Hi Dan and Greg, 

Thanks for your answers on this.  So far I have managed to make things work 
following Dan's suggestion ... except that I can't seem to get my configuration 
data file to install into tool-data.  I'm not sure why this might be since all 
my XXX.loc.sample files install into tool-data fine.  I tried adding a file to 
my tool repository under tool-data/protk_site_config.txt.sample ... and had 
hoped it would result in a file being installed (when the tools are installed) 
into tool-data/protk_site_config.txt .. but unfortunately this doesn't happen.  
If I hack things and copy the file in place manually then Dan's instructions 
work (after modifying my display applications). 

Anyway, I'll investigate this a bit more tomorrow. Hopefully you can shed some 
light on why my .loc.sample files are copied fine, but my other file is not.  
Does galaxy only install tool-data files with the .loc.sample naming 
convention? Or is there some other internal filter/check that could be stopping 
my config file being installed.

Thanks
Ira





On 03/05/2012, at 8:35 PM, Greg Von Kuster wrote:

> 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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