Pull Request 431`_
* Fix ``run_tests.sh`` example API test command. `Pull Request 432`_
* Fixed typo in Tool Shed docstring. (Thanks to `@peterjc
  <https://github.com/peterjc>`__.) `Pull Request 438`_
* Various Trackster fixes. `Pull Request 446`_
* Fix job query to allow admins to view other histories. `Pull Request 465`_
* Fix ``dbkey`` filtering of multiple input targets. `Pull Request 534`_
* Fixes for ``DeleteIntermediatesAction``. `Pull Request 547`_
* Fix overriding the name variable in Tool Shed index code. `Pull Request 566`_
* Fix batch mode input in new tool form UI. (Thanks to `@ericenns
  <https://github.com/ericenns>`__.) `Pull Request 568`_
* CSV/SAM sniff order fix. `Pull Request 571`_
* Show field for entering remote/home url when managing a Tool Shed repository.
  `Pull Request 580`_
* Fix regenerating repository metadata when coming from batch interface.
  `Pull Request 600`_


.. github_links
.. _Pull Request 80: https://github.com/galaxyproject/galaxy/pull/80
.. _Pull Request 132: https://github.com/galaxyproject/galaxy/pull/132
.. _Pull Request 137: https://github.com/galaxyproject/galaxy/pull/137
.. _Pull Request 148: https://github.com/galaxyproject/galaxy/pull/148
.. _Pull Request 149: https://github.com/galaxyproject/galaxy/pull/149
.. _Pull Request 150: https://github.com/galaxyproject/galaxy/pull/150
.. _Pull Request 151: https://github.com/galaxyproject/galaxy/pull/151
.. _Pull Request 159: https://github.com/galaxyproject/galaxy/pull/159
.. _Pull Request 160: https://github.com/galaxyproject/galaxy/pull/160
.. _Pull Request 161: https://github.com/galaxyproject/galaxy/pull/161
.. _Pull Request 163: https://github.com/galaxyproject/galaxy/pull/163
.. _Pull Request 172: https://github.com/galaxyproject/galaxy/pull/172
.. _Pull Request 173: https://github.com/galaxyproject/galaxy/pull/173
.. _Pull Request 181: https://github.com/galaxyproject/galaxy/pull/181
.. _Pull Request 182: https://github.com/galaxyproject/galaxy/pull/182
.. _Pull Request 183: https://github.com/galaxyproject/galaxy/pull/183
.. _Pull Request 186: https://github.com/galaxyproject/galaxy/pull/186
.. _Pull Request 190: https://github.com/galaxyproject/galaxy/pull/190
.. _Pull Request 191: https://github.com/galaxyproject/galaxy/pull/191
.. _Pull Request 197: https://github.com/galaxyproject/galaxy/pull/197
.. _Pull Request 200: https://github.com/galaxyproject/galaxy/pull/200
.. _Pull Request 202: https://github.com/galaxyproject/galaxy/pull/202
.. _Pull Request 204: https://github.com/galaxyproject/galaxy/pull/204
.. _Pull Request 208: https://github.com/galaxyproject/galaxy/pull/208
.. _Pull Request 218: https://github.com/galaxyproject/galaxy/pull/218
.. _Pull Request 219: https://github.com/galaxyproject/galaxy/pull/219
.. _Pull Request 221: https://github.com/galaxyproject/galaxy/pull/221
.. _Pull Request 223: https://github.com/galaxyproject/galaxy/pull/223
.. _Pull Request 225: https://github.com/galaxyproject/galaxy/pull/225
.. _Pull Request 229: https://github.com/galaxyproject/galaxy/pull/229
.. _Pull Request 230: https://github.com/galaxyproject/galaxy/pull/230
.. _Pull Request 233: https://github.com/galaxyproject/galaxy/pull/233
.. _Pull Request 239: https://github.com/galaxyproject/galaxy/pull/239
.. _Pull Request 240: https://github.com/galaxyproject/galaxy/pull/240
.. _Pull Request 241: https://github.com/galaxyproject/galaxy/pull/241
.. _Pull Request 243: https://github.com/galaxyproject/galaxy/pull/243
.. _Pull Request 246: https://github.com/galaxyproject/galaxy/pull/246
.. _Pull Request 248: https://github.com/galaxyproject/galaxy/pull/248
