Hi james,


49: 1.bigwig
20.7 KB
format: bigwig, database: ?
uploaded bigwig file
display in IGB Local Web 


 I have uploaded 1.bigwig  file  in this https://main.g2.bx.psu.edu/ galaxy . 
but when i clicked Web  option . it creates a ".jnlp" file . I am not able to 
see anything on web .  how the local option works in this case ?

regards
shashi

________________________________
 From: shashi shekhar <me_shash...@yahoo.co.in>
To: James Taylor <ja...@taylorlab.org> 
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> 
Sent: Thursday, 20 June 2013 11:50 AM
Subject: Re: [galaxy-dev] visulaization tool
 


Hi james,

can you  share some examples of display application . and in which tool you use 
for display application in galaxy ?


Regards
shashi


________________________________
 From: James Taylor <ja...@taylorlab.org>
To: shashi shekhar <me_shash...@yahoo.co.in> 
Cc: Ross <ross.laza...@gmail.com>; "galaxy-dev@lists.bx.psu.edu" 
<galaxy-dev@lists.bx.psu.edu> 
Sent: Wednesday, 19 June 2013 7:03 PM
Subject: Re: [galaxy-dev] visulaization tool
 


Tightly integrated interactive visualizations like Trackster need to be web 
based (implemented in Javascript). See our paper that just came out in BMC 
genomics. Note there is already a phylogenetic tree visualization tool 
(phyloviz) that was built by Tomithy Too. Extensions to that for additional 
features would be welcome.

For a Java based visualization tool you need to take a completely different 
approach. Look at Display Applications support, specifically examples like IGB 
and IGV.

On Jun 19, 2013, at 7:56 AM, shashi shekhar <me_shash...@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.laza...@gmail.com>
>To: shashi shekhar <me_shash...@yahoo.co.in> 
>Cc: Hans-Rudolf Hotz <h...@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_shash...@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.laza...@gmail.com>
>>To: shashi shekhar <me_shash...@yahoo.co.in> 
>>Cc: Hans-Rudolf Hotz <h...@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_shash...@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 <h...@fmi.ch>
>>>To: shashi shekhar <me_shash...@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
>>>
>
>
>
>
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