Galaxy March Release Summary
$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable
$ hg pull
Starting with this distribution, an updated Galaxy release versioning system has been implemented. The versioning scheme is Ubuntu-style.
Releases versioning details are as follows:
A version_major key has been added to /api/configuration.
The file version.py is the source of version_major.
- "Point" releases will be created periodically with updates to the release.
"Point" releases are versioned as YY.MM.point, where ».point« begins at .1 and increments for each point release.
- The first version is »15.03«, where the tag for the release is »v15.03«.
- Stable updates to »15.03« will be »15.03.1«, »15.03.2«, where the tag for the release is formatted as »v15.03.1«.
- Backwards compatibility: The tag »latest_15.03« in Bitbucket will always point to the newest »15.03« changeset.
The Github master branch is similar to the former Bitbucket stable branch. The difference is that whereas individual commits to the current stable release were previously applied to the stable branch, they are now only applied in a group, when a "point" release is made (e.g. 15.03.1).
- The Bitbucket stable branch now works the same way as the Github master branch.
Permanent named branches are now created for each release. The 15.03 release is in the release_15.03 branch, which will be updated with additional changes throughout the lifecycle of this release, as was done with the Bitbucket stable branch in the past. When the Galaxy Team determines that a "point" release is necessary, this branch is merged to master and a point release tag is created. This branch exists in both the Github and Bitbucket versions of Galaxy.
Thus, if you would like to upgrade to the 15.03 release and ensure you do not subsequently upgrade to the release after 15.03 (i.e. 15.05) when it is made, you can use the release_15.03 branch. If you would always like to run the latest release (recommended), you should use the master (Git) or stable (Bitbucket) branch.
Much of Galaxy’s core tool set has been redesigned. Several contain new functionality. These tools are included in the Tool Shed and many are ready for use on Galaxy Main. Older Workflows may contain tools that automatically map to the new tools or Workflows may need minor adjustments. c6Lkejro
Be sure to check out the new Galaxy NGS 101 wiki (in progress).
Galaxy development has moved to Github, but stable/release changes are mirrored to Bitbucket. Deployers can continue to use Bitbucket as they have done in the past.
An invalid API key will now always return a »403« error. Triggers: API key is not found, is expired, or is not associated with an active account. n59kZhXk
New options that permits tools to access their $REPOSITORY_INSTALL_DIR location via PATH. 0pgF5PBQ
To preserve the original deployment state, a new option to disable runtime egg fetching was created (a configurable environment variable - see ticket for details). lthRjVZq
Enhancement to permit configuration to disable egg fetching or the use of eggs entirely. gfm6jilm
Six egg added to eggs.galaxyproject.org. Pv84VVZR
Reloading an external display application from disk can be done now without restarting Galaxy. 4ZlsSGA4
Functional tool tests now output xunit or nosetests style XML. dpfrNZDq
Expanded on Base, History, and HDA managers to provide a consistent facade for common model operations. 3A8nocpN
Removed use of the elementtree package and move to lxml.etree. JJDxFdzK
New configuration option to isolate tool commands in their own shell. kyS9dF0s
Added a new configuration, template_cache_path, to reports_wsgi.ini.sample. Thank you Trevor Wennblom. 5vJ4EsDI
Allow reloading External Display applications without restarting Galaxy. 02W1lMw7
Restructured mvc/ui.js. HnnBFJy0
Improved use of a SELECT statement to reliably retrieve table column names. Thank you James Johnson. oYkjj4T3
Made installation of tool repositories more robust by setting time to "Epoch" instead of throwing server error when repository_metadata.time_last_tested is unset. o09VBhr1
Change to allow anonymous users (those not logged into a Galaxy account) to view Pages with embedded Histories. 9Om6Odj2
The GET /api/jobs request/response functionality has been expanded. Details in ticket. Thank you Thomas McGowan. H0Bvd737
Moved blastdb_p.loc.sample to the NCBI BLAST Tool Shed repository. Thanks to Lance Parsons. lpZNmEzj
Clearer error messages where parameter validation fails. Thanks to Peter Cock. dRaX5reV
Added pkg_resources to load required Mako packages. Thanks to Lance Parsons. JdxJ11U0
Added a new API method to remove items from tool data tables. Thanks to Anthony Bretaud. 51JsMj0b
Create attribute »optional« for data column parameters. A compliment to »force_select«. G5YtpQZK
Enhanced the collect_primary_datasets() method to allow assignment of the defined output parameter for 3rd-party tools that manage tool outputs internally. pncHLXdw
New and Improved
Data Source/Provider Functions: filtering of transferred lines based on parsed column values. jBMtQm0w
New Multiple Histories View. XLkP9pCr
Enhanced the Data Managers' reference genome retrieval protocol to function better with UCSC's updated file naming/paths. Created a new Data Manager for dbkeys/Genome Builds. Find these in the Tool Shed. kPkwDHmi pmd6gSS6
External Display Applications can now use Tool Data Tables. b5kX6Eje
Data Managers can now populate Tool Data Tables that are undeclared. 2FV2aVIH
Tool Data Tables can load from a URL instead of a path. xTsc9ojY
Tuned and enhanced the determine_output_formats() method for tools. jeMaAiap
- Many changes have been made in order to support full usability of Dataset Collections in the near term. Latest progress includes:
Tools may now use $input.element_identifier during tool evaluation for input data parameters (useful for Workflows/Dataset Collections). W5IChoLS
Implementation of Dataset Collections »list of pairs«. Additional work is in-progress (see ticket). 8hEO00xj
Dataset Collections updated to permit »Drag & Drop« functionality (»copy datasets« is still an option). Zmy8aiFP
New datatypes. Thanks to Björn Grüning.
