.. to_doc

16.04
===============================

.. announce_start

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

.. major_feature

* Overhaul of Tools and Jobs
  `Pull Request 1688`_
* Implement an Embedded Pulsar Job Runner
  `Pull Request 2057`_
* Use the API to install repositories instead of loading the
  Tool Shed in an iframe. (Beta)
  `Pull Request 1392`_

.. feature

* Phinch interactive environment
  (thanks to `@shiltemann <https://github.com/shiltemann>`__.)
  `Pull Request 1647`_
* Add iobio external display applications for BAM and VCF.
  `Pull Request 1926`_
* add chemical datatypes
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1941`_
* Scratchbook tour
  `Pull Request 1463`_
* Work toward automating release management.
  `Pull Request 1613`_
* Basic tool error Sentry reporting.
  `Pull Request 1900`_
* disable 'hg push' to TS repositories
  `Pull Request 2033`_
* Generic GIE Launcher, GIE Image Chooser, multiple datasets
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1403`_
* The entire Python source code is now continuously checked with flake8 for
  PEP-8 style consistency and common errors. The last 3500 errors were fixed in
  this release
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1489`_, `Pull Request 1713`_, `Pull Request 1755`_

.. enhancement

* Implement new GIE proxy
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1807`_
* Workflow editor overview click navigation
  `Pull Request 1843`_
* API, history contents: allow filters, limit/offset, and ordering
  `Pull Request 1602`_
* datalibs: introduce folder management; fix various glitches; refactor
  `Pull Request 1562`_
* Add makefile target for release process
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1433`_
* libraries: provide select all/none options when importing
  `Pull Request 1970`_
* libraries: add 'create history &import to it' feature
  `Pull Request 2017`_
* Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type
  (thanks to `@markiskander <https://github.com/markiskander>`__.)
  `Pull Request 1148`_
* Update SnpEffDb and SnpSiftDbNSFP for SnpEff v4.1
  (thanks to `@jj-umn <https://github.com/jj-umn>`__.)
  `Pull Request 1280`_
* Docker Testing - Newer versions of phantomjs and casperjs, in container
  wheels.
  `Pull Request 1449`_
* Add run_toolshed_tests.html to .gitignore .
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1456`_
* Allow sorting of discover_datasets elements.
  `Pull Request 1512`_
* Cleanup common ui elements, add test cases
  `Pull Request 1519`_
* add minor styling to tour popover
  `Pull Request 1539`_
* Code design and legacy cleanup of datatypes and metadata.
  `Pull Request 1556`_
* show_params input walking
  `Pull Request 1561`_
* Add API endpoint for fetching all metadata for a repository.
  `Pull Request 1565`_
* Fix parameter validation
  `Pull Request 1572`_
* Remove recovery hack for REALLY old jobs.
  `Pull Request 1574`_
* Clarify area github tags.
  `Pull Request 1579`_
* update pinned-requirements.txt
  (thanks to `@matthdsm <https://github.com/matthdsm>`__.)
  `Pull Request 1605`_
* Improve dbkey handling for discovered datasets.
  `Pull Request 1610`_
* Various improvements to the heartbeat
  `Pull Request 1614`_
* Visualization plugins: add routes that more closely match potential static assets.
  `Pull Request 1615`_
* Disable individual file metadata changes in upload
  `Pull Request 1625`_
* added resolver dependency display to the tool view page
  (thanks to `@zipho <https://github.com/zipho>`__.)
  `Pull Request 1632`_
* Cherry-picked changes from pull request `#1392
  <https://github.com/galaxyproject/galaxy/issues/1392>`__.
  `Pull Request 1821`_
* Export toolshed repository information for workflow portability
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1636`_
* Lint optional handling on conditional test parameters.
  `Pull Request 1639`_
* Updated hashes for bioblend v0.7.0
  (thanks to `@matthdsm <https://github.com/matthdsm>`__.)
  `Pull Request 1646`_
* Add tox startup (run.sh) test and test on OS X and linux
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1649`_
* Optionally pass dataset lists as a single file within tool wrappers
  (thanks to `@einon <https://github.com/einon>`__.)
  `Pull Request 1658`_
* add a zip datatype which won't be extracted
  (thanks to `@lecorguille <https://github.com/lecorguille>`__.)
  `Pull Request 1665`_
* Tour improvements and bugfixes
  `Pull Request 1671`_
* Add Marius van den Beek to Galaxy committer group.
  `Pull Request 1699`_
* Revise tool parameter handling, remove redundancies
  `Pull Request 1711`_
* Python 2/3 string handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1731`_
* workaround for error message on tool lookup in case original toolshed had
  been disabled
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1738`_
* Make api/tools return tool_shed_repository information.
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1752`_
* Use visit inputs for check_and_update_param_values
  `Pull Request 1764`_
* Update makefile and add the script I used to apply security patches for
  16.01
  `Pull Request 1793`_
* Implement dataset empty input validator.
  `Pull Request 1808`_
* Makefile help target + formatting
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1824`_
* Add license and repository information to package.json.
  `Pull Request 1829`_
* Improved logging during tool executions.
  `Pull Request 1832`_
* Do not access the history when loading the workflow editor
  `Pull Request 1861`_
* Tones down the warning message about tool changes
  (thanks to `@bwlang <https://github.com/bwlang>`__.)
  `Pull Request 1893`_
* Use shared value serialization for tool model
  `Pull Request 1901`_
* adding contrib init for reports and modifying status check to have output by process in case multiprocess
  (thanks to `@miloaec <https://github.com/miloaec>`__.)
  `Pull Request 1911`_
* Retrieve authentification also for long urls
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1912`_
* Modify run.sh to add --restart option, for a more consistent use of parameters.
  (thanks to `@remimarenco <https://github.com/remimarenco>`__.)
  `Pull Request 1914`_
* Rename tool_shed_get to url_get.
  `Pull Request 1918`_
* Allow testing element counts in tool output collections.
  `Pull Request 1942`_
* Use database query rather than dataset iteration to compute dataset counts in saved histories grid.
  `Pull Request 1948`_
* Add "new" state to list of dataset states in saved history list.
  `Pull Request 1949`_
* Add IUC as a new default bioconda channel
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1950`_
* More job related timing logging.
  `Pull Request 1956`_
* Improvements to workflow scaling performance testing scripts.
  `Pull Request 1958`_
* Optimization for discovering datasets for dynamic output collection.
  `Pull Request 1959`_
* Improve tabular datatypes.
  (thanks to `@brenninc <https://github.com/brenninc>`__ and `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1968`_, `Pull Request 2317`_
* Optimize adding datasets to large histories.
  `Pull Request 1983`_
* Much more friendly route mapping.
  `Pull Request 2002`_
* Revise content selection, add test cases
  `Pull Request 2011`_
* Don't setup a default tool_data_table_config_path in the shed.
  `Pull Request 2025`_
* data_column to json config file
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 2026`_
* Revise input wrapper, add test cases
  `Pull Request 2027`_
* enable obfs datatype during upload
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 2028`_
* Better element_identifier handling in repeat sections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 2029`_
* Pulsar-As-A-Dependency
  `Pull Request 2052`_
* Simplify Workflow sharing menu
  (thanks to `@nturaga <https://github.com/nturaga>`__.)
  `Pull Request 2060`_
* Add Phinch as an external display application.
  `Pull Request 2069`_
* For non-shed tool data - read loc from sample if available.
  `Pull Request 2070`_
* tool lineage for versionless toolshed tool_ids
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 2082`_
* make new beta TS tools installation via API configurable
  `Pull Request 2088`_
* Patch in visual separation of section parameters
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 2091`_
* Add sample supervisor config
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 2096`_
* Fix cli runner: use embed_metadata_in_job parameter
  (thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__.)
  `Pull Request 2107`_
* Switch Dockerized commands to use sh instead of bash.
  `Pull Request 2282`_

