Hi Clint, Xiaofei,

There are no current plans to include additional genomes to the SnpEff tool on the public Main Galaxy instance at http://usegalaxy.org.


The best solution is to either run a local Galaxy (with sufficient resources) or what is probably easier and more practical for many scientific end users, a cloud Galaxy or possibly a Slipstream Appliance. The tool wrapper is in the Tool Shed, so it can be installed and used within your Galaxy, where you can add in any genome that you want that has the appropriate reference data available.

Help to get started is in these links:
https://wiki.galaxyproject.org/BigPicture/Choices
https://wiki.galaxyproject.org/Tool%20Shed

Hopefully one of these solutions will work out for both of you!

Jen
Galaxy team

On 2/17/14 8:20 AM, Wang, Xiaofei wrote:
I have the same question. But, I want to use it on Drosophila and use SnpEff 
for CloudMap pipeline.
________________________________________
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of Clint Christensen [cli...@txbiomedgenetics.org]
Sent: Monday, February 17, 2014 10:01 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Reference Genome in snpEff Tool

Howdy!

I only see the "Caenorhabditis elegans: WS220.64" reference genome listed in the 
"Genome" drop down menu in the snpEff tool.  If possible, I would like to use the latest 
human genome hg19.  Can it be added as an option?  Thanks in advance.

Not: I did follow the link to the developer's site, but would prefer to use the 
tool from within Galaxy.

Clint Christensen
Research Assistant, Department of Genetics
Texas Biomedical Research Institute
7620 NW Loop 410
San Antonio, TX  78245
210-258-9779
cli...@txbiomedgenetics.org



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http://galaxyproject.org

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