API updated to include options for selecting data from or downloading (as a tar ball) tool-data content. Thank you Kyle Ellrott. 1874DlBw
Upload UI enhancements that added »select all« functionality to severall operations. Contributed by Jennifer Cabral. X4WscBt8
Modified API protocol when removing or refreshing a data table. x2DLSNlN
- History API Prototypes:
Updated location for new Tool’s »Tool Shed URL«: Tool Options pull down menu. (see graphic at right) 8GdLuEj2
Tool Panel »search« function optimized. 6Bvbduci
Allowing Workflow step dependencies when no input/output files exist. h5qZlgU8
Workflow steps are now assigned UUIDs. 4U9e1och
Updated the Workflow API by replacing preferred usage terminology (s/usage/invocation). XNInq5KH
Tuning for History panel functions: Dataset search, multi-select Datasets to perform batch operations, related database modifications. D4nLl5Ky
Load the »Available Genomes« list from data tables for visualizations (Trackster). Thanks to Anthony Bretaudeau. x8LMSD7Z
The History »Options« menu has been updated to better compliment other recent UI changes. EEsM0abM
Several improvements to the History list view. ltNMDNbZ
Added tool tests functions to assert properties about command, standard output, and standard error. kNgOADAF
Fixed tool shed tests by creating database directory when one is missing from the repository. Thank you Jennifer Cabral. mKBDDG8j
Fixed provenance API request bug when data element has job == None. Thank you Kyle Ellrott. fPVKzBZ6
Resolved a bug in Users API preventing administrators from creating users when allow_user_creation was False. aLqEOOyd
Fixed a GATK Evaluation Bug. PXClb3PT
Corrected an "over-sanitized" info message after renaming a history (html was displaying). MtAQNOqC
Discovered and fixed issue with Paired list collection creator (key renaming broken). QklilFk3
Fix for preventing non-admins from running Data Managers through the API.EeHJP167
Egg-fetching related bugfixes. 9L0HlQ0u
Small fixes for updated workflow scheduler. fF7pUNIG
Change to use samtools version 1.x to generate BAM indexes if it is first in $PATH. UOVlg7nL
Removed displayed paragraph tags from history/rename feedback messages V4VMvDeY
Fixed Picard index Data Manager so that it no longer indicates failure (red dataset result in admin history) when it is actually successful. b1cHiIw0
Corrected certain UI confirmation dialogs that were non-functional. LWkgOJRV
Fetching zip-safe eggs that depend on other eggs were failing - this has been corrected. HWuxsftB
Logging out through External authentication external_auth_logout_url now resets impersonation correctly (logs out of impersonated account). 4SX0BZKA
Fixed tabular dataset display so that it sets the correct extension and mime-type when preview=False and to_ext is not provided. uZnZdFGu
Additions to the js environment by require.js now correctly apply cache busting (avoiding user errors). s2klR2Bb
Corrected a re-run operation that was reporting incorrect dataset names. eniXoRB6
Fixed a history dataset counter that was not updating after a tool run. 2slkkPQW
Several Fixes for Tool Data Tables. scA7eWKH
Fixed History, HDA, and UI post-managers-refactoring. UPiay3qr
Corrected Workflow/Visualization links that were including an extraneous slash »/». dtccfVRK
Replaced missing get_initial_value function in LibraryDatasetToolParameter. MVOasuZY
Correction for Tool Shed not having config.shed_tool_data_path. Og1WxqSA
Resolved processing naming conflicts with uWSGI and Control Queues. ahDk0lx4
News and Community
Two Hackathons are now scheduled to occur before and during GCC 2015.
Teach resources are an exciting, growing, and key area for expansion throughout 2015, check out what is new!
Follow current development real-time and create, comment, and vote on active Trello tickets. As an open source project, we very much welcome community involvement. Not sure how to get involved or how to create an account? We have guidance available here..., that includes a form to aid with quick ticket submission.
Community resources. Overview about how we value and seek your input. Have your voice heard and get involved!
Galaxy Project home page (hub for all resources, those listed above and more!)
See our wiki's right side bar menu → for more links to areas of interest to you
- Our wiki is absolutely open for community contributions and improvements.
Various low-vulnerability-level security fixes. U6yj2pPr
Galaxy logs no longer leak database connection information. VjEqTxlT
The email for resetting an account password is now a link. SKjU40t6
Review instructions for core build: Getting the Stable Distribution
Review reset for Toolshed repos: Resetting Metadata For Installed Repositories