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September 2017 Galaxy Release (v 17.09)

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Highlights

Singularity

Tool execution using the HPC-friendly container technology Singularity is now supported. Custom containers can be specified by the Galaxy admin on a per job destination basis or standardized containers corresponding to Conda requirements can be built or downloaded automatically using the mulled toolkit built into Galaxy (just like is possible for Docker). For more information checkout this presentation from the 2017 Galaxy Community Conference. Pull Request 4175

Download entire collection

Downloading whole colections is now possible from the history interface. Pull Request 4098 Thanks to @mvdbeek.

Switch tool versions in workflows

You can now select exactly what version of tool you want to use when building workflows. Pull Request 4373 Thanks to @mvdbeek.

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_17.09 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git checkout release_17.09 && git pull --ff-only origin release_17.09

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

Security

The 17.09 Galaxy version includes many security patches. Per our new Security Policy some of these have been applied to Galaxy releases going back 12 months.

Details of the vulnerabilities that have been backported can be found in the Security patch details section of these release notes. Some issues have only been addressed in 17.09, for this reason if security is important to your Galaxy instance we strongly recommend upgrading to this latest release as soon as possible.

If you maintain a publicly accessible Galaxy please consider signing up for this mailing list to receive the future security patches in advance of the public disclosure.

Deprecation Notices

  • The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In the next releases we will remove it completely. Related PRs:#4526 #4872 .

  • The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release.

  • Workflows API: When exposing WorkflowInvocationSteps state will no longer be available.

  • The refresh_on_change attribute of a <param> tag in the tool syntax can no longer be set to a value of another parameter. Use boolean instead (e.g. refresh_on_change="True"). Details

  • The endpoint /api/configuration/toolbox is now deprecated and will be removed in the future. All tools are now watched for changes and this feature became obsolete.

Release Notes

Enhancements

Fixes

Security patch details

Limited Galaxy Data Library unauthorized filesystem access

Tracked as GX-2017-0001

A medium severity security vulnerability in Galaxy Data Libraries was recently discovered by Jelle Scholtalbers. This vulnerability allows the following unauthorized actions:

  1. Any user that has been granted the permission to add datasets to a library, library folder, or to modify an existing library dataset (an “authorized user”), is able to import any file on the system that is readable by the user running the Galaxy server.

  2. Anyone can create libraries and library folders (but not add datasets to them)

The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this commit

Arbitrary code execution for Galaxy servers with Galaxy Interactive Environments enabled

Tracked as GX-2017-0002

A high severity security vulnerability was recently discovered in Galaxy Interactive Environments (GIEs) by the Galaxy Committers Team. Anyone with a Galaxy account can exploit this vulnerability to execute arbitrary code on the Galaxy server as the user running the Galaxy server process.

The vulnerability only affects Galaxy servers on which Galaxy Interactive Environments are enabled (by setting the interactive_environment_plugins_directory option in galaxy.ini). Because the vulnerability can be exploited to execute arbitrary code, the impact for affected servers is severe.

Administrators of Galaxy servers where GIEs are enabled should update immediately.

The fix for this issue has been applied to Galaxy releases back to 17.05 and can be found in this commit

Unauthorized filesystem access via data source tools

Tracked as GX-2017-0003

A medium severity security vulnerability in tools utilizing the Galaxy data source protocol was recently discovered by the Galaxy Committers Team. Anyone who is able to run an external data source tool can access any file that is readable by the user running Galaxy jobs on the host where the job runs.

Many such “external data source” tools are provided with the Galaxy distribution and are enabled by default (most tools under the “Get Data” section of the tool panel), meaning that its exploitability is fairly high, as only one such tool needs to be enabled to be vulnerable, including any custom data source tools (any tool that uses tools/data_source/data_source.py). What files are readable depends entirely upon what the job’s user has access to read on the host(s) where jobs run.

The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this commit

Cross site scripting and session fixation

Disclosed on the mailing list in August 2017.

Vulnerabilities were found by Helena Rasche and Manabu Ishii respectively. Detailed descriptions of these categories of vulnerabilities can be found at:

The fix for these issues has been applied to Galaxy releases back to 16.10 and can be found in this diff

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