Hi Ira,

You'll want to set this up as a dynamic display application, where the link id, name, url, port, etc are defined in an external tab-delimited file. Most of the displays included in the dist are set up this way, one example would be the display_applications/ucsc/bam.xml. 

For an example where the external display application needs to access Galaxy's datasets directly on a shared filesystem have a look at display_applications/genetrack.xml.

Thanks for using Galaxy,

Dan

On May 2, 2012, at 10:58 PM, Ira Cooke wrote:

Dear All,

Our toolshed tools include a custom display application.  Although the display application is open source ( https://bitbucket.org/Andrew_Brock/proteomics-visualise ) we do not yet have a public server for it.  Actually, at present it isn't possible to have the application work properly if it is running on a completely separate server because it needs access to galaxy's database/files directory (I'll leave that for another question).  For now I just need to be able to provide a way for administrators of a local galaxy to configure the url to this display application. 

At the moment we have it hard coded .. like this;

 <url target_frame="galaxy_main">http://${galaxy_url.qp}:8500/init_local?file=${encoded_filename.qp}&amp;type=mzml</url>

Using the galaxy_url (because we are on the same server) .. and hard coding the port.

What would be the best way to allow local admins to configure this? 

Thanks

Ira

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