Hi Ross i got the file registry.py in lib/galaxy/visualization directory .. here four built in visualization is mentioned ..in the same way i want to add one more VISUALIZATION in galaxy ...this is my question . i wanted tom know that from which files i should start . class VisualizationsRegistry( object ): """ Main responsibilities are: - testing if an object has a visualization that can be applied to it - generating a link to controllers.visualization.render with the appropriate params - validating and parsing params into resources (based on a context) used in the visualization template """ # these should be handled somewhat differently - and be passed onto their resp. methods in ctrl.visualization #TODO: change/remove if/when they can be updated to use this system BUILT_IN_VISUALIZATIONS = [ ] # where to search for visualiztion templates (relative to templates/webapps/galaxy) # this can be overridden individually in the config entries Regards shashi ________________________________ From: Ross <ross.lazarus@gmail.com> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Sent: Wednesday, 19 June 2013 5:32 PM Subject: Re: [galaxy-dev] visulaization tool Shashi, Beats me. Cloning the visualisation code would be a good start I'd guess. It will not be trivial. Others may have better ideas. On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar <me_shashi29@yahoo.co.in> wrote: Hi Ross,
Actually i have to add the visualization which will be interactive . it will take dataset from galaxy .it will be in the same way as tracker works . in stead of tracker i want to add my own visualization tool. from wehere should i start to replace tracker with my own visulization tool. Regards shashi
________________________________ From: Ross <ross.lazarus@gmail.com> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: Hans-Rudolf Hotz <hrh@fmi.ch>; "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Sent: Wednesday, 19 June 2013 5:02 PM
Subject: Re: [galaxy-dev] visulaization tool
Shashi, Thanks for the additional information. AFAIK: If it's command line driven and spews out pdf's, adapt any similar tool that spews out pdfs like fastqc. Galaxy tool execution is isolated from the user and from Galaxy itself, so communication is just not possible if it's interactive - unless you hack the tool into Galaxy itself or something. There is no documentation for that.
On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar <me_shashi29@yahoo.co.in> wrote:
Hi Ross,
thanks for the reply . actually i want to use TreeView as visulaization tool.
TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It allows one to order the branches of the trees, and to export the trees in SVG format.
i have to add treeviewx in galaxy..
Regardsshashi
________________________________ From: Ross <ross.lazarus@gmail.com> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: Hans-Rudolf Hotz <hrh@fmi.ch>; "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Sent: Wednesday, 19 June 2013 3:28 PM
Subject: Re: [galaxy-dev] visulaization tool
Shashi, Hans made a brave guess based on your vague question, but you'll probably get better answers if you do us all a favour and make an effort to provide unambiguous detail about exactly what you want to achieve.
If there is a working Galaxy tool that does what you need but using a different "visualisation program" (whatever you mean by that vague term), substituting your executable will probably be relatively trivial. eg do you consider the Html object produced by the fastqc or the image from the scatterplot tool to be "visualisation program" outputs? If so, clone a working tool.
On Wed, Jun 19, 2013 at 5:37 PM, shashi shekhar <me_shashi29@yahoo.co.in> wrote:
Hi,
I want to add the the complete separate tool in galaxy . how will i do it ..i don't want to use existing visulaization tool.
Regardsshashi
________________________________ From: Hans-Rudolf Hotz <hrh@fmi.ch> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Sent: Wednesday, 19 June 2013 12:29 PM Subject: Re: [galaxy-dev] visulaization tool
Hi Shashi
Have a look at:
http://wiki.galaxyproject.org/Learn/Visualization http://wiki.galaxyproject.org/Visualization%20Setup
Regards, Hans-Rudolf
On 06/19/2013 08:07 AM, shashi shekhar wrote:
Hi,
i want to add new visualization tool in galaxy . can i get the required documents ?
can u send me the details how can i add the visualization tool in galaxy .
Regards shashi