This site does not seem to be working for getting patches.
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone:  617-627-5319
Fax: 617-627-3667

From: galaxy-dev 
 on behalf of Nate Coraor <<>>
Date: Thursday, December 15, 2016 at 3:13 PM
Cc: Galaxy Committers 
 Galaxy Dev List 
Subject: [galaxy-dev] Galaxy Security Vulnerability - Arbitrary code execution


A security vulnerability was recently discovered by David Wyde in two Galaxy 
tools that are provided with and enabled by default in the Galaxy server. These 
vulnerabilities allow malicious actors to execute arbitrary code as the user 
running the Galaxy server.

The vulnerable tools are "Filter GFF data by attribute" and "Filter GFF data by 
feature count", two tools which share code with each other and the more general 
"Filter data on any column using simple expressions" tool. The latter was fixed 
in a previous security disclosure but these GFF variants of the tool were 
missed when updating the Filter tool.

These tools use the Python `eval` and `exec` functions and do not properly 
sanitize input to these functions.

Additionally, an XSS vulnerability with the upload tool: An uploaded file's 
name was not properly sanitized, and so a specially crafted filename uploaded 
to the Galaxy server could be used as an XSS attack vector. This vulnerability 
has already been fixed in the 16.07 and 16.10 Galaxy releases.

The Galaxy Committers would like to thank David for disclosing these 
vulnerabilities. If you discover security vulnerabilities in Galaxy, please 
report them to the Galaxy Committers at<>.


These arbitrary code execution vulnerability is present in all known releases 
of Galaxy using the default tool config or a tool config in which these tools 
are loaded. To determine if your Galaxy server is affected, check your 
tool_conf.xml for the following lines:

    <tool file="filters/gff/gff_filter_by_attribute.xml" />
    <tool file="filters/gff/gff_filter_by_feature_count.xml" />

If you are unsure, you can also check to see if the tools have loaded by 
searching for them in your Galaxy server logs, e.g.:

  % grep gff_filter paster.log DEBUG 2016-12-08 13:25:16,930 Loaded tool id: 
gff_filter_by_attribute, version: 0.1 into tool panel.. DEBUG 2016-12-08 13:25:16,930 Loaded tool id: 
gff_filter_by_feature_count, version: 0.1 into tool panel..


This vulnerability can be exploited to execute arbitrary code as the user that 
runs Galaxy jobs on any system where Galaxy runs those jobs (potentially a 
cluster). Such code can be used to provide a remote shell to an attacker, or 
read/write/delete files that the Galaxy user has appropriate permissions on.


Multiple solutions exist for the arbitrary code execution vulnerability:

1. Update your Galaxy code. A fix for the issue has been applied to stable 
releases of Galaxy back to version 14.10.

2. Disable the affected tools.

3. Patch the affected tools. Patches to fix the vulnerabilities (depending on 
the version of Galaxy that you are running) can be found below.


1. To apply the fix, first identify your current Galaxy release version using 
the `git branch` command. If you are on a 'release_YY.MM' branch, you can 
update with:

  % git pull

The process above can also be used to update to the 16.10 release if you are on 
the 'master' git branch. If you are on the 'master' 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 fetch origin
  % git checkout -b release_YY.MM origin/release_YY.MM
  % git pull

2. To disable the tools, locate and remove the following lines from your 
tool_conf.xml, then restart Galaxy:

    <tool file="filters/gff/gff_filter_by_attribute.xml" />
    <tool file="filters/gff/gff_filter_by_feature_count.xml" />

3. To manually patch the tools, use the appropriate patch file below:

For Galaxy releases 16.01 to dev:

For Galaxy releases 15.07 to 15.10:

For Galaxy releases 14.10 to 15.05:

To apply the patch, navigate to the root of your Galaxy directory, then execute 
(replacing <patch_url> with the url above appropriate for your current Galaxy 

  % wget -O filter_security.patch <patch_url>


  % curl -o filter_security.patch <patch_url>

and then test applying the patch:

  % patch -p1 --dry-run < filter_security.patch
  checking file tools/filters/gff/
  checking file tools/filters/gff/gff_filter_by_attribute.xml
  checking file tools/filters/gff/
  checking file tools/filters/gff/gff_filter_by_feature_count.xml

If this succeeds without error (applying successfully with fuzz/offset is
fine), apply with:

  % patch -p1 < filter_security.patch
  patching file tools/filters/gff/
  patching file tools/filters/gff/gff_filter_by_attribute.xml
  patching file tools/filters/gff/
  patching file tools/filters/gff/gff_filter_by_feature_count.xml

In all cases, for the changes to take effect, *YOU MUST RESTART ALL GALAXY

On behalf of the Galaxy Committers,
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