May 2022 Galaxy Release (v 22.05)¶
The New History is Here
A quick switcher, letting you switch between recent histories
Easily find dataset inputs
Improved history search interface
Check it out now!
Storage Dashboard (beta)
Have you ever been over your quota? 250 GB sure goes fast! Now with the new Storage Dashboard you can get a quick overview of ways to help clean up deleted datasets and recover some of that quota allocation. This is a beta version of this interface, let us know if you have any issues. In future versions, it will be expanded to help you understand how your allocation is being used, and which histories and datasets should be cleaned up first.
Bulk History Operations
The new history allows for improved bulk operations, selecting dozens or hundreds of datasets to retag or change database key automatically, a process that used to require using collections or doing them one by one.
Deferred dataset resolution enables running workflows and tools without importing data into Galaxy first
It is now possible to defer dataset resolution for datasets imported via URLs and the “Choose remote files” dialog. This means that the deferred dataset will only be downloaded as it is needed during job execution. Deferred datasets will not count towards your storage quota, as the data is not stored by Galaxy. To enable deferred dataset resolution click on “Settings” in the upload dialog.
You can now see all invocations of a specific workflow, across all of your histories.
This is especially useful if you run a single workflow across multiple datasets, and keep them nicely separated in multiple histories. You can see all of the results in a single centralised location.
Additional workflow improvements have been made, e.g. numbering of steps in a workflow. Improvements have been made to the internal representation of the workflow that should make the saved .ga and .gxwf.yml files easier to compare across changes.
Workflows can also now be zoomed in and out via scrolling, this interface should be more familiar for anyone who has used Google Maps:
Do you use the Rule Based Uploader (RBU)? (If not, learn how today!) The RBU now has a very convenient recently used rule listing, sorted by how recently they were used. You can hover over each entry to also list a preview of what steps were done in that RBU invocation:
The scratchbook has been updated to a new implementation. Now your views of datasets can overlap, you have much more freedom in the size of each window, and you can minimize datasets like minimizing a window to the taskbar in Windows.
The Galaxy API is going through an upgrade to FastAPI, which allows us to generate OpenAPI documentation. If you’re an API consumer, either via BioBlend or via another system, you can use this to see all of the APIs available from Galaxy and try them out live.
Builtin Tool Updates¶
Overhaul and improve the Jupyter Interactive Tool, providing many new interface options (thanks to @blankenberg). Pull Request 13606 * You can specify any number of user-defined inputs using the repeat input, providing name value, selecting the type of input, and then providing values. * You can make the JupyTool reusable in a workflow, by allowing the user to specify input values for the defined input blocks. * Inputs can be accessed by name from the automatically provided GALAXY_INPUTS dictionary. * Outputs can be written automatically to the user’s history by writing to the outputs directory for one individual file or to the outputs/collection directory for multiple files. * Using collection tools, you can parse out the individual elements from the collection, as needed.
Release Testing Team¶
A special thanks to the release testing team for testing many of the new features and reporting many bugs:
Ahmed Awan <https://github.com/ahmedhamidawan>
Catherine Bromhead <https://github.com/cat-bro>
Fabio Cumbo <https://github.com/cumbof>
Jennifer Hillman-Jackson <https://github.com/jennaj>
John Davis <https://github.com/jdavcs>
Simon Bray <https://github.com/simonbray>
Tyler Collins <https://github.com/tcollins2011>
User facing release notes compiled by Helena Rasche.
Please see the full release notes for more details.
You can always chat with us on Matrix.
Thanks for using Galaxy!