So tool_conf.xml only contains references to the other tool wrapper files. Those tools are either be in the distribution (which you can find in your galaxy-central/tools directory) or in the toolshed, at toolshed.g2.bx.psu.edu. -Dannon On Tue, May 28, 2013 at 1:32 PM, vijayalakshmi <vijiraghs@gmail.com> wrote:

I am trying to integrate the following tools in galaxy but I am not able to find their corresponding code in the "tool_conf.xml" file. If you can point me to those, it'd we swell.

1) NGS: Variant detection 2) NGS: Picard(beta) 3) BEDTools 4) SnpEff

Thanks, VJ.

On Tue, May 28, 2013 at 12:42 PM, Dannon Baker <dannon.baker@gmail.com>wrote:

...

I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration as a reference. Some of these components are installed via the tool shed, and others may have been manually added to main and are not included in the base tool_conf.xml.sample. I may be able to point you in the right direction, though -- what is it that you're trying to do?

-Dannon

On Tue, May 21, 2013 at 3:31 PM, vijayalakshmi <vijiraghs@gmail.com>wrote:

...

Hi all,

I am trying to get the *"tool_conf.xml"* <section> code corresponding to the following topics listed below. I am unable to find it in both the default build and the stable build in bitbucket. If you can point me to where I can find it, it'd be swell.

1) NGS: Variant detection 2) NGS: Picard(beta) 3) BEDTools 4) SnpEff

Thanks, VJ.

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