Re: [galaxy-dev] visulaization tool
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
Re: [galaxy-dev] visulaization tool
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
Re: [galaxy-dev] visulaization tool
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
urlhttp://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}amp;position=${position.qp}amp;hgt.customText=${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.laza...@gmail.com
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 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_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
___
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/
Re: [galaxy-dev] visulaization tool
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_shash...@yahoo.co.inwrote:
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
urlhttp://genome.ucsc.edu/cgi-bin/hgTracks?db=${qp($bed_file.dbkey)}amp;position=${position.qp}amp;hgt.customText=${bed_file.qp}
http://genome.ucsc.edu/cgi-bin/hgTracks?db=$%7Bqp($bed_file.dbkey)%7Dposition=$%7Bposition.qp%7Dhgt.customText=$%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.laza...@gmail.com
*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 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_shash...@yahoo.co.inwrote:
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.inwrote:
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
[galaxy-dev] visulaization tool
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/
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/
Re: [galaxy-dev] visulaization tool
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/
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.inwrote: 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/
Re: [galaxy-dev] visulaization tool
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. 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 ___ 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/
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.inwrote: 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.inwrote: 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/
Re: [galaxy-dev] visulaization tool
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 ___ 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/
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_shash...@yahoo.co.inwrote: 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.inwrote: 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.inwrote: 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/
Re: [galaxy-dev] visulaization tool
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.laza...@gmail.com 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 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_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 ___ Please keep all replies on the list by using reply all
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/
