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May 2018 Galaxy Release (v 18.05)

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Highlights

New Interface Style Library

The design of many components of the Galaxy user interface has been subtly improved as the result of upgrading to the Bootstrap 4 style library. The upgrade process was a large community effort with commits from six contributors and testing and bug reports from many others. A huge thanks goes out to everyone who helped - it is a great step forward toward a more standardized Galaxy client infrastructure built on reactive VueJS components. Read more about whats new and changed in the underlying Bootstrap 4 JavaScript library here.

Pull Request 5807, Galaxy Project Board for Bootstrap 4.

Unlimited Browser Upload Size

Support for chunked and resumable file uploads out-of-the-box. This should effectively eliminate browser-based limitations on the size of files that can be uploaded to Galaxy.

Pull Request 5516

New Powerful Rule-Based Data Uploader

Galaxy now features a powerful new interface for manipulating lists of rules for processing metadata that can be used to describe the upload of arbitrarily complex collections as well as individual datasets. These rules can be used to build collections from lists of URLs, FTP directory contents, data library folders, and tabular sample sheets or exports from external data sources. The same technique can be applied to the metadata of an existing collection, enabling very flexible filtering, sorting, relabelling, grouping, flattening, and general re-organization of collections. This client widget is backed by a powerful new hierarchical upload API and a new collection operation tool.

Check out this tutorial describing new techniques for loading large numbers of datasets and complex collections into Galaxy.

Pull Request 5365, Pull Request 5220, Pull Request 5819, Pull Request 5823, Pull Request 5929, Pull Request 5940

GDPR Beta Mode

We introduce beta GDPR privacy mode. Admins can enable it to help them comply with the European Union law known as General Data Protection Regulation, which goes into effect on May 25, 2018. Thanks to @hexylena.

Pull Request 6069

New HIV-TRACE Plugin

Integration of a new visualization plugin - HIV-TRACE. Thanks to @veg!

Pull Request 5869

Visualization Frameworks Unified

The charts and generic visualization frameworks have been merged together into a single coherent one. You can use a new menu option to list and search all available visualizations.

Pull Request 5633, Pull Request 5505

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_18.05 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_18.05 && git pull --ff-only origin release_18.05

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

Security

vcffilter by devteam allowed RCE

Tracked as GX-2018-0004.

Older versions of the VCF filter tool in the vcffilter repository by devteam allowed remote code execution due to missing character escaping. If you have this repository installed in your Galaxy, please update to the revision 4:6b935ab36d7b or newer and disable/uninstall all older versions.

Breaking Changes

  • The charts repository that powers Galaxy built-in visualizations that need backend computation has been moved to the IUC account. In order for these visualization options to keep working, admins need to install the following repository: iuc/charts.

  • Removed support for the Graphite statistics middleware. We continue to further support the statsd middleware.

  • We reworked how compressed archives (zip, gz, bz etc.) are being defined and handled in Galaxy. As a result, if you have a custom datatypes_conf.xml configuration file, you should remove the compressed sniffers that used to be in the sample file but now are not. Otherwise you will encounter non-breaking errors in the logs.

  • We have removed the deprecated symlink static/scripts/packed -> . If you used it please change your (proxy) configuration. An example can be seen here.

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