Multiple security vulnerabilities were recently 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
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
The Galaxy Committers would like to thank Youri Hoogstrate at the Erasmus
MC, Rotterdam, who initially reported a similar vulnerability in the Tool
Shed. Through additional auditing based on this attack vector, we
discovered the other vulnerabilities.
This issue affects all known releases of Galaxy in at least the last 3
The read and write vulnerabilities can be exploited to write to any path on
the Galaxy server writable by the Galaxy user, which can be potentially
destructive to Galaxy configuration files and data.
Additionally, they can be used to read any file available on the system
that is readable by the user running the Galaxy server, including Galaxy
config files, data, system config files, contents of /proc, etc.
As such, Galaxy administrators are strongly encouraged to update
The arbitrary code execution vulnerability can be exploited to execute any
shell command as the Galaxy user, which is also very dangerous. If your
Galaxy instance has had an external service configured at any point in the
past, you are strongly encouraged to update immediately.
Fixes for these vulnerabilities have been applied to the 14.10 and newer
release branches in the public GitHub and Bitbucket repositories. Galaxy
versions older than 14.10 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
'master'/'stable' branch and wish to remain on your current Galaxy major
release, check the 'lib/galaxy/version.py' 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
For the changes to take effect, *YOU MUST RESTART ALL GALAXY SERVER
On behalf of the Galaxy Committers,