October 2016 Galaxy Release (v 16.10)

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Highlights

Galaxu UI plugins - Webhooks
We introduce Galaxy Webhooks - optional plugins for the web UI that allow for better customization of your instance. See the documentation. Includes work from @bgruening, @anatskiy, and Joachim Wolff @joachimwolff. Implemented in Pull Request 3040.
Workflow run form replaced
The workflow run form has been replaced by one backed by the new tool form and the API. Nicer, faster, standardized. Implemented in Pull Request 2669, Pull Request 2720, Pull Request 2766, Pull Request 2776, Pull Request 2770, Pull Request 2895, Pull Request 2935, Pull Request 3007, Pull Request 2969, Pull Request 2799, Pull Request 3082, Pull Request 2672, Pull Request 2920, Pull Request 2777, Pull Request 2902.
Automatic tool reload after installation
Galaxy does not need to be restarted after tool installation anymore. This provides a smoother experience for the users. Yay! Thanks to @mvdbeek. Implemented in Pull Request 2840, Pull Request 3025.

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_16.10 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git checkout release_16.10 && git pull --ff-only origin release_16.10

See our wiki for additional details regarding the source code location.

Deprecation Notices

  • API-like endpoints (returning JSON) that start with <galaxy>/root/ in the URL are now deprecated and will be removed in future releases. Please use proper API (e.g. /api/histories or /api/tools) to replace your implementations.
  • The jsonp parameter for search API endpoints in Tool Shed is deprecated and will be removed in the future. Instead the presence of a callback argument will trigger the JSONP format to be returned.

Security

An arbitrary code execution vulnerability in two tools and an XSS vulnerability with the upload tool were identified this release cycle and have been fixed concurrently with the release. In addition, the fixes have been backported to older releases.

The Galaxy Committers would like to thank David Wyde for disclosing these vulnerabilities. Details follow:

  1. The vulnerable tools are “Filter GFF data by attribute” and “Filter GFF data by feature count”, both of which are provided with and enabled by default in the Galaxy server. These two tools share code with each other and the more general “Filter data on any column using simple expressions” tool. The latter was fixed in a previous security disclosure but these GFF variants of the tool were missed when updating the Filter tool. These tools use the Python eval and exec functions and do not properly sanitize input to these functions. The fix for this issue has been applied to Galaxy releases back to v14.10 and can be found in Commit c1e3087
  2. An uploaded file’s name was not properly sanitized, and so a specially crafted filename uploaded to the Galaxy server could be used as an XSS attack vector. The fix for this issue has been applied to Galaxy releases back to v16.07 and can be found in Pull Request 3278.

Release Notes

Highlighted Enhancements

Security

  • Fix an ACE vulnerability with gff filter tools (thanks to David Wyde). Commit c1e3087
  • Escape filename in upload dialog, default and composite (thanks to David Wyde). Pull Request 3278

Enhancements

Fixes

To stay up to date with Galaxy’s progress watch our screencasts, visit our community hub, and follow @galaxyproject on Twitter.

You can always reach us on Gitter or IRC.

Thanks for using Galaxy!

The Galaxy Team