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
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/
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 <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
___________________________________________________________ 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/
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.
Regards shashi
------------------------------ *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
___________________________________________________________ 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/
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.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
___________________________________________________________
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/
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..
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 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.
Regards shashi
------------------------------ *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
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
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..
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 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.
Regards shashi
------------------------------ *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
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
Hi Ross, i am using display application as visualization in galaxy. display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC"> <link id="main" name="main"> <url>http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp}</url> <param type="data" name="bed_file" url="galaxy.bed" format="bedstrict"/> <!-- Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, UCSC does not: force use of converter which will make strict BED6+ file --> <param type="template" name="position" strip="True" > what is the meaninng <param type="template" name="position" strip="True" /> and what is the use of url="galaxy.bed" ? 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
Hello, Shashi It looks like TreeViewX was written in C++ as a desktop program. In this case, there is no way that it can be used with the display_application code without major modification. One option is to not use TreeViewX from within Galaxy but simply have it installed on your users' computers and have them load their Galaxy data into it after downloading to their local machines. Other options may include other phylogenetic tree viewers and formatters. There are many excellent programs and libraries available: FigTree http://tree.bio.ed.ac.uk/software/figtree/ Archaeopteryx https://sites.google.com/site/cmzmasek/home/software/archaeopteryx and jsPhyloSVG (javascript) http://www.jsphylosvg.com/ If you need to produce phylogenetic trees within Galaxy, the phyloviz visualization is the best place for you to start. In order to modify it to get the features you'd need from it, however, you'll need to have some experience with programming in JavaScript, python, and a web development environment. There are many resources on the internet to help you. We'd like to add to add functionality to phyloviz at some point (such as saving to SVG, re-formatting the trees, etc.) so, if you're not able, we will be working on it. However, those improvements may not be done anytime soon. On Thu, Jun 20, 2013 at 7:36 AM, shashi shekhar <me_shashi29@yahoo.co.in>wrote:
Hi Ross,
i am using display application as visualization in galaxy.
display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC">
<link id="main" name="main"> <url>http://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}&position=${position.qp}&hgt.customText=${bed_file.qp} <http://genome.ucsc.edu/cgi-bin/hgTracks?db=$%7Bqp($bed_file.dbkey)%7D&position=$%7Bposition.qp%7D&hgt.customText=$%7Bbed_file.qp%7D></url> <param type="data" name="bed_file" url="galaxy.bed" format="bedstrict"/> <!-- Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, UCSC does not: force use of converter which will make strict BED6+ file --> <param type="template" name="position" strip="True" >
what is the meaninng <param type="template" name="position" strip="True" />
and what is the use of url="galaxy.bed" ?
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..
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 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.
Regards shashi
------------------------------ *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
___________________________________________________________ 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/
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_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..
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 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.
Regards shashi
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
___________________________________________________________ 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/
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 <james@taylorlab.org> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: Ross <ross.lazarus@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_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
___________________________________________________________
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/
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_shashi29@yahoo.co.in> To: James Taylor <james@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 <james@taylorlab.org> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: Ross <ross.lazarus@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_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
___________________________________________________________
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/
Display applications are extensively documented here: http://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%... -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Jun 20, 2013 at 2:20 AM, shashi shekhar <me_shashi29@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 <james@taylorlab.org> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: Ross <ross.lazarus@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_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..
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 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.
Regards shashi
________________________________ 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
___________________________________________________________ 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/
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_m.... 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 <james@taylorlab.org> To: shashi shekhar <me_shashi29@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%... -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Jun 20, 2013 at 2:20 AM, shashi shekhar <me_shashi29@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 <james@taylorlab.org> To: shashi shekhar <me_shashi29@yahoo.co.in> Cc: Ross <ross.lazarus@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_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..
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 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.
Regards shashi
________________________________ 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
___________________________________________________________ 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/
participants (5)
-
Carl Eberhard -
Hans-Rudolf Hotz -
James Taylor -
Ross -
shashi shekhar