Galaxy/Tool Shed Security Vulnerability - Read/write arbitrary filesystem paths

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Galaxy/Tool Shed Security Vulnerability - Read/write arbitrary filesystem paths

Nate Coraor (

Multiple security vulnerabilities were recently 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.

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.


These issues affect all known releases of the Tool Shed and Galaxy in at least the last 3 years.


This vulnerability can be exploited to read any file available on the system that is readable by the user running the Tool Shed or Galaxy server, including Galaxy/Tool Shed config files, data, system config files, contents of /proc, etc. As such, Tool Shed administrators are strongly encouraged to update immediately. For Galaxy administrators, the impact is not as great, unless Galaxy administrators do not have access to the Galaxy server command line.


Fixes for these vulnerabilities have been applied to the 15.01 and newer (14.10 in the case of the portion of the vulnerability affecting Galaxy) release branches in the public GitHub and Bitbucket repositories. Tool Shed versions older than 15.01 should upgrade (preferably to 16.01). To apply the fix, first identify your current Galaxy release version using the `git branch` or `hg branch` commands. If you are on a 'release_YY.MM' branch, you can update with:

  % git pull


  % hg pull -u

The process above can also be used to update to the 16.01 release if you are on the 'master' git branch or the 'stable' hg branch. If you are on the 'master'/'stable' branch and wish to remain on your current Galaxy major release, check the 'lib/galaxy/' file to determine your major release version, then update to the appropriate branch:

  % git checkout -b release_YY.MM origin/release_YY.MM
  % git pull


  % hg pull
  % hg update release_YY.MM


On behalf of the Galaxy Committers,

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