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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/