.. _Pull Request 249: https://github.com/galaxyproject/galaxy/pull/249
.. _Pull Request 250: https://github.com/galaxyproject/galaxy/pull/250
.. _Pull Request 257: https://github.com/galaxyproject/galaxy/pull/257
.. _Pull Request 259: https://github.com/galaxyproject/galaxy/pull/259
.. _Pull Request 261: https://github.com/galaxyproject/galaxy/pull/261
.. _Pull Request 263: https://github.com/galaxyproject/galaxy/pull/263
.. _Pull Request 264: https://github.com/galaxyproject/galaxy/pull/264
.. _Pull Request 266: https://github.com/galaxyproject/galaxy/pull/266
.. _Pull Request 267: https://github.com/galaxyproject/galaxy/pull/267
.. _Pull Request 268: https://github.com/galaxyproject/galaxy/pull/268
.. _Pull Request 269: https://github.com/galaxyproject/galaxy/pull/269
.. _Pull Request 270: https://github.com/galaxyproject/galaxy/pull/270
.. _Pull Request 272: https://github.com/galaxyproject/galaxy/pull/272
.. _Pull Request 274: https://github.com/galaxyproject/galaxy/pull/274
.. _Pull Request 277: https://github.com/galaxyproject/galaxy/pull/277
.. _Pull Request 279: https://github.com/galaxyproject/galaxy/pull/279
.. _Pull Request 280: https://github.com/galaxyproject/galaxy/pull/280
.. _Pull Request 284: https://github.com/galaxyproject/galaxy/pull/284
.. _Pull Request 285: https://github.com/galaxyproject/galaxy/pull/285
.. _Pull Request 286: https://github.com/galaxyproject/galaxy/pull/286
.. _Pull Request 287: https://github.com/galaxyproject/galaxy/pull/287
.. _Pull Request 289: https://github.com/galaxyproject/galaxy/pull/289
.. _Pull Request 290: https://github.com/galaxyproject/galaxy/pull/290
.. _Pull Request 291: https://github.com/galaxyproject/galaxy/pull/291
.. _Pull Request 294: https://github.com/galaxyproject/galaxy/pull/294
.. _Pull Request 295: https://github.com/galaxyproject/galaxy/pull/295
.. _Pull Request 296: https://github.com/galaxyproject/galaxy/pull/296
.. _Pull Request 297: https://github.com/galaxyproject/galaxy/pull/297
.. _Pull Request 299: https://github.com/galaxyproject/galaxy/pull/299
.. _Pull Request 301: https://github.com/galaxyproject/galaxy/pull/301
.. _Pull Request 302: https://github.com/galaxyproject/galaxy/pull/302
.. _Pull Request 303: https://github.com/galaxyproject/galaxy/pull/303
.. _Pull Request 306: https://github.com/galaxyproject/galaxy/pull/306
.. _Pull Request 307: https://github.com/galaxyproject/galaxy/pull/307
.. _Pull Request 308: https://github.com/galaxyproject/galaxy/pull/308
.. _Pull Request 309: https://github.com/galaxyproject/galaxy/pull/309
.. _Pull Request 311: https://github.com/galaxyproject/galaxy/pull/311
.. _Pull Request 312: https://github.com/galaxyproject/galaxy/pull/312
.. _Pull Request 314: https://github.com/galaxyproject/galaxy/pull/314
.. _Pull Request 316: https://github.com/galaxyproject/galaxy/pull/316
.. _Pull Request 318: https://github.com/galaxyproject/galaxy/pull/318
.. _Pull Request 319: https://github.com/galaxyproject/galaxy/pull/319
.. _Pull Request 322: https://github.com/galaxyproject/galaxy/pull/322
.. _Pull Request 323: https://github.com/galaxyproject/galaxy/pull/323
.. _Pull Request 325: https://github.com/galaxyproject/galaxy/pull/325
.. _Pull Request 326: https://github.com/galaxyproject/galaxy/pull/326
.. _Pull Request 328: https://github.com/galaxyproject/galaxy/pull/328
.. _Pull Request 329: https://github.com/galaxyproject/galaxy/pull/329
.. _Pull Request 330: https://github.com/galaxyproject/galaxy/pull/330
.. _Pull Request 332: https://github.com/galaxyproject/galaxy/pull/332
.. _Pull Request 333: https://github.com/galaxyproject/galaxy/pull/333
