Please note new upgrade syntax
$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable
$ hg pull
Python 2.5 Support Has Ended
As of this release, Galaxy no longer supports Python 2.5. More in the ticket: http://trello.com/c/OQT8Iun8
Required metadata reset for installed tool shed repositories
It is critical that you reset the metadata on your installed tool shed repositories when you upgrade your Galaxy instance to this revision!
When a tool shed repository is installed into your local Galaxy instance, metadata is generated for the repository as a part of the installation process and stored in the tool_shed_repository.metadatatable column in the Galaxy database. This automatic process inspects the contents of the specific revision of the installed repository and generates and stores important information about it. This metadata information is used by certain Galaxy features. As new features are added to Galaxy or the tool shed, the process that generates this installed tool shed repository metadata within the Galaxy instance may be enhanced to accommodate information about the new features. Read more…
New Tool Shed Features
Resetting metadata on your repositories
There may be occasions when the entire changelog should be inspected and all of the metadata reset on it. You can reset all metadata on a repository that you are authorized to change by selecting the Reset all repository metadata option from the Repository Actions menu. Sometimes it may be necessary to reset metadata on multiple repositories. For example, if metadata is changed for a repository that is a dependency of another repository, it may be necessary to reset all metadata on each of the repositories in the dependency chain. Read more…
Tool Shed feature enhancements
- Supported tags sets for the tool_dependencies.xml file
Several new tags and attributes are supported for tool dependency definitions. These tags and attributes are supported when installing repositories with tool dependencies in either a browser or using the enhanced Galaxy API. Read more…
- The bells and whistles of tool dependency definitions
In some cases, a dependency definition author may want to write a definition whose dependency package (e.g., osra) can require a previously compiled binary (e.g., graphicsmagick) during compilation as well as tool execution time when the tool is using the compiled [osra] binary. This is possible using a combination of three tool dependency definition tag sets, which must be defined in the tool_dependencies.xml file in the order discussed here. Read more…
- Framework enhancements that process repository_dependencies.xml files Several enhancements have been made to the Tool Shed framework that processes repository dependency definitions contained in a repository_dependencies.xml file in a repository. Both of the previously required "toolshed" and "changeset_revision" attributes are now optional, and a new tag attribute is supported for ordering the installation of repository dependencies. This new attribute named "prior_installation_required", and if set to True in the repository dependency definition for a certain repository XYZ, then Galaxy's repository installation process will ensure that the required repository (XYZ's defined repository dependency) is installed prior to the installation of XYZ. These enhancements are supported when installing repositories with repository dependencies in either a browser or using the enhanced Galaxy API.
- The automated tool test framework
The Tool Shed includes an extensive installation and test framework that works with repositories that contain valid tools. It is designed to be executed by cron regularly and sends email notification to a mail list when each run is completed. The framework is very flexible. It can be executed automatically or manually on a single repository revision or all revisions of all repositories in the tool shed. Read more…
- The Tool Shed API
The RESTful Tool Shed API has been significantly enhanced. Read more…
- Tool Shed Functional Test Framework
Many additional tests have been added to the tool shed functional test framework. Read more…
Miscellaneous Tool Shed fixes and enhancements
- Enhance the Repositories that contain tools with invalid functional tests grid to allow for sorting by repository owner. Enhance several of the repository review grids to enable sorting by repository owner.
- Clean up the main repositories by category grid and add a tools verified column.
Raise exceptions when tool dependency definition <install> and <set_environment> tags define an unsupported version attribute.
- Add more granular lists of writable repositories for the current user: repositories with missing tool test components, repositories with failing tool tests and repositories with no failing tool tests.
Move the My invalid tools menu item in the tool shed to a grid that filters to the latest metadata revision.
- The "Repository Actions" menu has been standardized so that the menu is virtually the same on all pages.
- Attempt to standardize the main page title for repository pages in the tool shed by displaying the repository name.
Enable dynamic configuration of message box content and visibility in the wsgi .ini file. Display the configured brand, if any, in the <title> element.
- For tool dependencies whose installation ended in an error, still display them when attempting to uninstall them.
- Enhancements for the tool shed repository View changeset page: display the commit message, display both the ctx rev and the changeset hash in the title bar, and add Previous changeset and Next changeset buttons to allow for easier scrolling through the repository changelog.
- Fix for reinstalling an uninstalled repository when leaving the no changes checkbox checked and entering text into the new tool panel section field.
Keep all contents (including comments) of dependency definition files when re-writing them to include missing toolshed and changeset_revision attributes.
Eliminate the use of Galaxy's elementree egg within the tool shed.
