[Gmod-ajax] get started with plugins

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[Gmod-ajax] get started with plugins

Sofia Robb
I was hoping to get pointed to some help in writing my first plugin.

Could someone point me to a tutorial for building a plugin or a very simple plugin that deals with feature sequence retrieval and display. I see the tutorial in the JBrowse Configuration guide, but i still don't know where to start with the code that I need to put into somewhere in the example main.js. 

I want to start with what i think should be a really simple plugin. I have a blast track, loaded with a url. It looks great. I would love to use the FeatureSequence plugin on this track. So I added a track config block to my trackList.json for all my blast tracks. When I try to use the Feature Sequence am getting an error 

main.js:136 Uncaught TypeError: Cannot read property 'browser' of undefined

I don't know how to fix this,

So I was thinking I just want to concatenate and display the sequence from the blast track, I could make my own plugin. But where do I start? Is there a list of methods I can use? How do I retrieve the coordinates of the feature track, how do I retrieve reference sequence from coordinates, how do I display this in a pretty box like the "view details"

Any help in getting me on the right track would be greatly appreciated.

Thanks,
Sofia




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Re: get started with plugins

nathandunn

Sofia,

I think you are right to start with an existing plugin (https://gmod.github.io/jbrowse-registry/) and make modifications.

This is a list of API’s:  http://jbrowse.org/api/

It might be easiest to create a new GH project to build a plugin based on one of these and then point folks to the proper place to go so they can check out the code themselves to help you.

Nathan

On Nov 10, 2016, at 12:34 PM, Sofia Robb <[hidden email]> wrote:

I was hoping to get pointed to some help in writing my first plugin.

Could someone point me to a tutorial for building a plugin or a very simple plugin that deals with feature sequence retrieval and display. I see the tutorial in the JBrowse Configuration guide, but i still don't know where to start with the code that I need to put into somewhere in the example main.js. 

I want to start with what i think should be a really simple plugin. I have a blast track, loaded with a url. It looks great. I would love to use the FeatureSequence plugin on this track. So I added a track config block to my trackList.json for all my blast tracks. When I try to use the Feature Sequence am getting an error 

main.js:136 Uncaught TypeError: Cannot read property 'browser' of undefined

I don't know how to fix this,

So I was thinking I just want to concatenate and display the sequence from the blast track, I could make my own plugin. But where do I start? Is there a list of methods I can use? How do I retrieve the coordinates of the feature track, how do I retrieve reference sequence from coordinates, how do I display this in a pretty box like the "view details"

Any help in getting me on the right track would be greatly appreciated.

Thanks,
Sofia



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Re: get started with plugins

Eric Yao
Hi Sofia,
There are a number of different kinds of plugins here too:
https://github.com/GMOD/jbrowse/tree/master/plugins

This one I'm working on is a more involved blast result viewer (needs a lot more documentation and cleanup) and is integrated with our jbserver and galaxy.

Eric



On Thu, Nov 10, 2016 at 1:37 PM, Nathan Dunn <[hidden email]> wrote:

Sofia,

I think you are right to start with an existing plugin (https://gmod.github.io/jbrowse-registry/) and make modifications.

This is a list of API’s:  http://jbrowse.org/api/

It might be easiest to create a new GH project to build a plugin based on one of these and then point folks to the proper place to go so they can check out the code themselves to help you.

Nathan

On Nov 10, 2016, at 12:34 PM, Sofia Robb <[hidden email]> wrote:

I was hoping to get pointed to some help in writing my first plugin.

Could someone point me to a tutorial for building a plugin or a very simple plugin that deals with feature sequence retrieval and display. I see the tutorial in the JBrowse Configuration guide, but i still don't know where to start with the code that I need to put into somewhere in the example main.js. 

I want to start with what i think should be a really simple plugin. I have a blast track, loaded with a url. It looks great. I would love to use the FeatureSequence plugin on this track. So I added a track config block to my trackList.json for all my blast tracks. When I try to use the Feature Sequence am getting an error 

main.js:136 Uncaught TypeError: Cannot read property 'browser' of undefined

I don't know how to fix this,

So I was thinking I just want to concatenate and display the sequence from the blast track, I could make my own plugin. But where do I start? Is there a list of methods I can use? How do I retrieve the coordinates of the feature track, how do I retrieve reference sequence from coordinates, how do I display this in a pretty box like the "view details"

Any help in getting me on the right track would be greatly appreciated.

Thanks,
Sofia



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Training and support from Colfax.
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Re: get started with plugins

Saari, Travis

Hi Sofia,

 

Have you gotten the FeatureSequence plugin to work for any of your other tracks? I’m wondering if you were receiving the error due to the track loading from a URL. Either way, I think all of the code for the functionality you desire is in the FeatureSequence plugin, it’s just a matter of finding a way of calling it from the blast track.

 

This has always been the tricky part for me building the plugin – the use of the call function in trackList.json is the only way that I could think of to make this option available on certain tracks and not others.

 

Let me know and we can hopefully find a way to make it work for you. Otherwise, Eric’s plugin might be another option.

