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_converter...

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}&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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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_converter...

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}&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/

___________________________________________________________ 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/