Blast Output Visualizers in Galaxy

3.3 years ago by

Germany

Bjoern Gruening ♦ 5.1k wrote:

Have a look at this issue report with some alternative we have and will develop: https://github.com/peterjc/galaxy_blast/issues/60

For more information please see the Visualization wiki page @ https://wiki.galaxyproject.org/VisualizationsRegistry/Cookbook

If you want to have a way have a look how we do it in our Docker Flavours: https://github.com/bgruening/galaxy-rna-workbench/blob/master/Dockerfile#L11

Cheers,

Bjoern

ADD COMMENT • link modified 3.3 years ago • written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern,

this is great! Would you happen to know where in the galaxy source code I can embed this in and have it work on my local galaxy instance? I'm trying to see how Trackster does their visualizations in the source code.

I am familiar w/ the basics of bootstrap, if that helps. Thanks. -Roy

ADD REPLY • link written 3.3 years ago by rlee03 • 50

I updated my post with more informations. Hope this gets you started!

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern,

I don't have a background in JS, and starting out w/ Python/Unix

1) Are you referring to this link?

Link 1 https://github.com/peterjc/galaxy_blast/pull/61 <https: github.com="" peterjc="" galaxy_blast="" pull="" 61="">

Link 2 https://github.com/peterjc/galaxy_blast/pull/61/files#r30315209 <https: github.com="" peterjc="" galaxy_blast="" pull="" 61="" files#r30315209="">

2a) What would I need to implement this? 2b) XML files? Python Files? 2c) Is there a trigger I need to activate the JS once the user clicks on a link? 2d) Also, DO I need to have a Javascript background?

Thanks.

ADD REPLY • link written 3.3 years ago by rlee03 • 50

You don't need any backgroud. Ideally you should be able to drag and drop crossbio_blast into your visualization directory and you should be ready to go.

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

I'm using these files

https://github.com/bgruening/galaxy_blast/tree/b324ba9efa9e9d579445bf4fd352d2b0c39990fd/visualizations/crossbio_blast

. I pasted them in my visualizations folder of my galaxy instance directly. Still no results.

I added the first two lines in your XML file

1 2 <https: wiki.galaxyproject.org="" visualizationsregistry#ca-adf70f9509e82baee0f6049fab46c2f2476b5f5e_2=""> *

I also have a separate tool that produces Blast output in an XML format in the central panel of the web browser, how would I connect my blast output this crossbio tool? It's running on a docker container.

Thanks for all of your help.

ADD REPLY • link written 3.3 years ago by rlee03 • 50

You only see it on special datatypes, in this case I think it was blastxml.

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

1) I'm sorry, but may you please clarify your response. "You only see it on special datatypes, in this case I think it was blastxml."

What is the "it" you are referring to?

So......

2) Cross Bio Receives Blast XML files as input.

How can I load the Blast XML input file so Cross Bio reads it?

3) I followed your instructions by pasting the Cross bio folder into the visualizations folder,

but it does NOT show up in galaxy. May you give me some ideas on why this is the case?

Thanks.

ADD REPLY • link written 3.3 years ago by rlee03 • 50

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