 

Best,


Travis Saari

 

From: Eric Yao [mailto:[hidden email]]
Sent: Tuesday, November 15, 2016 6:59 PM
To: Nathan Dunn <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] get started with plugins

 

Hi Sofia,

There are a number of different kinds of plugins here too:

https://github.com/GMOD/jbrowse/tree/master/plugins

 

This one I'm working on is a more involved blast result viewer (needs a lot more documentation and cleanup) and is integrated with our jbserver and galaxy.

 

Eric

 

 

 

On Thu, Nov 10, 2016 at 1:37 PM, Nathan Dunn <[hidden email]> wrote:

 

Sofia,

 

I think you are right to start with an existing plugin (https://gmod.github.io/jbrowse-registry/) and make modifications.

 

This is a list of API’s:  http://jbrowse.org/api/

 

It might be easiest to create a new GH project to build a plugin based on one of these and then point folks to the proper place to go so they can check out the code themselves to help you.

 

Nathan

 

On Nov 10, 2016, at 12:34 PM, Sofia Robb <[hidden email]> wrote:

 

I was hoping to get pointed to some help in writing my first plugin.

 

Could someone point me to a tutorial for building a plugin or a very simple plugin that deals with feature sequence retrieval and display. I see the tutorial in the JBrowse Configuration guide, but i still don't know where to start with the code that I need to put into somewhere in the example main.js. 

 

I want to start with what i think should be a really simple plugin. I have a blast track, loaded with a url. It looks great. I would love to use the FeatureSequence plugin on this track. So I added a track config block to my trackList.json for all my blast tracks. When I try to use the Feature Sequence am getting an error 

 

main.js:136 Uncaught TypeError: Cannot read property 'browser' of undefined

 

I don't know how to fix this,

 

So I was thinking I just want to concatenate and display the sequence from the blast track, I could make my own plugin. But where do I start? Is there a list of methods I can use? How do I retrieve the coordinates of the feature track, how do I retrieve reference sequence from coordinates, how do I display this in a pretty box like the "view details"

 

Any help in getting me on the right track would be greatly appreciated.

 

Thanks,

Sofia

 

 

 

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With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
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With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
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Re: get started with plugins

Sofia Robb
Thank you all for the advice. I will be trying all of the mentioned options. I will try to again with the FeatureSequence plugin, I will try out Eric's blast result viewer as well as the other examples. I am sure I will be emailing the list again with questions during my progress. I am hoping to find some time soon to sit down and really work on this.

Thanks again!
Sofia


On Wed, Nov 16, 2016 at 8:47 AM, Saari, Travis <[hidden email]> wrote:

Hi Sofia,

 

Have you gotten the FeatureSequence plugin to work for any of your other tracks? I’m wondering if you were receiving the error due to the track loading from a URL. Either way, I think all of the code for the functionality you desire is in the FeatureSequence plugin, it’s just a matter of finding a way of calling it from the blast track.

 

This has always been the tricky part for me building the plugin – the use of the call function in trackList.json is the only way that I could think of to make this option available on certain tracks and not others.

 

Let me know and we can hopefully find a way to make it work for you. Otherwise, Eric’s plugin might be another option.

 

Best,


Travis Saari

 

From: Eric Yao [mailto:[hidden email]]
Sent: Tuesday, November 15, 2016 6:59 PM
To: Nathan Dunn <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] get started with plugins

 

Hi Sofia,

There are a number of different kinds of plugins here too:

https://github.com/GMOD/jbrowse/tree/master/plugins

 

This one I'm working on is a more involved blast result viewer (needs a lot more documentation and cleanup) and is integrated with our jbserver and galaxy.

 

Eric

 

 

 

On Thu, Nov 10, 2016 at 1:37 PM, Nathan Dunn <[hidden email]> wrote:

 

Sofia,

 

I think you are right to start with an existing plugin (https://gmod.github.io/jbrowse-registry/) and make modifications.

 

This is a list of API’s:  http://jbrowse.org/api/

 

It might be easiest to create a new GH project to build a plugin based on one of these and then point folks to the proper place to go so they can check out the code themselves to help you.

 

Nathan

 

On Nov 10, 2016, at 12:34 PM, Sofia Robb <[hidden email]> wrote:

 

I was hoping to get pointed to some help in writing my first plugin.

 

Could someone point me to a tutorial for building a plugin or a very simple plugin that deals with feature sequence retrieval and display. I see the tutorial in the JBrowse Configuration guide, but i still don't know where to start with the code that I need to put into somewhere in the example main.js. 

 

I want to start with what i think should be a really simple plugin. I have a blast track, loaded with a url. It looks great. I would love to use the FeatureSequence plugin on this track. So I added a track config block to my trackList.json for all my blast tracks. When I try to use the Feature Sequence am getting an error 

 

main.js:136 Uncaught TypeError: Cannot read property 'browser' of undefined

 

I don't know how to fix this,

 

So I was thinking I just want to concatenate and display the sequence from the blast track, I could make my own plugin. But where do I start? Is there a list of methods I can use? How do I retrieve the coordinates of the feature track, how do I retrieve reference sequence from coordinates, how do I display this in a pretty box like the "view details"

 

Any help in getting me on the right track would be greatly appreciated.

 

Thanks,

Sofia

 

 

 

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

 


------------------------------------------------------------------------------
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With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
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