Re: [galaxy-dev] Ucsc bigbed display tool does not show up on local installation

[Jeremy Villalobos]

Thanks for your response.  I figured out it was some extra text at the end
of the xml file that was preventing galaxy from reading the file.

I also was confused about how to setup the proxy.  For Ubuntu, the apache2
configuration file is in /etc/apache2/sites-available/default (using
virtual servers by default)

I was initially working with /etc/apache2/httpd.conf which I think may be
the standard in other distros.



Jeremy


On Thu, Nov 3, 2011 at 7:23 PM, Jennifer Jackson  wrote:

> Hello Jeremy,
>
> Galaxy does not come with a display tool for UCSC. There is an integrated
> display tool, under Visualization, commonly called "Trackster". The icon
> for Trackster is a set of colored, stacked bars that when hovered over is
> labeled "Visualize in Trackster".
>
> If you do want to display at the public (or a local mirror) UCSC browser,
> then some additional set-up is required. Here are the links to the details,
> including a tutorial:
>
> http://wiki.g2.bx.psu.edu/**Admin/Config/Apache%20Proxy(scroll
>  to Display at UCSC)
>
> http://wiki.g2.bx.psu.edu/**Admin/Tools/External%**
> 20Display%20Applications%**20Tutorial
>
> http://wiki.g2.bx.psu.edu/**Admin 
>
> Hopefully this helps to get you started,
>
> Jen
> Galaxy team
>
>
> On 11/2/11 3:52 PM, Jeremy Villalobos wrote:
>
>> Hello:
>>
>> The display tool for UCSC that comes with the local installation package
>> does not work.  uploading a bigbed file (from the test-data that comes
>> with the package) does not trigger the webapp to show an option to view
>> the file using UCSC's viewer.
>>
>> How do I enable this ?
>>
>> To reproduce the issue, simply download galaxy using mercurial.  change
>> the host address to 0.0.0.0.  and load the bigbed file from the
>> test-data directory.
>> Once the file uploads, the user should expect to see a display tool
>> added to the files description (on the right), but nothing is shown.
>>
>> Thanks
>>
>> Jeremy
>> UNCC
>>
>>
>> __**_
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>>
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/**Support
>
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Re: [galaxy-dev] Ucsc bigbed display tool does not show up on local installation

[Jennifer Jackson]

Hello Jeremy,

Galaxy does not come with a display tool for UCSC. There is an 
integrated display tool, under Visualization, commonly called 
"Trackster". The icon for Trackster is a set of colored, stacked bars 
that when hovered over is labeled "Visualize in Trackster".


If you do want to display at the public (or a local mirror) UCSC 
browser, then some additional set-up is required. Here are the links to 
the details, including a tutorial:


http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy (scroll to Display 
at UCSC)


http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial

http://wiki.g2.bx.psu.edu/Admin

Hopefully this helps to get you started,

Jen
Galaxy team

On 11/2/11 3:52 PM, Jeremy Villalobos wrote:

Hello:

The display tool for UCSC that comes with the local installation package
does not work.  uploading a bigbed file (from the test-data that comes
with the package) does not trigger the webapp to show an option to view
the file using UCSC's viewer.

How do I enable this ?

To reproduce the issue, simply download galaxy using mercurial.  change
the host address to 0.0.0.0.  and load the bigbed file from the
test-data directory.
Once the file uploads, the user should expect to see a display tool
added to the files description (on the right), but nothing is shown.

Thanks

Jeremy
UNCC


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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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