May 2015 Galaxy Release (v 15.05)

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Highlights

Authentication Plugins
Galaxy now has native support for LDAP and Active Directory via a new community developed authentication plugin system.
Tool Sections
Tool parameters may now be groupped into collapsable sections.
Collection Creators
New widgets have been added that allow much more flexibility when creating simple dataset pair and list collections.

Github

New
% git clone -b master https://github.com/galaxyproject/galaxy.git
Update to latest stable release
% git checkout master && pull --ff-only origin master
Update to exact version
% git checkout v15.05

BitBucket

Upgrade
% hg pull
% hg update latest_15.05

See our wiki for additional details regarding the source code locations.

Release Notes

Enhancements

Fixes

  • During the 15.05 development cycle dozens of fixes were pushed to the release_15.03 branch of Galaxy. These are all included in 15.05 and summarized here (with special thanks to Björn Grüning and Marius van den Beek).
  • Fix race condition that would occasionally prevent Galaxy from starting properly. Pull Request 198, Trello
  • Fix scatter plot API communications for certain proxied Galaxy instances - thanks to @yhoogstrate. Pull Request 89
  • Fix bug in collectl job metrics plugin - thanks to Carrie Ganote. Pull Request 231
  • Fix late validation of tool parameters. Pull Request 115
  • Fix fasta_to_tabular_converter.py (for implicit conversion) - thanks to Peter Cock. Pull Request 11
  • Fix to eliminate race condition by collecting extra files before declaring dataset’s OK. Pull Request 48
  • Fix setting current history for certain proxied Galaxy instances - thanks to @wezen. 6946e46.
  • Fix typo in tool failure testing example - thanks to Peter Cock. Pull Request 18.
  • Fix Galaxy to default to using SSL for communicating with Tool Sheds. 0b037a2
  • Fix data source tools to open in _top window. Pull Request 17
  • Fix to fallback to name for tool parameters without labels. Pull Request 189, Trello
  • Fix to remove redundant version ids in tool version selector. Pull Request 244
  • Fix for downloading metadata files. Pull Request 234
  • Fix for history failing to render if it contains more exotic dataset collection types. Pull Request 196
  • Fixes for BaseURLToolParameter. Pull Request 247
  • Fix to suppress pysam binary incompatibility warning when using datatypes in binary.py. Pull Request 252
  • Fix for library UI duplication bug. Pull Request 179
  • Fix for Backbone.js loading as AMD. 4e5218f
  • Other small Tool Shed fixes. 815f86f, 76e0915
  • Fix file closing in lped_to_pbed_converter. 182b67f
  • Fix undefined variables in Tool Shed add_repository_entry API script. 47e6f08
  • Fix user registration to respect use_panels when in the Galaxy app. 7ac8631, Trello
  • Fix bug in scramble exception, incorrect reference to source_path 79d50d8
  • Fix error handling in pbed_to_lped. 7aecd7a
  • Fix error handling in Tool Shed step handler for chmod action. 1454396
  • Fix __safe_string_wrapper in tool evaluation object_wrapper. ab6f13e
  • Fixes for data types and data providers. c1d2d1f, 8da70bb, 0b83b1e
  • Fixes for Tool Shed commit and mercurial handling modules. 6102edf, b639bc0, debea9d
  • Fix to clean working directory during job re-submission. Pull Request 236
  • Fix bug when task splitting jobs fail. Pull Request 214
  • Fix some minor typos in comment docs in config/galaxy.ini.sample. Pull Request 210
  • Fix admin disk usage message. Pull Request 205, Trello
  • Fix to sessionStorage Model to suppress QUOTA DOMExceptions when Safari users are in private browsing mode. 0c94f04

To stay up to date with Galaxy’s progress watch our screencasts, visit our community hub, and follow @galaxyproject on Twitter.

You can always reach us on Gitter or IRC.

Thanks for using Galaxy!

The Galaxy Team