Accepted Tool Shed pull requests
Tool Shed Tickets
GenomeSpace: Update serverurl.properties file location to work around issue with jumbo frames. https://trello.com/c/7tZli0PH
MAF to BED corrected to fix problem with false error states. https://trello.com/c/y55KbTRt
STDERR and STDOUT will now show beginning and end of contents, instead of just the beginning, when truncated. https://trello.com/c/v31ECJPr
Fix displaying STDERR and STDOUT links in dataset info. https://trello.com/c/2ZTg6Tiq
Auto Focus on first item on forms. https://trello.com/c/etlSFyEr
Clarify tool tip FASTQ Summary Statistics. https://trello.com/c/LX0ma0uQ
Resolve BSD/GNU grep version behavior differences. https://trello.com/c/dPUZ9zEA
Filter and Sort: "Select" tool, improved handling of special characters. https://trello.com/c/cwrBpNP9
Change file-merging to use copy.copyfileobj() rather than cat and mv. https://trello.com/c/Gaqoc6H8
Data Manager: Fix for detecting job error in data manager tools; needed as a result of recent job flow changes. https://trello.com/c/EtXd4zqq
Enhancements to handlers, display, and data input parsing. https://trello.com/c/5jk3k7Td
Composite track improvements. https://trello.com/c/hPcrKfJl
Insert a button for Trackster Visualization into data display viewer. https://trello.com/c/KGNfWZEH
Add Bigwig support for BAM coverage. https://trello.com/c/GV7nTlg9
VCF visualization in trackster. https://trello.com/c/1dj3lTtU
Histories & Datasets
Delete Hidden Datasets menu option. https://trello.com/c/0SoREcMn
When copying datasets to the current history always refresh history. https://trello.com/c/jY5HSdu1
Library API problem in galaxy-central default but not stable. https://trello.com/c/TbWP1tad
Unicode fixes for previewing large datasets. https://trello.com/c/BHRKkcaw
Unicode fixes for uploading by file in upload tool. https://trello.com/c/O0M8W8X8
Unicode fixes for displaying saved workflows in Tool Menu. https://trello.com/c/dAuDcE99
Unicode fixes for form builder and toolparameters. https://trello.com/c/nVldKDiL
Fix for TabularToolDataTable.get_column_name_list() when value column is overloaded by e.g. name. https://trello.com/c/6fPCLwn5
Tool Parameter Validator: MetadataInDataTableColumnValidator fix issue where validator's list of valid options would become stale when e.g. a Data Manager was run. https://trello.com/c/dSEOinly
Stop jobs on history deletion. https://trello.com/c/LBZxfcjx
Track down decorator import failure that shows on some machines (see ticket). https://trello.com/c/It6q5Ul8
Do not allow deleted datasets to be viewed / downloaded. https://trello.com/c/elIs7IHc
Reports app: Fix util clash due to bad imports. https://trello.com/c/5d7EeeTq
Unify Web/API Transactions. https://trello.com/c/c5wZPVGd
Eliminate PasteScript startup. https://trello.com/c/Q4bJNZuo
Upgraded SQLAlchemy. https://trello.com/c/Q6kBeByD
Error Logging with Sentry. https://trello.com/c/Yc1LXXTR
Pull Requests Merged
Significantly enhance job resource definitions. https://trello.com/c/uNpYoYov
More even distribution of job scheduling. https://trello.com/c/wBDXGcx2
Although there are no specific known security fixes in this distribution, all Galaxy instance maintainers are strongly encouraged to run the latest release to take advantage of other improvements and fixes.
Dataset display now honors preview flag. https://trello.com/c/p7zeJHlX
Bug fix to report's web application. https://trello.com/c/o0S3klAF
Fix problem where jobs were unable to run when job limits were set. https://trello.com/c/6vxkqdjT
Fix Bug causing both upload_async_message and tool_executed.mako to refresh the history panel on upload. https://trello.com/c/8urL3hGW
Fix Tophat2 Wrapper to properly quote read group attribute values. https://trello.com/c/nDBz5eoR
Fix bug admin jobs 'AttributeError: 'NoopQueue' object has no attribute 'job_lock'. https://trello.com/c/uBlCbOFs
ToolDataTables: Fix loading .loc files from locations other than galaxy's tool_data. https://trello.com/c/Xedp7bo5
Fix API External Authentication. https://trello.com/c/UjBbWw4A
Fix non-persistent workflow step hiding. https://trello.com/c/sVKvrw67
Fix problem with search in workflow editor. https://trello.com/c/sAsC6lAK
Fix to add confirm on delete permanently (footer button), saved histories. https://trello.com/c/8nUlUMew
"Stop job" function in jobs admin interface corrected (as of April 2013 release). https://trello.com/c/3vkBCaWf
Have a suggestion? Please see Using the Galaxy Issue Board.