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 Helena Rasche. Pull Request 30

• Expose category list in show call for Tool Shed repositories - thanks to Helena 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 Helena 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 Helena 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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Thanks for using Galaxy!

The Galaxy Team