A security vulnerability was recently discovered by John Chilton with Galaxy's "Filter data on any column using simple expressions" and "Filter on ambiguities in polymorphism datasets" tools that can allow for arbitrary execution of code on the command line.
The fix for these tools has been committed to the Galaxy source. The timing of this commit coincides with the next Galaxy stable release (which has also been pushed out today).
To apply the fix and simultaneously update to the new Galaxy stable release, ensure you are on the stable branch and upgrade to the latest changeset:
% hg branch
% hg pull -u
For Galaxy installations that administrators are not yet ready to upgrade to the latest release, there are three workarounds.
First, for Galaxy installations running on a relatively new version of the stable release (e.g. release_2013.08.12), Galaxy can be updated to the specific changeset that that contains the fix. This will include all of the stable (non-feature) commits that have been accumulated since the 8/12 release plus any new features included with (and prior to) the 8/12 release, but without all of the new features included in the 11/4 release. Ensure you are on the stable branch and then upgrade to the specific changeset:
% hg pull -u -r e094c73fed4d
Second, the patch can be downloaded and applied manually:
% wget -o security.patch https://bitbucket.org/galaxy/galaxy-central/commits/e094c73fed4dc66b58993...
% hg patch security.patch
% patch -p1 < security.patch
Third, the tools can be completely disabled by removing them from the tool configuration file (by default, tool_conf.xml) and restarting all Galaxy server processes. The relevant lines in tool_conf.xml are:
<tool file="stats/dna_filtering.xml" />
<tool file="stats/filtering.xml" />
The full 11/4 Galaxy Distribution News Brief will be available later today and will contain details of changes since the last release.