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2023 Galaxy Release (v 23.0)

Get Galaxy

Highlights

This release includes significant user interface changes enhancing accessibility and usability. This includes a new tool search, modernized multi-history view, new tag displays, theme support, and better drag and drop handling across the application. There are also brand new ‘Datatypes’ and ‘About This Galaxy’ interfaces. Interactive Tools are more seamlessly integrated into the user interface and Galaxy also comes with a new MGnify Notebook IT. The workflow editor has been completely overhauled with significant improvements to usability and extensibility, including new conditional workflow step functionality.

Check out the 23.0 user release notes for all the details. Are you an admin? See the Administration Notes below, and check out some admin relevant PRs.

Get Galaxy

The code lives at GitHub and you should have Git to obtain it.

To get a new Galaxy repository run:
$ git clone -b release_23.0 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_23.0 && git pull --ff-only origin release_23.0

See the community hub for additional details on source code locations.

Administration Notes

Dependencies for various built-in converter tools have been changed from pysam to samtools. Please make sure you install these dependencies through the admin panel or manually. See more details on the PR here.

Configuration default values are no longer read from the sample files – they now come directly from the config schema. If you are relying on local changes to sample files, be aware that you will need to adjust your configuration. See more details on configuration changes on the PR here.

Configuration Changes

Added

The following configuration options are new

config/galaxy.yml.sample

  • gravity

config/galaxy.yml.sample:galaxy

  • mapping.tool_shed.mapping.bootstrap_admin_api_key

  • mapping.tool_shed.mapping.sentry_traces_sample_rate

Changed

The following configuration options have been changed

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.job_config_file.default has changed from

    job_conf.xml

    to

    job_conf.yml

  • mapping.galaxy.mapping.logo_src.default has changed from

    /static/favicon.png

    to

    /static/favicon.svg

  • mapping.galaxy.mapping.tool_recommendation_model_path.default has changed from

    https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5

    to

    https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model_v_0.2.hdf5

  • mapping.galaxy.mapping.topk_recommendations.default has changed from

    10

    to

    20

Removed

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy

  • mapping.reports.mapping.debug

  • mapping.reports.mapping.use_lint

  • mapping.reports.mapping.use_profile

New Configuration Files

The following files are new, or recently converted to yaml

  • config/themes_conf.yml.sample

Deprecation Notices

Trackster is deprecated and will be removed in the next release. This functionality will be provided by other visualization plugins (IGV.js, JBrowse).

Workflow exports to myexperiment.org are deprecated and will be removed in the next release.

Release Notes

Enhancements

Fixes

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!

The Galaxy Team