Hi Ira,

You'll need to include an entry for the display application in a 
datatype_conf.xml file in the tool shed repository- this will result in the 
display application being properly installed with the repository and made 
functional in the local Galaxy instance.  For details about this, see the 
following section of the tool shed wiki.

http://wiki.g2.bx.psu.edu/Tool%20Shed#Tool_Shed.Including_datatype_converters_and_display_applications

Let me know if you have any questions on this.
Thanks!

On May 2, 2012, at 11:19 PM, Daniel Blankenberg wrote:

> 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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