Hi Greg, 

Thanks ... that's great.  It's all working now.

Ira

On 04/05/2012, at 3:41 AM, Greg Von Kuster wrote:

> Hi Ira,
> 
> Sample fiel handling for installed tool shed repositories was restricted to 
> .loc.sample files as you discovered.  I've enhanced this feature to copy all 
> appropriate .sample files contained in the installed repository to the 
> tool-data directory of the Galaxy instance to which the repository was 
> installed.   This enhancement is available in change set 7145:ea9f3c25a415 in 
> our central repository.  Thanks for reporting this problem!
> 
> Greg Von Kuster
> 
> On May 3, 2012, at 6:49 AM, Ira Cooke wrote:
> 
>> 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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>> 
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