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January 2016 Galaxy Release (v 16.01)

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Highlights

Interactive Tours

The interactive tours framework allows developers and deployers to build interactive tutorials for users superimposed on the actual Galaxy web front end. Unlike video tutorials, these will not become stale and are truly interactive (allowing users to actually navigate and interact with Galaxy). Galaxy 16.01 ships with two example tours and new ones can easily be added by creating a small YAML file describing the tour. Try the Galaxy UI tour on Main.

Wheels

Galaxy’s Python dependencies have traditionally been distributed as eggs using custom dependency management code to enable Galaxy to distribute binary dependencies (enabling quick downloads and minimal system requirements). With this release all of that infrastructure has been replaced with a modern Python infrastructure based on pip and wheels. Work done as part of this to enable binary dependencies on Linux has been included with the recently released pip 8.

Detailed documentation on these changes and their impact under a variety of Galaxy deployment scenarios can be found in the Framework Dependencies section of the Admin documentation.

Nested Workflows

Workflows may now run other workflows as a single abstract step in the parent workflow. This allows for reusing or subworkflows in your analyses.

Github

New
% git clone -b master https://github.com/galaxyproject/galaxy.git
Update to latest stable release
% git checkout master && pull --ff-only origin master
Update to exact version
% git checkout v16.01

BitBucket

Upgrade
% hg pull
% hg update latest_16.01

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

Deprecation Notices

Barring a strong outcry from deployers, 16.01 will be the last release of Galaxy to support Python 2.6. For more information, see Galaxy Github Issue #1596.

Security

Multiple security vulnerabilities were identified during this release cycle and fixed concurrently with the release. In addition, the fixes have been backported to older releases.

The Galaxy Committers would like to thank Youri Hoogstrate at the Erasmus MC, Rotterdam, who initially reported the hg push vulnerability. Through additional auditing based on this attack vector, we discovered the other vulnerabilities.

Galaxy

Multiple security vulnerabilities were discovered in Galaxy that allow malicious actors to read and write files on the Galaxy server. Additionally, Galaxy servers on which a rarely used feature has been enabled are vulnerable to an arbitrary code execution exploit.

  1. A write vulnerability exists in the history import mechanism. It is possible to create a history tar archive that contains files with parent directory components in the file path (e.g. foo/../../bar would extract to ../bar), and these archive members would be written if the user running the Galaxy server had write permission to the given path.

  2. A read vulnerability exists in the object store path composition code. Galaxy allows clients to add elements to the end of a path to “extra” files associated with a dataset (as is the case with composite datatypes). These elements were not being checked to ensure they did not contain relative parent references (..) or did not start with an absolute path character (/). Because of this, the dataset display methods could be manipulated to return the contents of any files for which the Galaxy server user had read permission.

  3. An arbitrary code execution vulnerability exists in the Galaxy sample tracking system. The sample tracking system included a feature which allowed administrators to browse remote “external services” (such as sequencers) to choose files to transfer to the Galaxy server. This browsing code used a shell invocation which did not sanitize user input. However, this code is only reachable if at least one external service has ever been defined.

Fixes for all three issues have been applied to Galaxy releases back to v14.10.

Tool Shed

Multiple security vulnerabilities were discovered in the Tool Shed that allow malicious actors to read and write files on the Tool Shed server outside of normal Tool Shed repository directories.

  1. A write vulnerability exists in the Tool Shed tarball and capsule upload functionality. It is possible to create a tar archive that contains files with parent directory components in the file path (e.g. foo/../../bar would extract to ../bar), and these archive members would be written if the user running the Tool Shed had write permission to the given path. The Tool Shed tarball handling code checked for invalid characters (/ or ..) at the beginning of the path but not for .. in the middle of a path.

  2. A read vulnerability exists in multiple places. The first is in the (now deprecated) hg push functionality for updating Tool Shed repositories. This method allows malicious actors to push symlinks whose targets are outside the repository (either via an absolute or relative path). The contents of the targets would then be visible in the Tool Shed repository contents viewer, if the Tool Shed user has read permission on the target.

  3. A second read vulnerability exists in the Tool Shed repository contents viewer. The viewer would allow a malicious actor to specify a path outside the repository, and if the Tool Shed system user had read permissions on that path, it would be displayed. The viewer also did not check to ensure that the targets of symlinks in a repository did not point outside the repository.

The repository contents viewer read vulnerability also exists in Galaxy, but is only reachable/exploitable by admin users. Fixes for vulnerability #3 have been applied to Galaxy/Tool Shed releases back to v14.10, and issues #1 and #2 have been applied to releases back to v15.01.

Release Notes

Enhancements

Security

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