Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

2015-12-07 Thread rbrown1422 
Good morning Bjorn,


The way I understand Galaxy is worksteps involve a tool using History inputs 
and creates History output files.   I view the results from the tool one 
click's on the eyeball to see the output file content.

In following this same flow, I was trying to have my datatype display my 
heatmap when the user clicks on the eyeball after creating the history output 
file from the HM creation tool.

Similar to how one can display an image file or csv by clicking on the eyeball.

Thanks again,
bob

- Original Message -From: rbrown1422@comcast.netTo: Bjrn 
Grning Sent: Sun, 06 Dec 2015 15:49:56 - 
(UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype 
to display a webpage if eyeball is clicked?

Good morning and thanks Bjorn,

One question  on your statement ...This does not work with the eyeball, but 
with the visualization buttonassociated to every dataset.  How is this invoked 
so the dataset is displayed if not by the eyeball?

Let me digest this info and hopefully I can take it from here.

cheers,
bob

- Original Message -From: Bjrn Grning 
To: rbrown1...@comcast.net, galaxy-dev 
Sent: Fri, 04 Dec 2015 18:14:51 - 
(UTC)Subject: Re: [galaxy-dev] How does one create a viewer for a new datatype 
to display a webpage if eyeball is clicked?

Hi Bob,

you could write a special visualisation for your specific datatype. Thisdoes 
not work with the eyeball, but with the visualisation buttonassociated to every 
dataset.

For a few visualisation examples please see the following links:

*https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations*
 https://github.com/bgruening/galaxytools/tree/master/visualisations* 
https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook

Hope this gets you started!Bjoern

> Good afternoon,> > I am trying create a display module for a special binary 
> datatype.> When someone requests to view the output file in the History 
> using> the eyeball it will kick off my code to create an HTML display in the> 
> Galaxy center section. I am looking at binary.py but I am not sure> if this 
> is it. Is there sample or existing code to look at?> > I hope this makes 
> sense to someone on the team.> > Thanks, bob> > > > 
> ___ 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] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

2015-12-07 Thread Björn Grüning 

Hi Bob,

> Good morning Bjorn,
> 
> 
> The way I understand Galaxy is worksteps involve a tool using History
> inputs and creates History output files.   I view the results from
> the tool one click's on the eyeball to see the output file content.
> 
> In following this same flow, I was trying to have my datatype display
> my heatmap when the user clicks on the eyeball after creating the
> history output file from the HM creation tool.

So the eyeall is trying to display the real data. If this is an image we
render the image, if it's a csv we try to visualise the tabular data.

If you want to visualise your data in a non-standard way, you can write
your own visualisations and append them to a specific datatype. For
example we added an interactive BAM visualisation.

Have a look at this video, to see a list of visualisations:

https://www.youtube.com/watch?v=jQDyTuYnn1k

Sorry, have not found a better example. IPython is not a real
visualisation but uses the same menue.

Cheers,
Bjoern

> Similar to how one can display an image file or csv by clicking on
> the eyeball.
> 
> Thanks again, bob
> 
> - Original Message -From: rbrown1422@comcast.netTo:
> Bjrn Grning Sent: Sun, 06 Dec
> 2015 15:49:56 - (UTC)Subject: Re: [galaxy-dev] How does one
> create a viewer for a new datatype to display a webpage if eyeball is
> clicked?
> 
> Good morning and thanks Bjorn,
> 
> One question  on your statement ...This does not work with the
> eyeball, but with the visualization buttonassociated to every
> dataset.  How is this invoked so the dataset is displayed if not by
> the eyeball?
> 
> Let me digest this info and hopefully I can take it from here.
> 
> cheers, bob
> 
> - Original Message -From: Bjrn Grning
> To: rbrown1...@comcast.net, galaxy-dev
> Sent: Fri, 04 Dec 2015 18:14:51
> - (UTC)Subject: Re: [galaxy-dev] How does one create a viewer for
> a new datatype to display a webpage if eyeball is clicked?
> 
> Hi Bob,
> 
> you could write a special visualisation for your specific datatype.
> Thisdoes not work with the eyeball, but with the visualisation
> buttonassociated to every dataset.
> 
> For a few visualisation examples please see the following links:
> 
> *https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/visualizations*
> https://github.com/bgruening/galaxytools/tree/master/visualisations*
> https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook
> 
> Hope this gets you started!Bjoern
> 
>> Good afternoon,> > I am trying create a display module for a
>> special binary datatype.> When someone requests to view the output
>> file in the History using> the eyeball it will kick off my code to
>> create an HTML display in the> Galaxy center section. I am looking
>> at binary.py but I am not sure> if this is it. Is there sample or
>> existing code to look at?> > I hope this makes sense to someone on
>> the team.> > Thanks, bob> > > >
>> ___ 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:
>> https://lists.galaxyproject.org/> > To search Galaxy mailing lists
>> use the unified search at: >
>> http://galaxyproject.org/search/mailinglists/>
> 
> 
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/