.. small_enhancement

* Remove IPython IE, which was replaced by Jupyter IE.
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 1402`_
* Added py34-lint tox target but forgot to update .travis.yml.
  `Pull Request 1457`_
* fix old jobparam hack for importing files to library
  `Pull Request 1488`_
* An attempt to add limit/offset to history contents
  `Pull Request 1490`_
* Revise label handling in form
  `Pull Request 1496`_
* History UI: clean up.
  `Pull Request 1522`_
* Client-build, Webpack: add tasks to grunt for the common webpack tasks,
  update readme
  `Pull Request 1523`_
* Remove handlebars and rely solely on underscore templates
  `Pull Request 1537`_
* disable email notifications from travis
  `Pull Request 1592`_
* Remove unnecessary variable and assignment of job command
  (thanks to `@einon <https://github.com/einon>`__.)
  `Pull Request 1616`_
* Implement the ratable mixin
  `Pull Request 1618`_
* Tour cleanup, remove a few globals.
  `Pull Request 1621`_
* Refactor workflow loading.
  `Pull Request 1735`_
* Swapping from svgfig to svgwrite
  `Pull Request 1747`_
* various libraries refactoring and bugfixes
  `Pull Request 1751`_
* Refactor the Html Datatype Class into text.py instead of images.py
  (thanks to `@remimarenco <https://github.com/remimarenco>`__.)
  `Pull Request 1760`_
* Drop python2.6 (deprecated, will not be supported in 16.04) from testing.
  `Pull Request 1785`_
* Rework history updating
  `Pull Request 1788`_
* Tests for some of the 16.01 security vulnerabilities
  `Pull Request 1794`_
* Reduce the use of mutable types in toolshed test framework's method
  definitions.
  `Pull Request 1813`_
* Remove decryption/encryption of tool states
  `Pull Request 1838`_
* Do not import dumps and loads from galaxy.util.json .
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1840`_
* Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship.
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1868`_
* Cosmetic comma fixes :)
  (thanks to `@remimarenco <https://github.com/remimarenco>`__.)
  `Pull Request 1874`_
* More debugging for transiently failing tool shed test.
  `Pull Request 1939`_
* Improve logging and retry  for another TS test...
  `Pull Request 1961`_
* Add page layout test cases
  `Pull Request 1991`_
* Fix inconsistency in update state handling for tool modules
  `Pull Request 1993`_
* Functional Test Drivers Overhaul
  `Pull Request 2016`_
* Remove install and test code.
  `Pull Request 2018`_
* Remove twill functional tests we don't actively run.
  `Pull Request 2019`_
* Fix transiently failing tool shed tests.
  `Pull Request 2030`_
* Libraries: faster, refactored, cleaned
  `Pull Request 2031`_
* Adjust testing directories so no python root is ever "tool_shed".
  `Pull Request 2067`_
* Fix pbs runner file touch.
  `Pull Request 2074`_
* Move scripts out of lib/tool_shed.
  `Pull Request 2093`_
* Consolidate duplicated method in tool_shed/model.
  `Pull Request 2099`_
* Remove redundant ui divs, move masthead into #everything
  `Pull Request 2182`_
* Remove SLURM memory limit warning from stderr if the job was successful
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2309`_


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

.. major_bug

* upgrade mercurial wheel to latest (fixing CVE issues)
  `Pull Request 2045`_
* Add changeset_revision to tool attributes, avoid self.tool_shed_repository.
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1802`_
* Do not convert spaces to tabs when importing datasets into a library
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 1985`_