.. _Pull Request 334: https://github.com/galaxyproject/galaxy/pull/334
.. _Pull Request 335: https://github.com/galaxyproject/galaxy/pull/335
.. _Pull Request 336: https://github.com/galaxyproject/galaxy/pull/336
.. _Pull Request 337: https://github.com/galaxyproject/galaxy/pull/337
.. _Pull Request 338: https://github.com/galaxyproject/galaxy/pull/338
.. _Pull Request 339: https://github.com/galaxyproject/galaxy/pull/339
.. _Pull Request 340: https://github.com/galaxyproject/galaxy/pull/340
.. _Pull Request 341: https://github.com/galaxyproject/galaxy/pull/341
.. _Pull Request 342: https://github.com/galaxyproject/galaxy/pull/342
.. _Pull Request 344: https://github.com/galaxyproject/galaxy/pull/344
.. _Pull Request 345: https://github.com/galaxyproject/galaxy/pull/345
.. _Pull Request 346: https://github.com/galaxyproject/galaxy/pull/346
.. _Pull Request 347: https://github.com/galaxyproject/galaxy/pull/347
.. _Pull Request 349: https://github.com/galaxyproject/galaxy/pull/349
.. _Pull Request 350: https://github.com/galaxyproject/galaxy/pull/350
.. _Pull Request 351: https://github.com/galaxyproject/galaxy/pull/351
.. _Pull Request 352: https://github.com/galaxyproject/galaxy/pull/352
.. _Pull Request 354: https://github.com/galaxyproject/galaxy/pull/354
.. _Pull Request 355: https://github.com/galaxyproject/galaxy/pull/355
.. _Pull Request 356: https://github.com/galaxyproject/galaxy/pull/356
.. _Pull Request 362: https://github.com/galaxyproject/galaxy/pull/362
.. _Pull Request 364: https://github.com/galaxyproject/galaxy/pull/364
.. _Pull Request 366: https://github.com/galaxyproject/galaxy/pull/366
.. _Pull Request 368: https://github.com/galaxyproject/galaxy/pull/368
.. _Pull Request 369: https://github.com/galaxyproject/galaxy/pull/369
.. _Pull Request 370: https://github.com/galaxyproject/galaxy/pull/370
.. _Pull Request 371: https://github.com/galaxyproject/galaxy/pull/371
.. _Pull Request 373: https://github.com/galaxyproject/galaxy/pull/373
.. _Pull Request 374: https://github.com/galaxyproject/galaxy/pull/374
.. _Pull Request 376: https://github.com/galaxyproject/galaxy/pull/376
.. _Pull Request 381: https://github.com/galaxyproject/galaxy/pull/381
.. _Pull Request 383: https://github.com/galaxyproject/galaxy/pull/383
.. _Pull Request 384: https://github.com/galaxyproject/galaxy/pull/384
.. _Pull Request 386: https://github.com/galaxyproject/galaxy/pull/386
.. _Pull Request 389: https://github.com/galaxyproject/galaxy/pull/389
.. _Pull Request 390: https://github.com/galaxyproject/galaxy/pull/390
.. _Pull Request 392: https://github.com/galaxyproject/galaxy/pull/392
.. _Pull Request 394: https://github.com/galaxyproject/galaxy/pull/394
.. _Pull Request 395: https://github.com/galaxyproject/galaxy/pull/395
.. _Pull Request 397: https://github.com/galaxyproject/galaxy/pull/397
.. _Pull Request 398: https://github.com/galaxyproject/galaxy/pull/398
.. _Pull Request 399: https://github.com/galaxyproject/galaxy/pull/399
.. _Pull Request 402: https://github.com/galaxyproject/galaxy/pull/402
.. _Pull Request 403: https://github.com/galaxyproject/galaxy/pull/403
.. _Pull Request 405: https://github.com/galaxyproject/galaxy/pull/405
.. _Pull Request 406: https://github.com/galaxyproject/galaxy/pull/406
.. _Pull Request 407: https://github.com/galaxyproject/galaxy/pull/407
.. _Pull Request 410: https://github.com/galaxyproject/galaxy/pull/410
.. _Pull Request 412: https://github.com/galaxyproject/galaxy/pull/412
.. _Pull Request 414: https://github.com/galaxyproject/galaxy/pull/414
.. _Pull Request 416: https://github.com/galaxyproject/galaxy/pull/416
.. _Pull Request 419: https://github.com/galaxyproject/galaxy/pull/419
