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June 2023 Galaxy Release (v 23.1)¶
Highlights¶
Activity Bar Interface¶
23.1 introduces the Activity Bar, a new customizable interface element designed for swift navigation through various sections of the application. The feature is currently opt-in, and you can try it today by enabling it in User Preferences. Upcoming releases will enable this by default for all users, and will extend functionality with new activities and by allowing users to drag items such as datasets and workflows directly from the UI into the activity bar component.
Carbon Emissions Reporting¶
Monitor your environmental impact with our new Carbon Emissions Reporting feature. This feature is available on the job information page, allowing users to track their carbon footprint in real-time. The calculations assume global average values for carbon intensity and power usage effectiveness. Monitor your carbon footprint and become inspired to better your relationship with the environment!
History Archival Feature¶
The history menu has a new option to move a history out of your active histories and into an archive. When archiving a history, you will be presented with two options: either to “Keep the Storage Space” or to “Free the Storage Space” taken up by the history. Keeping the storage space will keep the contents of the history where they are, allowing them to be restored at any moment, but will prevent the UI from allowing certain operations on the history. Freeing the storage space will prompt you to package and export the history to a permanent remote source as a backup snapshot, and then will purge the history and its contents to free up storage space. There will be a simple list, titled Archived Histories, for you to explore your archived histories and restore and reimport them, as needed!
Visualize HDF5 Datasets¶
Users can now visualize their HDF5 datasets directly in Galaxy, thanks to the integration of the h5web visualizer (https://h5web.panosc.eu/)!
Galaxy Notification Framework¶
Galaxy now contains a universal notification framework. This will facilitate sending notifications about a wide variety of scenarios like job completion, artifact sharing, server updates, and more. Users have control over their notifications, including the option to subscribe/unsubscribe from certain types of notifications. The new notification system also supports broadcast notifications, allowing administrators to send server-wide announcements, such as server maintenance or downtime notifications.
New Visualizations¶
H5web updates (thanks to @dannon). Pull Request 16509
Update galaxyproject/charts utilizing visualizations (thanks to @dannon). Pull Request 16674
Add support for visualizing HDF5 datasets (thanks to @jarrah42). Pull Request 15394
Phylocanvas rebuild (thanks to @dannon). Pull Request 15521
Gitignore update (thanks to @ElectronicBlueberry). Pull Request 16046
Fixes the parcel2 build for hdf5 viz when using node18. (thanks to @dannon). Pull Request 16047
FITS file visualization plugin (thanks to @francoismg). Pull Request 16187
Small test decorator improvements (thanks to @jmchilton). Pull Request 16220
New Datatypes¶
Fix bad auto-merge of dev (thanks to @jmchilton). Pull Request 15386
Follow up to #15186 (thanks to @jdavcs). Pull Request 15388
Add support for visualizing HDF5 datasets (thanks to @jarrah42). Pull Request 15394
Merge 23.0 into dev (thanks to @mvdbeek). Pull Request 15594
Enable
strict_equality
mypy option (thanks to @nsoranzo). Pull Request 15808FITS data format (thanks to @volodymyrss). Pull Request 15905
Improve display chunk generation for BAMs (thanks to @wm75). Pull Request 15972
Code cleanups from ruff and pyupgrade (thanks to @nsoranzo). Pull Request 16035
Dataset chunking tests (and small fixes) (thanks to @jmchilton). Pull Request 16069
Merge release_23.0 into dev (thanks to @nsoranzo). Pull Request 16088
Improve robustness of collection edit E2E test (thanks to @jmchilton). Pull Request 16092
Add hdf4 datatype (thanks to @TheoMathurin). Pull Request 16105
Fix linting of FITS datatype code (thanks to @mvdbeek). Pull Request 16169
Add zipped mongodb and genenotebook datatypes (thanks to @abretaud). Pull Request 16173
Add Visium datatype for squidpy and spatialomics tools (thanks to @astrovsky01). Pull Request 16255
Builtin Tool Updates¶
Remove render.py script from iSEE (thanks to @neoformit). Pull Request 16616
FileInput no longer accept ‘U’ in the file mode (thanks to @bgruening). Pull Request 16704
Deprecate tools/evolution (thanks to @bernt-matthias). Pull Request 15656
Allow pending inputs in some collection operation tools (thanks to @mvdbeek). Pull Request 15892
Updates MGnify interactive tool to v1.1.0 (thanks to @SandyRogers). Pull Request 16179
Remove various fallback behaviors (thanks to @mvdbeek). Pull Request 16199
Release Testing Team¶
A special thanks to the release testing team for testing many of the new features:
Release Notes¶
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 @galaxyproject@mstdn.science on Mastodon or @galaxyproject on Twitter.
You can always chat with us on Matrix.
Thanks for using Galaxy!