.. bug

* Fix that typo in relation_builder.
  `Pull Request 1453`_
* URL generation tweaks for utils.js
  `Pull Request 1478`_
* Fix project linting for new pep8
  `Pull Request 1483`_
* Fix Python 3 problem causing Travis failure of dev.
  `Pull Request 1505`_
* catch Exception and properly log errors
  `Pull Request 1510`_
* Change python print() format to be backward compatible with older versions.
  (thanks to `@einon <https://github.com/einon>`__.)
  `Pull Request 1520`_
* Add js for mako based masthead
  `Pull Request 1533`_
* restrict blue popover to tours
  `Pull Request 1577`_
* small spelling error
  (thanks to `@matthdsm <https://github.com/matthdsm>`__.)
  `Pull Request 1582`_
* Fix installation of repository suites outside of tool panel section
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1601`_
* Fixes `<param argument="--set" />` not working when `help=""` is not set
  (thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
  `Pull Request 1650`_
* Fix validation for data source tools
  `Pull Request 1654`_
* Better fix for missing element identifier
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1693`_
* Update david identifier types
  (thanks to `@pavanvidem <https://github.com/pavanvidem>`__.)
  `Pull Request 1696`_
* Drop Ross from the committers group.
  `Pull Request 1698`_
* Wrap conditional test parameters
  `Pull Request 1714`_
* Remove len(stderr), breaks on recent docker versions
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1769`_
* Strip URL of download_file and download_by_url install actions.
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1775`_
* Fix tool form rendering of sections
  `Pull Request 1783`_
* Fix unused import.
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 1796`_
* Fix tool shed tests for commit e4a1d5727805168a9fd15aca1cdd21630ada2bbc
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 1798`_
* Checks for api_key before checking for header from SSO.
  (thanks to `@MatthewRalston <https://github.com/MatthewRalston>`__.)
  `Pull Request 1801`_
* Ensure tool.changeset_revision is set...
  `Pull Request 1806`_
* Change many job mapped properties to lazy loads
  `Pull Request 1809`_
* Whitelist logging tweaks
  `Pull Request 1819`_
* Fix upload tool routing
  `Pull Request 1827`_
* Using node 5.7, 'grunt style' fails with the error:
  `Pull Request 1841`_
* Do not create text values for failed inputs
  `Pull Request 1844`_
* Prevent tours from kicking off within iframes
  `Pull Request 1846`_
* Fix repeat prefix
  `Pull Request 1848`_
* also update rrda when repairing or updating a repository
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 1850`_
* Fix regex validator
  `Pull Request 1862`_
* Tour routing overhaul
  `Pull Request 1870`_
* Add dedicated client endpoint to the root controller.
  `Pull Request 1879`_
* Update check_python.py now dropping Python 2.6
  (thanks to `@peterjc <https://github.com/peterjc>`__.)
  `Pull Request 1883`_
* Fix citation-model to fail silently/gracefully
  `Pull Request 1884`_
* Change to sentry middleware to work with modern raven clients.
  `Pull Request 1895`_
* svgfig->svgwrite in unpinned requirements
  `Pull Request 1896`_
* Fix icon sizes
  `Pull Request 1934`_
* Fix tool downloads in tool form
  `Pull Request 1935`_
* Fixing error in run.sh script
  (thanks to `@kellrott <https://github.com/kellrott>`__.)
  `Pull Request 1954`_
* Fix typo: send-->sent
  `Pull Request 1965`_
* Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako .
  `Pull Request 1972`_
* Remove duplicate help target
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 1980`_
* Fix booleans in workflow editor
  `Pull Request 1990`_
* libraries: change default size of fa in iconspans
  `Pull Request 2000`_
* libraries: move text out of icon spans for library dataset view
  `Pull Request 2008`_
* Fix unbound error that is possible if using tool bursting.
  `Pull Request 2009`_
* Fix multiple flag for workflow dataset inputs
  `Pull Request 2021`_
* fix duplication of select2 entries
  `Pull Request 2022`_
* Fix fluent query log serialization when datetime types are in use.
  `Pull Request 2039`_
* Workflow import fix when tools are missing.
  `Pull Request 2048`_
* Managers: remove UTC zone when parsing dates
  (thanks also to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2042`_, `Pull Request 2062`_, `Pull Request 2065`_
