link from alignment page to jbrowse

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link from alignment page to jbrowse

Sofia Robb
Hello,

Is there a way to generate a link in the alignment page of a feature to link to jbrowse? how about including an embedded  jbrowse image of the alignment of the feature.

Thanks,
Sofia

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Re: link from alignment page to jbrowse

vkrishna
Hi Sofia,

I’m assuming yes, there should be a way to link out from the Tripal Alignment page to JBrowse. The relevant code would be in the following template:

In the Alignment table, you can either convert the alignment location column to a JBrowse link-out of the form (or just add a new column with the URL): <a href="http://hostname/jbrowse/?data=$dataset&loc=$feature_loc” target=“_blank”>$feature_loc</a>

You could also extend the template to include an iframe embed of your JBrowse instance, utilizing the $feature_loc from the Alignments table.

I hope that I have understood you question properly.

Thank you.
Vivek

On Mar 10, 2016, at 1:27 PM, Sofia Robb <[hidden email]> wrote:

Hello,

Is there a way to generate a link in the alignment page of a feature to link to jbrowse? how about including an embedded  jbrowse image of the alignment of the feature.

Thanks,
Sofia
------------------------------------------------------------------------------
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Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
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Re: link from alignment page to jbrowse

Sofia Robb
Hi Vivek,

Thanks for pointing me in the right direction, this is exactly my question. This gives me a place to start.

Thank!
Sofia


On Thu, Mar 10, 2016 at 12:12 PM, Krishnakumar, Vivek <[hidden email]> wrote:
Hi Sofia,

I’m assuming yes, there should be a way to link out from the Tripal Alignment page to JBrowse. The relevant code would be in the following template:

In the Alignment table, you can either convert the alignment location column to a JBrowse link-out of the form (or just add a new column with the URL): <a href="http://hostname/jbrowse/?data=$dataset&loc=$feature_loc” target=“_blank”>$feature_loc</a>

You could also extend the template to include an iframe embed of your JBrowse instance, utilizing the $feature_loc from the Alignments table.

I hope that I have understood you question properly.

Thank you.
Vivek

On Mar 10, 2016, at 1:27 PM, Sofia Robb <[hidden email]> wrote:

Hello,

Is there a way to generate a link in the alignment page of a feature to link to jbrowse? how about including an embedded  jbrowse image of the alignment of the feature.

Thanks,
Sofia
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
Gmod-tripal mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-tripal



------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
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Re: link from alignment page to jbrowse

Sofia Robb
Thank you!! I now have links to my features in jbrowse. I expanded the feature object to include the records from the feature_dbxref table, and use the urlprefix to form my link if the db name has JBrowse in the name.

Thanks again,
Sofia



On Thu, Mar 10, 2016 at 12:28 PM, Sofia Robb <[hidden email]> wrote:
Hi Vivek,

Thanks for pointing me in the right direction, this is exactly my question. This gives me a place to start.

Thank!
Sofia


On Thu, Mar 10, 2016 at 12:12 PM, Krishnakumar, Vivek <[hidden email]> wrote:
Hi Sofia,

I’m assuming yes, there should be a way to link out from the Tripal Alignment page to JBrowse. The relevant code would be in the following template:

In the Alignment table, you can either convert the alignment location column to a JBrowse link-out of the form (or just add a new column with the URL): <a href="http://hostname/jbrowse/?data=$dataset&loc=$feature_loc” target=“_blank”>$feature_loc</a>

You could also extend the template to include an iframe embed of your JBrowse instance, utilizing the $feature_loc from the Alignments table.

I hope that I have understood you question properly.

Thank you.
Vivek

On Mar 10, 2016, at 1:27 PM, Sofia Robb <[hidden email]> wrote:

Hello,

Is there a way to generate a link in the alignment page of a feature to link to jbrowse? how about including an embedded  jbrowse image of the alignment of the feature.

Thanks,
Sofia
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
_______________________________________________
Gmod-tripal mailing list
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