.. _Pull Request 420: https://github.com/galaxyproject/galaxy/pull/420
.. _Pull Request 421: https://github.com/galaxyproject/galaxy/pull/421
.. _Pull Request 422: https://github.com/galaxyproject/galaxy/pull/422
.. _Pull Request 423: https://github.com/galaxyproject/galaxy/pull/423
.. _Pull Request 424: https://github.com/galaxyproject/galaxy/pull/424
.. _Pull Request 426: https://github.com/galaxyproject/galaxy/pull/426
.. _Pull Request 427: https://github.com/galaxyproject/galaxy/pull/427
.. _Pull Request 429: https://github.com/galaxyproject/galaxy/pull/429
.. _Pull Request 431: https://github.com/galaxyproject/galaxy/pull/431
.. _Pull Request 432: https://github.com/galaxyproject/galaxy/pull/432
.. _Pull Request 433: https://github.com/galaxyproject/galaxy/pull/433
.. _Pull Request 438: https://github.com/galaxyproject/galaxy/pull/438
.. _Pull Request 439: https://github.com/galaxyproject/galaxy/pull/439
.. _Pull Request 440: https://github.com/galaxyproject/galaxy/pull/440
.. _Pull Request 441: https://github.com/galaxyproject/galaxy/pull/441
.. _Pull Request 443: https://github.com/galaxyproject/galaxy/pull/443
.. _Pull Request 444: https://github.com/galaxyproject/galaxy/pull/444
.. _Pull Request 446: https://github.com/galaxyproject/galaxy/pull/446
.. _Pull Request 449: https://github.com/galaxyproject/galaxy/pull/449
.. _Pull Request 452: https://github.com/galaxyproject/galaxy/pull/452
.. _Pull Request 453: https://github.com/galaxyproject/galaxy/pull/453
.. _Pull Request 454: https://github.com/galaxyproject/galaxy/pull/454
.. _Pull Request 455: https://github.com/galaxyproject/galaxy/pull/455
.. _Pull Request 458: https://github.com/galaxyproject/galaxy/pull/458
.. _Pull Request 459: https://github.com/galaxyproject/galaxy/pull/459
.. _Pull Request 462: https://github.com/galaxyproject/galaxy/pull/462
.. _Pull Request 463: https://github.com/galaxyproject/galaxy/pull/463
.. _Pull Request 465: https://github.com/galaxyproject/galaxy/pull/465
.. _Pull Request 470: https://github.com/galaxyproject/galaxy/pull/470
.. _Pull Request 472: https://github.com/galaxyproject/galaxy/pull/472
.. _Pull Request 473: https://github.com/galaxyproject/galaxy/pull/473
.. _Pull Request 478: https://github.com/galaxyproject/galaxy/pull/478
.. _Pull Request 479: https://github.com/galaxyproject/galaxy/pull/479
.. _Pull Request 480: https://github.com/galaxyproject/galaxy/pull/480
.. _Pull Request 481: https://github.com/galaxyproject/galaxy/pull/481
.. _Pull Request 482: https://github.com/galaxyproject/galaxy/pull/482
.. _Pull Request 484: https://github.com/galaxyproject/galaxy/pull/484
.. _Pull Request 485: https://github.com/galaxyproject/galaxy/pull/485
.. _Pull Request 486: https://github.com/galaxyproject/galaxy/pull/486
.. _Pull Request 487: https://github.com/galaxyproject/galaxy/pull/487
.. _Pull Request 488: https://github.com/galaxyproject/galaxy/pull/488
.. _Pull Request 490: https://github.com/galaxyproject/galaxy/pull/490
.. _Pull Request 491: https://github.com/galaxyproject/galaxy/pull/491
.. _Pull Request 492: https://github.com/galaxyproject/galaxy/pull/492
.. _Pull Request 493: https://github.com/galaxyproject/galaxy/pull/493
.. _Pull Request 494: https://github.com/galaxyproject/galaxy/pull/494
.. _Pull Request 495: https://github.com/galaxyproject/galaxy/pull/495
.. _Pull Request 496: https://github.com/galaxyproject/galaxy/pull/496
.. _Pull Request 499: https://github.com/galaxyproject/galaxy/pull/499
.. _Pull Request 500: https://github.com/galaxyproject/galaxy/pull/500
.. _Pull Request 509: https://github.com/galaxyproject/galaxy/pull/509