* Change user disk usage pgcalc function up a bit to make a slightly safer dry-run.
  `Pull Request 2063`_
* Allow tool confs with a tool_path to not be interpreted as shed confs.
  `Pull Request 2066`_
* Fix deps.command.download_command on Mac OS X.
  `Pull Request 2075`_
* Show sections in workflow run
  `Pull Request 2087`_
* Workflow section fix backport
  (thanks to `@hexylena <https://github.com/hexylena>`__.)
  `Pull Request 2092`_
* Run external local set_metadata jobs in the job's working directory
  `Pull Request 2094`_
* make dependencies browsable again
  `Pull Request 2101`_
* Convert the DRMAA runner to use Pulsar's DRMAA session wrapper
  `Pull Request 2102`_
* Updated to Dependency change in b167a741a444c3988447b0d63a1ba3dc5e4e62f5
  (thanks to `@Christian-B <https://github.com/Christian-B>`__.)
  `Pull Request 2104`_
* Fix datatype list in workflow editor
  `Pull Request 2105`_
* Workaround for the toolshed's hgweb.
  `Pull Request 2106`_
* Update debian init script
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
  `Pull Request 2109`_
* Rev Pulsar to 0.7.0.dev3.
  `Pull Request 2122`_
* change run_tool_shed.py to see the file in the correct lcoation
  (thanks to `@nturaga <https://github.com/nturaga>`__.)
  `Pull Request 2131`_
* Fixes due to `#2093 <https://github.com/galaxyproject/galaxy/issues/2093>`__
  and `#2018 <https://github.com/galaxyproject/galaxy/issues/2018>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 2133`_
* markupsafe.escape() in Python2 does not work on str containing non-ASCII
  characters
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 2138`_
* load options from config, not from options
  `Pull Request 2139`_
* fix/replace biomart data source
  `Pull Request 2149`_
* Add tool parameters back to parameters and expose for certain tools
  `Pull Request 2156`_
* Fix wrapper issue, overload __ne__
  `Pull Request 2161`_
* Fix grouping tool and enhance performance when removing lines.
  `Pull Request 2166`_
* libraries: always fetch new permissions as we are reusing the view
  `Pull Request 2176`_
* Fix for redirecting a non-user when a tool has require_login=True.
  `Pull Request 2180`_
* Fix.published history long titles have to be truncated
  `Pull Request 2189`_
* fix a bug with missing history_id in libraries dataset import
  `Pull Request 2190`_
* Fix message in legacy panel mako
  `Pull Request 2191`_
* Prepass on remote user header based on maildomain and normalize config.
  `Pull Request 2195`_
* Extend to_json for dataset tool parameters
  `Pull Request 2196`_
* Pages parser fix
  `Pull Request 2197`_
* Translate data source tool parameters on parameter expansion
  `Pull Request 2201`_
* Sync job_script module with Pulsar to fix doctest.
  `Pull Request 2203`_
* Improve error message for data source tools, executed through the
  tool_runner controller
  `Pull Request 2204`_
* Add fixed validation check for data_source tools URL parameter
  `Pull Request 2208`_
* Fix tool action redirect url for non-default tools
  `Pull Request 2211`_
* Browse library date handling for non-ascii month abbreviations
  `Pull Request 2214`_
* Avoid reset of cursor position for input fields during manual entry
  `Pull Request 2218`_
* Add conditional statsd requirement
  `Pull Request 2227`_
* Fix js value validator
  `Pull Request 2234`_
* Encode collection reduce in serializable fashion
  `Pull Request 2238`_
* Update `_condarc` automatically
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 2255`_
* Truncate job name in DRMAA runner by default for PBSPro.
  `Pull Request 2265`_
* Cherrypick of encoding fix
  `Pull Request 2266`_
* If a Slurm post-mortem determines that a job is in a non-terminal state,
  return the job to the monitor queue
  `Pull Request 2311`_
* Unicodify pretty datetimes which can contain non-ASCII chars
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 2312`_
* Relax default value acceptance condition
  `Pull Request 2316`_
* Fixes the proxy naming
  (thanks to `@bgruening <https://github.com/bgruening>`__.)
  `Pull Request 2333`_
* Re-fix the bug with multiple preceding '/' characters in the GIE proxy
  prefix
  `Pull Request 2339`_
* Do not pollute param_dict with a non JSONifiable dict
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
  `Pull Request 2345`_

