December 2016 - galaxy-announce - lists.galaxyproject.org

Announcing the October 2016 (v16.10) Galaxy Release
by Nate Coraor 15 Dec '16

15 Dec '16

The Galaxy Committers team <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> is pleased to announce the *October 2016 (v16.10) release of Galaxy <https://docs.galaxyproject.org/en/master/releases/16.10_announce.html>*. Security <https://docs.galaxyproject.org/en/master/releases/16.10_announce.html#secur…> An arbitrary code execution vulnerability in two tools and an XSS vulnerability with the upload tool were identified this release cycle and have been fixed concurrently with the release. In addition, the fixes have been backported to older releases. The Galaxy Committers would like to thank David Wyde for disclosing these vulnerabilities. Details follow: 1. The vulnerable tools are “Filter GFF data by attribute” and “Filter GFF data by feature count”, both of which are provided with and enabled by default in the Galaxy server. These two tools 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. The fix for this issue has been applied to Galaxy releases back to v14.10 and can be found in Commit c1e3087 2. 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. The fix for this issue has been applied to Galaxy releases back to v16.07 and can be found in Pull Request 3278. Highlighted Enhancements <https://docs.galaxyproject.org/en/master/releases/16.10_announce.html#highl…> - Overhaul of charts visualization - more visualizations, more options, and better user interface. - Paginate contents of large histories. - Implement a collection operation tool for merging collections (thanks to @Takadonet). - Replace reference documentation for tool XML files with automatically generated documentation from a now official Galaxy XSD documentation (with help from many). - Add a password strength evaluation bar (thanks to @benfulton). - Implement a GoDocker job runner (thanks to @varunshankar). - Support for API batch requests. - Allow JSONP to be returned from API endpoints. - Add “Save as” as an option in the workflow editor (thanks to @tmcgowan). - Allow naming input datasets and collections during workflow extraction. - Various enhancements for API driven installation of tool shed repositories. Get Galaxy <http://getgalaxy.org/> The code lives at Github <https://github.com/galaxyproject/galaxy> and you should have Git <https://git-scm.com/> to obtain it. *To get a new Galaxy repository run:* $ git clone -b release_16.10 https://github.com/galaxyproject/galaxy.git *To update an existing Galaxy repository run:* $ git checkout release_16.10 && git pull --ff-only origin release_16.10 Release Notes <https://docs.galaxyproject.org/en/master/releases/16.10_announce.html> For full details on all of the enhancements and fixes in this release, please see the full release notes <https://docs.galaxyproject.org/en/master/releases/16.10_announce.html>. On behalf of the Galaxy Committers <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> , *Thanks for using Galaxy!* --nate

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Galaxy Security Vulnerability - Arbitrary code execution
by Nate Coraor 15 Dec '16

15 Dec '16

*DESCRIPTION* 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 galaxy-committers(a)lists.galaxyproject.org. *AFFECTED VERSIONS* 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 galaxy.tools.toolbox.base DEBUG 2016-12-08 13:25:16,930 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-12-08 13:25:16,930 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel.. *IMPACT* 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. *SOLUTION* 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. *INSTRUCTIONS* 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/version.py' 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: https://depot.galaxyproject.org/patch/filter_security_16_01.patch For Galaxy releases 15.07 to 15.10: https://depot.galaxyproject.org/patch/filter_security_15_07.patch For Galaxy releases 14.10 to 15.05: https://depot.galaxyproject.org/patch/filter_security_14_10.patch 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 release): % wget -O filter_security.patch <patch_url> or: % 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/gff_filter_by_attribute.py checking file tools/filters/gff/gff_filter_by_attribute.xml checking file tools/filters/gff/gff_filter_by_feature_count.py 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/gff_filter_by_attribute.py patching file tools/filters/gff/gff_filter_by_attribute.xml patching file tools/filters/gff/gff_filter_by_feature_count.py 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 SERVER PROCESSES*. On behalf of the Galaxy Committers, --nate

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December Galaxy News: New web site, GAMe deadline extended
by Dave Clements 06 Dec '16

06 Dec '16

Hello all, The *December Galaxy News <https://new.galaxyproject.org/GalaxyUpdates/2016_12/>* is hot off the press, *and is was produced on a a hot new press. *Highlights this month include: - The *Galaxy Community Hub (the Hub) <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#galaxy-community-hub-t…>* will be the new home for Galaxy Community documentation, replacing the current wiki. - And we are asking for help to get it ready for it's official launch <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#the-community-hub-cont…> - *Galaxy Australasia Meeting (GAMe 2017) <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#galaxy-australasia-mee…>*: February 3-9, Melbourne, Victoria, Australia. - *Talk abstract submission extended to 14 December.* - *Early registration ends 31 December.* - And of course, other upcoming events <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#all-upcoming-events> too There are also 60 new publications (including eight featured pubs), four open positions, two new public Galaxy servers, new releases of Planemo & Pulsar, and other news too. Dave Clements and the Galaxy Team -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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