Hi James,
galaxy.pdb is a dataset in galaxy , which is shown by this url ....
http://10.180.8.54:9098/display_application/1fad1eaf5f4f1766/jmol_pdb/jmol_main/5da8464cb811e1a6/data/galaxy.pdb.
i want to download this link in galaxy by using python or java . after
downloading,downloaded file contains only html tags ..not the actual content .
it wont's display the actual contents.
Regards
shashi
________________________________
From: James Taylor <ja...@taylorlab.org>
To: shashi shekhar <me_shash...@yahoo.co.in>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Sent: Thursday, 20 June 2013 8:57 PM
Subject: Re: [galaxy-dev] visulaization tool
Display applications are extensively documented here:
http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Jun 20, 2013 at 2:20 AM, shashi shekhar <me_shash...@yahoo.co.in> wrote:
> 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..
>
> 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 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.
>
> Regards
> shashi
>
> ________________________________
> 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
>
>
>
>
>
> ___________________________________________________________
> 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/
>
> 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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