.. github_links
.. _Pull Request 1148: https://github.com/galaxyproject/galaxy/pull/1148
.. _Pull Request 1280: https://github.com/galaxyproject/galaxy/pull/1280
.. _Pull Request 1331: https://github.com/galaxyproject/galaxy/pull/1331
.. _Pull Request 1357: https://github.com/galaxyproject/galaxy/pull/1357
.. _Pull Request 1392: https://github.com/galaxyproject/galaxy/pull/1392
.. _Pull Request 1402: https://github.com/galaxyproject/galaxy/pull/1402
.. _Pull Request 1403: https://github.com/galaxyproject/galaxy/pull/1403
.. _Pull Request 1431: https://github.com/galaxyproject/galaxy/pull/1431
.. _Pull Request 1433: https://github.com/galaxyproject/galaxy/pull/1433
.. _Pull Request 1449: https://github.com/galaxyproject/galaxy/pull/1449
.. _Pull Request 1453: https://github.com/galaxyproject/galaxy/pull/1453
.. _Pull Request 1454: https://github.com/galaxyproject/galaxy/pull/1454
.. _Pull Request 1456: https://github.com/galaxyproject/galaxy/pull/1456
.. _Pull Request 1457: https://github.com/galaxyproject/galaxy/pull/1457
.. _Pull Request 1463: https://github.com/galaxyproject/galaxy/pull/1463
.. _Pull Request 1478: https://github.com/galaxyproject/galaxy/pull/1478
.. _Pull Request 1483: https://github.com/galaxyproject/galaxy/pull/1483
.. _Pull Request 1488: https://github.com/galaxyproject/galaxy/pull/1488
.. _Pull Request 1489: https://github.com/galaxyproject/galaxy/pull/1489
.. _Pull Request 1490: https://github.com/galaxyproject/galaxy/pull/1490
.. _Pull Request 1496: https://github.com/galaxyproject/galaxy/pull/1496
.. _Pull Request 1505: https://github.com/galaxyproject/galaxy/pull/1505
.. _Pull Request 1510: https://github.com/galaxyproject/galaxy/pull/1510
.. _Pull Request 1512: https://github.com/galaxyproject/galaxy/pull/1512
.. _Pull Request 1519: https://github.com/galaxyproject/galaxy/pull/1519
.. _Pull Request 1520: https://github.com/galaxyproject/galaxy/pull/1520
.. _Pull Request 1522: https://github.com/galaxyproject/galaxy/pull/1522
.. _Pull Request 1523: https://github.com/galaxyproject/galaxy/pull/1523
.. _Pull Request 1533: https://github.com/galaxyproject/galaxy/pull/1533
.. _Pull Request 1537: https://github.com/galaxyproject/galaxy/pull/1537
.. _Pull Request 1539: https://github.com/galaxyproject/galaxy/pull/1539
.. _Pull Request 1556: https://github.com/galaxyproject/galaxy/pull/1556
.. _Pull Request 1561: https://github.com/galaxyproject/galaxy/pull/1561
.. _Pull Request 1562: https://github.com/galaxyproject/galaxy/pull/1562
.. _Pull Request 1565: https://github.com/galaxyproject/galaxy/pull/1565
.. _Pull Request 1566: https://github.com/galaxyproject/galaxy/pull/1566
.. _Pull Request 1572: https://github.com/galaxyproject/galaxy/pull/1572
.. _Pull Request 1574: https://github.com/galaxyproject/galaxy/pull/1574
.. _Pull Request 1577: https://github.com/galaxyproject/galaxy/pull/1577
.. _Pull Request 1579: https://github.com/galaxyproject/galaxy/pull/1579
.. _Pull Request 1582: https://github.com/galaxyproject/galaxy/pull/1582
.. _Pull Request 1583: https://github.com/galaxyproject/galaxy/pull/1583
.. _Pull Request 1591: https://github.com/galaxyproject/galaxy/pull/1591
.. _Pull Request 1592: https://github.com/galaxyproject/galaxy/pull/1592
.. _Pull Request 1601: https://github.com/galaxyproject/galaxy/pull/1601
.. _Pull Request 1602: https://github.com/galaxyproject/galaxy/pull/1602
.. _Pull Request 1605: https://github.com/galaxyproject/galaxy/pull/1605
.. _Pull Request 1610: https://github.com/galaxyproject/galaxy/pull/1610
.. _Pull Request 1613: https://github.com/galaxyproject/galaxy/pull/1613
.. _Pull Request 1614: https://github.com/galaxyproject/galaxy/pull/1614
.. _Pull Request 1615: https://github.com/galaxyproject/galaxy/pull/1615
.. _Pull Request 1616: https://github.com/galaxyproject/galaxy/pull/1616
.. _Pull Request 1618: https://github.com/galaxyproject/galaxy/pull/1618
.. _Pull Request 1621: https://github.com/galaxyproject/galaxy/pull/1621
.. _Pull Request 1625: https://github.com/galaxyproject/galaxy/pull/1625
.. _Pull Request 1632: https://github.com/galaxyproject/galaxy/pull/1632
.. _Pull Request 1636: https://github.com/galaxyproject/galaxy/pull/1636
.. _Pull Request 1639: https://github.com/galaxyproject/galaxy/pull/1639
.. _Pull Request 1646: https://github.com/galaxyproject/galaxy/pull/1646
.. _Pull Request 1647: https://github.com/galaxyproject/galaxy/pull/1647
.. _Pull Request 1649: https://github.com/galaxyproject/galaxy/pull/1649
.. _Pull Request 1650: https://github.com/galaxyproject/galaxy/pull/1650
.. _Pull Request 1654: https://github.com/galaxyproject/galaxy/pull/1654
.. _Pull Request 1658: https://github.com/galaxyproject/galaxy/pull/1658
.. _Pull Request 1665: https://github.com/galaxyproject/galaxy/pull/1665
.. _Pull Request 1670: https://github.com/galaxyproject/galaxy/pull/1670
.. _Pull Request 1671: https://github.com/galaxyproject/galaxy/pull/1671
.. _Pull Request 1688: https://github.com/galaxyproject/galaxy/pull/1688
.. _Pull Request 1693: https://github.com/galaxyproject/galaxy/pull/1693
.. _Pull Request 1696: https://github.com/galaxyproject/galaxy/pull/1696
.. _Pull Request 1698: https://github.com/galaxyproject/galaxy/pull/1698
