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May 2022 Galaxy Release (v 22.05)

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Highlights

The New History is Here

After years of effort by the development team and community contributors, the new history is finally here. It’s a big improvement over the old history interface, both technically and in terms of user experience, but it might take some getting used to. It has a lot of great new features like:

  • A quick switcher, letting you switch between recent histories

  • Easily find dataset inputs

  • Improved history search interface

Check it out now!

Screenshot of a history, the top most dataset is expanded and a "sitemap" icon is clicked which is showing inputs for that dataset. Each of those inputs has a small upward arrow next to the dataset number. The 'end' dataset of those inputs has a checkmark icon next to the dataset number. The history is titled the beta history and there are a lot of new buttons at the top.

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.

Screenshot of the upload modal. The Settings menu is expanded and shows the "Deferred dataset resolution" checkbox.

Workflow Improvements

You can now see all invocations of a specific workflow, across all of your histories.

Screenshot of the drop down menu on a specific workflow, showing an invocation button. This is accessible via the workflow name in the workflow list.

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.

List of workflow invocations for a specific workflow named Annotation Pipeline. A single invocation is visible along with the results and associated report in the normal workflow invocation view that appears after submitting a job.

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:

Saved Rules

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:

Rule based uploader interface showing a list of recently used rules. The mouse hovers over the first one showing a short description of the rule mentioning filtering.

Scratchbook Upgraded

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.

OpenAPI Docs

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.

Screenshot of the OpenAPI autogenerated documentation listing all of the available Galaxy APIs. In each collapsed section there is an interface to try out the APIs with various values, live, in Galaxy.

New Visualizations

Screenshot of the new 3 dimensional PCA plot visualisation available in Galaxy.

New Datatypes

Builtin Tool Updates

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>

Release Notes

User facing release notes compiled by Helena Rasche.

Please see the full release notes for more details.

To stay up to date with Galaxy’s progress, watch our screencasts; visit our community Hub; and follow us on Bluesky, Mastodon, and LinkedIn.

You can always chat with us on Matrix.

Thanks for using Galaxy!

The Galaxy Team