Re: [galaxy-dev] Best way to allow users to configure a display application url for a toolshed tool
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_mainhttp://${galaxy_url.qp}:8500/init_local?file=${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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Re: [galaxy-dev] Best way to allow users to configure a display application url for a toolshed tool
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_mainhttp://${galaxy_url.qp}:8500/init_local?file=${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/
___
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/
Re: [galaxy-dev] Best way to allow users to configure a display application url for a toolshed tool
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_mainhttp://${galaxy_url.qp}:8500/init_local?file=${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/
___
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:
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Re: [galaxy-dev] Best way to allow users to configure a display application url for a toolshed tool
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_mainhttp://${galaxy_url.qp}:8500/init_local?file=${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/
___
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/
Re: [galaxy-dev] Best way to allow users to configure a display application url for a toolshed tool
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_mainhttp://${galaxy_url.qp}:8500/init_local?file=${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/