.. _Pull Request 1699: https://github.com/galaxyproject/galaxy/pull/1699
.. _Pull Request 1711: https://github.com/galaxyproject/galaxy/pull/1711
.. _Pull Request 1713: https://github.com/galaxyproject/galaxy/pull/1713
.. _Pull Request 1714: https://github.com/galaxyproject/galaxy/pull/1714
.. _Pull Request 1731: https://github.com/galaxyproject/galaxy/pull/1731
.. _Pull Request 1735: https://github.com/galaxyproject/galaxy/pull/1735
.. _Pull Request 1738: https://github.com/galaxyproject/galaxy/pull/1738
.. _Pull Request 1742: https://github.com/galaxyproject/galaxy/pull/1742
.. _Pull Request 1747: https://github.com/galaxyproject/galaxy/pull/1747
.. _Pull Request 1751: https://github.com/galaxyproject/galaxy/pull/1751
.. _Pull Request 1752: https://github.com/galaxyproject/galaxy/pull/1752
.. _Pull Request 1755: https://github.com/galaxyproject/galaxy/pull/1755
.. _Pull Request 1756: https://github.com/galaxyproject/galaxy/pull/1756
.. _Pull Request 1760: https://github.com/galaxyproject/galaxy/pull/1760
.. _Pull Request 1764: https://github.com/galaxyproject/galaxy/pull/1764
.. _Pull Request 1769: https://github.com/galaxyproject/galaxy/pull/1769
.. _Pull Request 1770: https://github.com/galaxyproject/galaxy/pull/1770
.. _Pull Request 1775: https://github.com/galaxyproject/galaxy/pull/1775
.. _Pull Request 1783: https://github.com/galaxyproject/galaxy/pull/1783
.. _Pull Request 1785: https://github.com/galaxyproject/galaxy/pull/1785
.. _Pull Request 1788: https://github.com/galaxyproject/galaxy/pull/1788
.. _Pull Request 1793: https://github.com/galaxyproject/galaxy/pull/1793
.. _Pull Request 1794: https://github.com/galaxyproject/galaxy/pull/1794
.. _Pull Request 1796: https://github.com/galaxyproject/galaxy/pull/1796
.. _Pull Request 1798: https://github.com/galaxyproject/galaxy/pull/1798
.. _Pull Request 1800: https://github.com/galaxyproject/galaxy/pull/1800
.. _Pull Request 1801: https://github.com/galaxyproject/galaxy/pull/1801
.. _Pull Request 1802: https://github.com/galaxyproject/galaxy/pull/1802
.. _Pull Request 1806: https://github.com/galaxyproject/galaxy/pull/1806
.. _Pull Request 1807: https://github.com/galaxyproject/galaxy/pull/1807
.. _Pull Request 1808: https://github.com/galaxyproject/galaxy/pull/1808
.. _Pull Request 1809: https://github.com/galaxyproject/galaxy/pull/1809
.. _Pull Request 1813: https://github.com/galaxyproject/galaxy/pull/1813
.. _Pull Request 1819: https://github.com/galaxyproject/galaxy/pull/1819
.. _Pull Request 1821: https://github.com/galaxyproject/galaxy/pull/1821
.. _Pull Request 1824: https://github.com/galaxyproject/galaxy/pull/1824
.. _Pull Request 1827: https://github.com/galaxyproject/galaxy/pull/1827
.. _Pull Request 1829: https://github.com/galaxyproject/galaxy/pull/1829
.. _Pull Request 1832: https://github.com/galaxyproject/galaxy/pull/1832
.. _Pull Request 1835: https://github.com/galaxyproject/galaxy/pull/1835
.. _Pull Request 1838: https://github.com/galaxyproject/galaxy/pull/1838
.. _Pull Request 1840: https://github.com/galaxyproject/galaxy/pull/1840
.. _Pull Request 1841: https://github.com/galaxyproject/galaxy/pull/1841
.. _Pull Request 1843: https://github.com/galaxyproject/galaxy/pull/1843
.. _Pull Request 1844: https://github.com/galaxyproject/galaxy/pull/1844
.. _Pull Request 1846: https://github.com/galaxyproject/galaxy/pull/1846
.. _Pull Request 1848: https://github.com/galaxyproject/galaxy/pull/1848
.. _Pull Request 1850: https://github.com/galaxyproject/galaxy/pull/1850
.. _Pull Request 1853: https://github.com/galaxyproject/galaxy/pull/1853
.. _Pull Request 1861: https://github.com/galaxyproject/galaxy/pull/1861
.. _Pull Request 1862: https://github.com/galaxyproject/galaxy/pull/1862
.. _Pull Request 1868: https://github.com/galaxyproject/galaxy/pull/1868
.. _Pull Request 1870: https://github.com/galaxyproject/galaxy/pull/1870
.. _Pull Request 1874: https://github.com/galaxyproject/galaxy/pull/1874
.. _Pull Request 1876: https://github.com/galaxyproject/galaxy/pull/1876
.. _Pull Request 1879: https://github.com/galaxyproject/galaxy/pull/1879
.. _Pull Request 1883: https://github.com/galaxyproject/galaxy/pull/1883
.. _Pull Request 1884: https://github.com/galaxyproject/galaxy/pull/1884
.. _Pull Request 1893: https://github.com/galaxyproject/galaxy/pull/1893
.. _Pull Request 1895: https://github.com/galaxyproject/galaxy/pull/1895
.. _Pull Request 1896: https://github.com/galaxyproject/galaxy/pull/1896
.. _Pull Request 1900: https://github.com/galaxyproject/galaxy/pull/1900
.. _Pull Request 1901: https://github.com/galaxyproject/galaxy/pull/1901
.. _Pull Request 1910: https://github.com/galaxyproject/galaxy/pull/1910
.. _Pull Request 1911: https://github.com/galaxyproject/galaxy/pull/1911
.. _Pull Request 1912: https://github.com/galaxyproject/galaxy/pull/1912
.. _Pull Request 1914: https://github.com/galaxyproject/galaxy/pull/1914
.. _Pull Request 1918: https://github.com/galaxyproject/galaxy/pull/1918
.. _Pull Request 1926: https://github.com/galaxyproject/galaxy/pull/1926
.. _Pull Request 1934: https://github.com/galaxyproject/galaxy/pull/1934
