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January 2022 Galaxy Release (v 22.01)
Highlights
New Colour Selector
Do you use tools which require colour inputs, like Circos? Previously we had a restricted colour input which gave you a very limited palette. Now, you have complete freedom of choice with the modern colour selector.
Improved File Export
If you’ve been exporting files from Galaxy lately, you’ve probably seen the amazing new remote file source export, which allows you to export files to FTP, Dropbox, and other locations.
Improved File Uploads
Previously, Galaxy servers used a variety of methods to let you upload large files easily, including some servers which required FTP for large files. We have replaced this with a new upload method, which will be enabled on all usegalaxy servers soon. This will make file uploads significantly smoother, and will be more tolerant of network failures and interruptions! You do not need to make any changes. See Pull Request 12656 for more information.
Beta History: Collection Improvements
If you’ve been trying out the beta history (which will be the default history next release!), it has been updated to indicate whether collections are homogeneous or heterogeneous. This will help you see more easily if you’ve accidentally included an incorrect dataset.
New Visualizations
Thanks to @neoformit, a new R shiny app “iSEE” has been added, which provides a UI for visualization of single-cell RNA datasets. See Pull Request 12650 for more information
New Datatypes
Add datatype iml_dataset subclassing html (thanks to @knutwa-ext). Pull Request 12099
Create sniffer for GRO file type (thanks to @simonbray). Pull Request 12885
Agp datatype Pull Request 12891
Add ludwig model datatype (thanks to @qiagu). Pull Request 13073
Add ampvis2 datatype (thanks to @bernt-matthias). Pull Request 13083
Add Neper and Gmsh datatypes (thanks to @jj-umn). Pull Request 13087
Add new datatype GRIB (thanks to @annefou). Pull Request 13175
Show yaml files in preview Pull Request 13176
Enable display of BAM data without sequence info (thanks to @wm75). Pull Request 13219
Add gz as datatype (thanks to @astrovsky01). Pull Request 13271
Add phyloseq datatype (thanks to @bernt-matthias). Pull Request 13462
Builtin Tool Updates
New interactive tool - iSEE (thanks to @neoformit). Pull Request 12650
Ignore type in unused function Pull Request 12694
Merge 21.09 -> dev Pull Request 12747
Set profile version of ncbi_datasets so it can run containerized Pull Request 12819
Downgrade bowtie requirement for CONVERTER_fasta_to_bowtie_color_index (thanks to @nsoranzo). Pull Request 12851
Fix containerized NCBI Datasets Genomes data source tool Pull Request 12915
Tighten type ignores (thanks to @common-workflow-lab). Pull Request 12965
Update interactivetool_pyiron.xml (thanks to @gmauro). Pull Request 12990
Don’t use triple-quoted strings as comments (thanks to @nsoranzo). Pull Request 13007
Add parquet to csv datatype converter Pull Request 13078
Drop tool migration scripts and related code Pull Request 13099
Allow any format in export tool (thanks to @astrovsky01). Pull Request 13151
Add dynamic step to FormNumber range slider (thanks to @davelopez). Pull Request 13233
FormNumber: notify value change on slider change (thanks to @davelopez). Pull Request 13260
Add bioconductor as valid xref for tools (thanks to @bgruening). Pull Request 13268
Release Testing Team
A special thanks to the release testing team for testing many of the new features and reporting many bugs:
Release Notes
User facing release notes compiled by Helena Rasche.
Please see the full release notes for more details.
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