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...

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 dengx@cdc.gov