.. _Pull Request 1935: https://github.com/galaxyproject/galaxy/pull/1935
.. _Pull Request 1936: https://github.com/galaxyproject/galaxy/pull/1936
.. _Pull Request 1939: https://github.com/galaxyproject/galaxy/pull/1939
.. _Pull Request 1941: https://github.com/galaxyproject/galaxy/pull/1941
.. _Pull Request 1942: https://github.com/galaxyproject/galaxy/pull/1942
.. _Pull Request 1943: https://github.com/galaxyproject/galaxy/pull/1943
.. _Pull Request 1948: https://github.com/galaxyproject/galaxy/pull/1948
.. _Pull Request 1949: https://github.com/galaxyproject/galaxy/pull/1949
.. _Pull Request 1950: https://github.com/galaxyproject/galaxy/pull/1950
.. _Pull Request 1953: https://github.com/galaxyproject/galaxy/pull/1953
.. _Pull Request 1954: https://github.com/galaxyproject/galaxy/pull/1954
.. _Pull Request 1956: https://github.com/galaxyproject/galaxy/pull/1956
.. _Pull Request 1958: https://github.com/galaxyproject/galaxy/pull/1958
.. _Pull Request 1959: https://github.com/galaxyproject/galaxy/pull/1959
.. _Pull Request 1961: https://github.com/galaxyproject/galaxy/pull/1961
.. _Pull Request 1962: https://github.com/galaxyproject/galaxy/pull/1962
.. _Pull Request 1963: https://github.com/galaxyproject/galaxy/pull/1963
.. _Pull Request 1965: https://github.com/galaxyproject/galaxy/pull/1965
.. _Pull Request 1968: https://github.com/galaxyproject/galaxy/pull/1968
.. _Pull Request 1969: https://github.com/galaxyproject/galaxy/pull/1969
.. _Pull Request 1970: https://github.com/galaxyproject/galaxy/pull/1970
.. _Pull Request 1971: https://github.com/galaxyproject/galaxy/pull/1971
.. _Pull Request 1972: https://github.com/galaxyproject/galaxy/pull/1972
.. _Pull Request 1974: https://github.com/galaxyproject/galaxy/pull/1974
.. _Pull Request 1980: https://github.com/galaxyproject/galaxy/pull/1980
.. _Pull Request 1983: https://github.com/galaxyproject/galaxy/pull/1983
.. _Pull Request 1985: https://github.com/galaxyproject/galaxy/pull/1985
.. _Pull Request 1990: https://github.com/galaxyproject/galaxy/pull/1990
.. _Pull Request 1991: https://github.com/galaxyproject/galaxy/pull/1991
.. _Pull Request 1993: https://github.com/galaxyproject/galaxy/pull/1993
.. _Pull Request 1996: https://github.com/galaxyproject/galaxy/pull/1996
.. _Pull Request 2000: https://github.com/galaxyproject/galaxy/pull/2000
.. _Pull Request 2002: https://github.com/galaxyproject/galaxy/pull/2002
.. _Pull Request 2004: https://github.com/galaxyproject/galaxy/pull/2004
.. _Pull Request 2008: https://github.com/galaxyproject/galaxy/pull/2008
.. _Pull Request 2009: https://github.com/galaxyproject/galaxy/pull/2009
.. _Pull Request 2010: https://github.com/galaxyproject/galaxy/pull/2010
.. _Pull Request 2011: https://github.com/galaxyproject/galaxy/pull/2011
.. _Pull Request 2015: https://github.com/galaxyproject/galaxy/pull/2015
.. _Pull Request 2016: https://github.com/galaxyproject/galaxy/pull/2016
.. _Pull Request 2017: https://github.com/galaxyproject/galaxy/pull/2017
.. _Pull Request 2018: https://github.com/galaxyproject/galaxy/pull/2018
.. _Pull Request 2019: https://github.com/galaxyproject/galaxy/pull/2019
.. _Pull Request 2020: https://github.com/galaxyproject/galaxy/pull/2020
.. _Pull Request 2021: https://github.com/galaxyproject/galaxy/pull/2021
.. _Pull Request 2022: https://github.com/galaxyproject/galaxy/pull/2022
.. _Pull Request 2025: https://github.com/galaxyproject/galaxy/pull/2025
.. _Pull Request 2026: https://github.com/galaxyproject/galaxy/pull/2026
.. _Pull Request 2027: https://github.com/galaxyproject/galaxy/pull/2027
.. _Pull Request 2028: https://github.com/galaxyproject/galaxy/pull/2028
.. _Pull Request 2029: https://github.com/galaxyproject/galaxy/pull/2029
.. _Pull Request 2030: https://github.com/galaxyproject/galaxy/pull/2030
.. _Pull Request 2031: https://github.com/galaxyproject/galaxy/pull/2031
.. _Pull Request 2033: https://github.com/galaxyproject/galaxy/pull/2033
.. _Pull Request 2039: https://github.com/galaxyproject/galaxy/pull/2039
.. _Pull Request 2040: https://github.com/galaxyproject/galaxy/pull/2040
.. _Pull Request 2042: https://github.com/galaxyproject/galaxy/pull/2042
.. _Pull Request 2044: https://github.com/galaxyproject/galaxy/pull/2044
.. _Pull Request 2045: https://github.com/galaxyproject/galaxy/pull/2045
.. _Pull Request 2048: https://github.com/galaxyproject/galaxy/pull/2048
.. _Pull Request 2052: https://github.com/galaxyproject/galaxy/pull/2052
.. _Pull Request 2055: https://github.com/galaxyproject/galaxy/pull/2055
.. _Pull Request 2057: https://github.com/galaxyproject/galaxy/pull/2057
.. _Pull Request 2060: https://github.com/galaxyproject/galaxy/pull/2060
.. _Pull Request 2061: https://github.com/galaxyproject/galaxy/pull/2061
.. _Pull Request 2062: https://github.com/galaxyproject/galaxy/pull/2062
.. _Pull Request 2063: https://github.com/galaxyproject/galaxy/pull/2063
.. _Pull Request 2065: https://github.com/galaxyproject/galaxy/pull/2065
.. _Pull Request 2066: https://github.com/galaxyproject/galaxy/pull/2066
.. _Pull Request 2067: https://github.com/galaxyproject/galaxy/pull/2067
.. _Pull Request 2069: https://github.com/galaxyproject/galaxy/pull/2069
