Hi Xiangyu,

This question is best directed to the galaxy development list, which I've cc'd.

In general, to integrate a tool into Galaxy, you'll want to write a tool 
wrapper:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

and then upload it to the Galaxy toolshed:

http://wiki.g2.bx.psu.edu/Tool%20Shed

You can also upload workflows to the tool shed as well:

http://wiki.g2.bx.psu.edu/Tool%20Shed#Enabling_workflow_sharing:_importing_a_workflow_via_a_URL

Feel free to email the galaxy-dev list with any questions you may have.

Best,
J.


On Apr 23, 2012, at 3:51 PM, Deng, Xiangyu (CDC/OID/NCEZID) (CTR) wrote:

> Hi Jeremy,
>  
> My name is Xiangyu, working across street at the enteric disease laboratory 
> branch, CDC. I built a SNP calling pipeline and want to put it somewhere with 
> a friendly GUI so our/other wet lab persons can use it. I wonder if I can do 
> it on Galaxy.
>  
> The pipeline, written in python, uses bowtie 2, samtools, velvet, biopython 
> and a perl program.
>  
> Thanks,
> Xiangyu
>  
> ---
> Xiang-yu Deng, Ph.D.
>  
> ASM Fellow
> Enteric Diseases Laboratory Branch
> Division of Foodborne, Waterborne and Environmental Diseases 
> National Center for Emerging and Zoonotic Infectious Diseases
> Centers for Disease Control and Prevention
> MS-C03, 1600 Clifton Road, Atlanta, GA 30333
> Office: 404-639-1036
> de...@cdc.gov
>  

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