Question: Blast Output Visualizers in Galaxy
0
gravatar for rlee03
2.4 years ago by
rlee0350
United States
rlee0350 wrote:

Hi, 

Does anyone know if there are any good blast output visualizers? 

Must be able to run on the command line (most important)

I am trying to put pretty html and other blast output on my local galaxy instance. 

Thanks.

-Roy

command line linux galaxy blast • 1.1k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by rlee0350
0
gravatar for Bjoern Gruening
2.4 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k 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 COMMENTlink modified 2.4 years ago • written 2.4 years ago by Bjoern Gruening4.8k

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 REPLYlink written 2.4 years ago by rlee0350

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

ADD REPLYlink written 2.4 years ago by Bjoern Gruening4.8k

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="">

or

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 REPLYlink written 2.4 years ago by rlee0350

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 REPLYlink written 2.4 years ago by Bjoern Gruening4.8k

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 REPLYlink written 2.4 years ago by rlee0350

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

ADD REPLYlink written 2.4 years ago by Bjoern Gruening4.8k

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 REPLYlink written 2.4 years ago by rlee0350
0
gravatar for rlee03
2.4 years ago by
rlee0350
United States
rlee0350 wrote:

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?

Cross Bio Receives Blast XML files as input.

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

Thanks.

 

ADD COMMENTlink written 2.4 years ago by rlee0350
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