.. _Pull Request 2070: https://github.com/galaxyproject/galaxy/pull/2070
.. _Pull Request 2071: https://github.com/galaxyproject/galaxy/pull/2071
.. _Pull Request 2074: https://github.com/galaxyproject/galaxy/pull/2074
.. _Pull Request 2075: https://github.com/galaxyproject/galaxy/pull/2075
.. _Pull Request 2078: https://github.com/galaxyproject/galaxy/pull/2078
.. _Pull Request 2082: https://github.com/galaxyproject/galaxy/pull/2082
.. _Pull Request 2087: https://github.com/galaxyproject/galaxy/pull/2087
.. _Pull Request 2088: https://github.com/galaxyproject/galaxy/pull/2088
.. _Pull Request 2089: https://github.com/galaxyproject/galaxy/pull/2089
.. _Pull Request 2091: https://github.com/galaxyproject/galaxy/pull/2091
.. _Pull Request 2092: https://github.com/galaxyproject/galaxy/pull/2092
.. _Pull Request 2093: https://github.com/galaxyproject/galaxy/pull/2093
.. _Pull Request 2094: https://github.com/galaxyproject/galaxy/pull/2094
.. _Pull Request 2096: https://github.com/galaxyproject/galaxy/pull/2096
.. _Pull Request 2099: https://github.com/galaxyproject/galaxy/pull/2099
.. _Pull Request 2101: https://github.com/galaxyproject/galaxy/pull/2101
.. _Pull Request 2102: https://github.com/galaxyproject/galaxy/pull/2102
.. _Pull Request 2104: https://github.com/galaxyproject/galaxy/pull/2104
.. _Pull Request 2105: https://github.com/galaxyproject/galaxy/pull/2105
.. _Pull Request 2106: https://github.com/galaxyproject/galaxy/pull/2106
.. _Pull Request 2107: https://github.com/galaxyproject/galaxy/pull/2107
.. _Pull Request 2109: https://github.com/galaxyproject/galaxy/pull/2109
.. _Pull Request 2118: https://github.com/galaxyproject/galaxy/pull/2118
.. _Pull Request 2122: https://github.com/galaxyproject/galaxy/pull/2122
.. _Pull Request 2131: https://github.com/galaxyproject/galaxy/pull/2131
.. _Pull Request 2133: https://github.com/galaxyproject/galaxy/pull/2133
.. _Pull Request 2138: https://github.com/galaxyproject/galaxy/pull/2138
.. _Pull Request 2139: https://github.com/galaxyproject/galaxy/pull/2139
.. _Pull Request 2141: https://github.com/galaxyproject/galaxy/pull/2141
.. _Pull Request 2149: https://github.com/galaxyproject/galaxy/pull/2149
.. _Pull Request 2150: https://github.com/galaxyproject/galaxy/pull/2150
.. _Pull Request 2154: https://github.com/galaxyproject/galaxy/pull/2154
.. _Pull Request 2156: https://github.com/galaxyproject/galaxy/pull/2156
.. _Pull Request 2161: https://github.com/galaxyproject/galaxy/pull/2161
.. _Pull Request 2164: https://github.com/galaxyproject/galaxy/pull/2164
.. _Pull Request 2166: https://github.com/galaxyproject/galaxy/pull/2166
.. _Pull Request 2176: https://github.com/galaxyproject/galaxy/pull/2176
.. _Pull Request 2180: https://github.com/galaxyproject/galaxy/pull/2180
.. _Pull Request 2182: https://github.com/galaxyproject/galaxy/pull/2182
.. _Pull Request 2184: https://github.com/galaxyproject/galaxy/pull/2184
.. _Pull Request 2186: https://github.com/galaxyproject/galaxy/pull/2186
.. _Pull Request 2189: https://github.com/galaxyproject/galaxy/pull/2189
.. _Pull Request 2190: https://github.com/galaxyproject/galaxy/pull/2190
.. _Pull Request 2191: https://github.com/galaxyproject/galaxy/pull/2191
.. _Pull Request 2195: https://github.com/galaxyproject/galaxy/pull/2195
.. _Pull Request 2196: https://github.com/galaxyproject/galaxy/pull/2196
.. _Pull Request 2197: https://github.com/galaxyproject/galaxy/pull/2197
.. _Pull Request 2201: https://github.com/galaxyproject/galaxy/pull/2201
.. _Pull Request 2203: https://github.com/galaxyproject/galaxy/pull/2203
.. _Pull Request 2204: https://github.com/galaxyproject/galaxy/pull/2204
.. _Pull Request 2208: https://github.com/galaxyproject/galaxy/pull/2208
.. _Pull Request 2211: https://github.com/galaxyproject/galaxy/pull/2211
.. _Pull Request 2214: https://github.com/galaxyproject/galaxy/pull/2214
.. _Pull Request 2218: https://github.com/galaxyproject/galaxy/pull/2218
.. _Pull Request 2220: https://github.com/galaxyproject/galaxy/pull/2220
.. _Pull Request 2227: https://github.com/galaxyproject/galaxy/pull/2227
.. _Pull Request 2234: https://github.com/galaxyproject/galaxy/pull/2234
.. _Pull Request 2238: https://github.com/galaxyproject/galaxy/pull/2238
.. _Pull Request 2255: https://github.com/galaxyproject/galaxy/pull/2255
.. _Pull Request 2265: https://github.com/galaxyproject/galaxy/pull/2265
.. _Pull Request 2266: https://github.com/galaxyproject/galaxy/pull/2266
.. _Pull Request 2282: https://github.com/galaxyproject/galaxy/pull/2282
.. _Pull Request 2284: https://github.com/galaxyproject/galaxy/pull/2284
.. _Pull Request 2309: https://github.com/galaxyproject/galaxy/pull/2309
.. _Pull Request 2311: https://github.com/galaxyproject/galaxy/pull/2311
.. _Pull Request 2312: https://github.com/galaxyproject/galaxy/pull/2312
.. _Pull Request 2316: https://github.com/galaxyproject/galaxy/pull/2316
.. _Pull Request 2317: https://github.com/galaxyproject/galaxy/pull/2317
.. _Pull Request 2333: https://github.com/galaxyproject/galaxy/pull/2333
.. _Pull Request 2339: https://github.com/galaxyproject/galaxy/pull/2339
.. _Pull Request 2345: https://github.com/galaxyproject/galaxy/pull/2345