.. _Pull Request 510: https://github.com/galaxyproject/galaxy/pull/510
.. _Pull Request 511: https://github.com/galaxyproject/galaxy/pull/511
.. _Pull Request 512: https://github.com/galaxyproject/galaxy/pull/512
.. _Pull Request 514: https://github.com/galaxyproject/galaxy/pull/514
.. _Pull Request 515: https://github.com/galaxyproject/galaxy/pull/515
.. _Pull Request 516: https://github.com/galaxyproject/galaxy/pull/516
.. _Pull Request 517: https://github.com/galaxyproject/galaxy/pull/517
.. _Pull Request 526: https://github.com/galaxyproject/galaxy/pull/526
.. _Pull Request 527: https://github.com/galaxyproject/galaxy/pull/527
.. _Pull Request 529: https://github.com/galaxyproject/galaxy/pull/529
.. _Pull Request 530: https://github.com/galaxyproject/galaxy/pull/530
.. _Pull Request 531: https://github.com/galaxyproject/galaxy/pull/531
.. _Pull Request 532: https://github.com/galaxyproject/galaxy/pull/532
.. _Pull Request 533: https://github.com/galaxyproject/galaxy/pull/533
.. _Pull Request 534: https://github.com/galaxyproject/galaxy/pull/534
.. _Pull Request 536: https://github.com/galaxyproject/galaxy/pull/536
.. _Pull Request 537: https://github.com/galaxyproject/galaxy/pull/537
.. _Pull Request 538: https://github.com/galaxyproject/galaxy/pull/538
.. _Pull Request 539: https://github.com/galaxyproject/galaxy/pull/539
.. _Pull Request 540: https://github.com/galaxyproject/galaxy/pull/540
.. _Pull Request 543: https://github.com/galaxyproject/galaxy/pull/543
.. _Pull Request 544: https://github.com/galaxyproject/galaxy/pull/544
.. _Pull Request 545: https://github.com/galaxyproject/galaxy/pull/545
.. _Pull Request 546: https://github.com/galaxyproject/galaxy/pull/546
.. _Pull Request 547: https://github.com/galaxyproject/galaxy/pull/547
.. _Pull Request 550: https://github.com/galaxyproject/galaxy/pull/550
.. _Pull Request 551: https://github.com/galaxyproject/galaxy/pull/551
.. _Pull Request 553: https://github.com/galaxyproject/galaxy/pull/553
.. _Pull Request 561: https://github.com/galaxyproject/galaxy/pull/561
.. _Pull Request 563: https://github.com/galaxyproject/galaxy/pull/563
.. _Pull Request 565: https://github.com/galaxyproject/galaxy/pull/565
.. _Pull Request 566: https://github.com/galaxyproject/galaxy/pull/566
.. _Pull Request 567: https://github.com/galaxyproject/galaxy/pull/567
.. _Pull Request 568: https://github.com/galaxyproject/galaxy/pull/568
.. _Pull Request 569: https://github.com/galaxyproject/galaxy/pull/569
.. _Pull Request 571: https://github.com/galaxyproject/galaxy/pull/571
.. _Pull Request 575: https://github.com/galaxyproject/galaxy/pull/575
.. _Pull Request 577: https://github.com/galaxyproject/galaxy/pull/577
.. _Pull Request 580: https://github.com/galaxyproject/galaxy/pull/580
.. _Pull Request 581: https://github.com/galaxyproject/galaxy/pull/581
.. _Pull Request 583: https://github.com/galaxyproject/galaxy/pull/583
.. _Pull Request 584: https://github.com/galaxyproject/galaxy/pull/584
.. _Pull Request 585: https://github.com/galaxyproject/galaxy/pull/585
.. _Pull Request 587: https://github.com/galaxyproject/galaxy/pull/587
.. _Pull Request 589: https://github.com/galaxyproject/galaxy/pull/589
.. _Pull Request 591: https://github.com/galaxyproject/galaxy/pull/591
.. _Pull Request 592: https://github.com/galaxyproject/galaxy/pull/592
.. _Pull Request 594: https://github.com/galaxyproject/galaxy/pull/594
.. _Pull Request 600: https://github.com/galaxyproject/galaxy/pull/600
.. _Pull Request 602: https://github.com/galaxyproject/galaxy/pull/602
.. _Pull Request 625: https://github.com/galaxyproject/galaxy/pull/625
