September 2018 Galaxy Release (v 18.09)

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Highlights

Extensive Workflow Enhancements

Workflows got a lot of love this time around, with new runtime parameters for subworkflows, exposed workflow versions, and zoom capability in the editor, to name a few. There were also a number of usability enhancements including better labeling, links, overhauled workflow import interfaces, and many more.

Pull Request 6664, Pull Request 6683, Pull Request 6142, Pull Request 6240, Pull Request 6290, Pull Request 6428, Pull Request 6441, Pull Request 6580, Pull Request 6596, Pull Request 6678, Pull Request 6076, Pull Request 6274, Pull Request 6570, Pull Request 6680, Pull Request 6774

Group Tags

Galaxy now contains powerful new features for multiple factor analysis of collections of datasets. The concept of group tags has been added to Galaxy. These are a special class of tags that describe key-value pairs that can be attached to the contents of a collection during upload or using collection operation tools. These tags can describe multiple sets of variables for the contents of a collection. Once set, these tags can be consumed intelligently by tools that need to divide collections into multiple overlapping factors or sets of datasets. A special thanks to @mvdbeek for devising and implementing this approach.

Pull Request 5457, Pull Request 6491, Pull Request 6661, Pull Request 6750, Pull Request 6499, Pull Request 6500, Pull Request 6572, Pull Request 6545

Python 3 Beta Support

After almost 3 years of work and more than 100 pull requests, we are proud to announce the Beta-stage support for running Galaxy under Python 3. Lint, unit, API, framework, integration and Selenium tests all pass, time for you to give it a try and report any bug you find!

Tracking issue

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_18.09 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_18.09 && git pull --ff-only origin release_18.09

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

Upgrade Warning for Admins

This release includes changes to the way that non-terminal jobs are handled that greatly improve performance and the user experience. As a result, when upgrading a Galaxy server with a large number of jobs in the new state, job handlers will block on first startup (jobs will not run) as these old new state jobs are migrated to a terminal state. This process will generate messages of the format:

galaxy.jobs DEBUG 2018-10-18 22:40:36,900 Pausing Job '995223', Execution of this dataset's job is paused because its input datasets are in an error state.

Once migration is complete, job handlers will resume normal operation.

For more details, see Pull Request 6036 and Issue 5944.

Security

Unauthorized File System Operations via New Upload API

Tracked as GX-2018-0006. Servers running Galaxy 18.05 should be updated as soon as possible. See the public announcement for full details.

Tool Vulnerabilities Discovered

Older versions of certain repositories in the Tool Shed were identified as vulnerable. All of these are owned and maintained by the iuc. The repository list follows:

  • gemini_query

  • gemini_stats

  • gemini_gene_wise

  • iqtree

  • shovill

  • fastq_dump

  • sam_dump

  • sra_pileup

If you have any of these repositories installed in your Galaxy, please update them to the latest revision immediately and disable/uninstall all older versions.

Galaxy Client Artifacts

New for 18.09, we no longer include pre-compiled JavaScript and other client-related artifacts in the GitHub repository. Instead, Galaxy now includes in its dependencies all the components necessary to build on startup when it detects changes in the client code. This will make it easier to integrate customizations to your local client, among other benefits moving forward with our continued client modernization.

This client building code executes automatically via the ‘common_startup.sh’ script, but if you run Galaxy in a way that doesn’t utilize that script, you should run it manually on deployment as documented in the General Update Procedures.

Deprecation Notice

With 19.01, all Galaxy users will be forced to have a username. This requirement has been enforced on user creation for years, though we have never taken steps to coerce users created in the past who did not have one. The 19.01 release will come with a migration script that will coerce this in the database, which will allow us to have consistent handling of this field.

Release Notes

Enhancements

Fixes

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