May 2015 Galaxy Release (v 15.05)¶

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¶

Pluggable framework to custom authentication (including new LDAP/Active Directory integration). Thanks to many including Andrew Robinson, Nicola Soranzo, and David Trudgian. Pull Request 1, Pull Request 33, Pull Request 51, Pull Request 75, Pull Request 98, Pull Request 216
Implement a new section tag for tool parameters. Pull Request 35, Trello
New UI widgets allowing much more flexibility when creating simple dataset pair and list collections. Pull Request 134, Trello
Improved JavaScript build system for client code and libraries (now using uglify and featuring Source Maps). 72c876c, 9a7f5fc, 648a623, 22f280f, Trello
Add an External Display Application for viewing GFF/GTF files with IGV. Pull Request 70, Trello
Use TravisCI and Tox for continuous integration testing. Pull Request 40, Pull Request 62, Pull Request 97, Pull Request 99, Pull Request 123, Pull Request 222, Pull Request 235,
Infrastructure for improved toolbox and Tool Shed searching. Pull Request 9, Pull Request 116, Pull Request 142, Pull Request 226, c2eb74c, 2bf52fe, ec549db, Trello, Trello
Enhance UI to allow renaming dataset collections. 21d1d6b
Improve highlighting of current/active content history panel. Pull Request 126
Improvements to UI and API for histories and collections. e36e51e, 1e55206, 0c79680
Update history dataset API to account for job re-submission. b4cf49a
Allow recalculating user disk usage from the admin interface. 964e081
Collect significantly more metadata for BAM files. Pull Request 107, Pull Request 108
Implement detect_errors attribute on command of tool XML. Pull Request 117
Allow setting auto_format="True" on tool output tags. Pull Request 130
Allow testing tool outputs based on MD5 hashes. Pull Request 125
Improved Cheetah type casting for int/float values. Pull Request 121
Add option to pass arbitrary parameters to gem install as part of the tool shed setup_ruby_environment Tool Shed install action - thanks to Björn Grüning. Pull Request 118
Add argument attribute to tool parameters. Pull Request 8
Improve link and message that appears after workflows are run. Pull Request 143
Add NCBI SRA datatype - thanks to Matt Shirley. Pull Request 87
Stronger toolbox filtering. Pull Request 119
Allow updating Tool Shed repositories via the API - thanks to Eric Rasche. Pull Request 30
Expose category list in show call for Tool Shed repositories - thanks to Eric Rasche. Pull Request 29
Add API endpoint to create Tool Shed repositories. Pull Request 2
Do not configure Galaxy to use the test Tool Shed by default. Pull Request 38
Add fields and improve display of Tool Shed repositories. a24e206, d6d61bc, Trello
Enhance multi-selection widgets to allow key combinations Ctrl-A and Ctrl-X. e8564d7, Trello
New, consistent button for displaying citation BibTeX. Pull Request 19
Improved README reflecting move to Github - thanks in part to Eric Rasche. PR #2 (old repo), 226e826, 2650d09, 7d5dde8
Update application to use new logo. 2748f9d, Pull Request 187, Pull Request 206
Update many documentation links to use https sites - thanks to Nicola Soranzo. 8254cab
Sync report options config with galaxy.ini - thanks to Björn Grüning. Pull Request 12
Eliminate need to use API key to list tools via API. cd7abe8
Restore function necessary for splitting sequence datatypes - thanks to Roberto Alonso. Pull Request 5
Suppress filenames in SAM merge using egrep - thanks to Peter Cock and Roberto Alonso. Pull Request 4
Option to sort counts in Count1 tool (tools/filters/uniq.xml) - thanks to Peter Cock. Pull Request 16
Preserve spaces in Count1 tool (tools/filters/uniq.xml) - thanks to Peter Cock. Pull Request 13
Interactive Environments improvements and fixes from multiple developers including Eric Rasche and Björn Grüning. Pull Request 69, Pull Request 73, Pull Request 131, Pull Request 135, Pull Request 152, Pull Request 197
Enable multi-part upload for exporting files with the GenomeSpace export tool. Pull Request 74, Trello
Large refactoring, expansion, and increase in test coverage for “managers”. Pull Request 76
Improved display of headers in tool help. 157eba6, Biostar
Uniform configuration of “From” field for sent emails - thanks to Nicola Soranzo. Pull Request 23
Allow setting job_conf.xml params via environment variables & galaxy.ini. dde2fc9
Allow a tool data table to declare that duplicate entries are not allowed. Pull Request 245
Add verbose test error flag option in run_tests.sh. 62f0495
Update .gitignore to include run_api_tests.html. b52cc98
Add experimental options to run tests in Docker. e99adb5
Improve run_test.sh --help documentation to detail running specific tests. Pull Request 86
Remove older, redundant history tests. Pull Request 120, Trello
Add test tool demonstrating citing a Github repository. 65def71
Add option to track all automated changes to the integrated tool panel. 10bb492
Make tool version explicit in all distribution tool - thanks to Peter Cock. Pull Request 14.
Relocate the external metadata setting script. Pull Request 7
Parameterize script used to pull new builds from the UCSC Browser. e4e5df0
Enhance jobs and workflow logging to report timings. 06346a4
Add debug message for dynamic options exceptions. Pull Request 91
Remove demo sequencer app. 3af3bf5
Tweaks to the Pulsar’s handling of async messages. Pull Request 109
Return more specific API authentication errors. 71a64ca
Upgrade Python dependency sqlalchemy to 1.0.0. d725aab, Pull Request 129
Upgrade Python dependency amqp to 1.4.6. Pull Request 128
Upgrade Python dependency kombu to 3.0.24. Pull Request 128
Upgrade JavaScript dependency raven.js to 1.1.17. bcd1701

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

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The Galaxy Team