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 <vijira...@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.ba...@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 <vijira...@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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>>
>
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