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peterjc / galaxy_blast

Galaxy wrappers for NCBI BLAST+ and related BLAST tools.
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BLAST visualizations #60

Open peterjc opened 9 years ago

peterjc commented 9 years ago

It would be great to offer some way of displaying BLAST output (ideally at least BLAST XML and tabular) using the Galaxy Visualizations framework (Goecks et al. 2013).

peterjc commented 9 years ago

See also the work from Gildas Le Corguillé presented at GCC2014:

bgruening commented 9 years ago

@peterjc the biojs project is working on a BlAST Vis. ping @greenify

wilzbach commented 9 years ago

Hey :)

I did work on this a couple of months ago as part of the crossb.io project.

Here's the current demo of the BLAST dashboard - however it is in a very early stage. It takes the BLAST XML as input. Let me know if you have ideas or specific requirements - I would be glad to help you guys ;-)

bgruening commented 9 years ago

Hi Seb,

I had a first docker image if this running at some point. Have you updated the code since then? Would you be interested in putting this into a VIS/IE? We need approximately a few hours together?

Cheers, Bjoern

wilzbach commented 9 years ago

Hi Björn,

I had a first docker image if this running at some point. Have you updated the code since then?

Nope - I did some minor modifications on the end of March, but only to get it work nicely with npm.

Would you be interested in putting this into a VIS/IE?

Sure - should we keep it as it is or do you want to modify some parts? As it is a npm package, I could use biojs2galaxy again :)

We need approximately a few hours together?

Yes - I do have time :)

bgruening commented 9 years ago

With the amazing help from @greenify we got this working:

blast

@peterjc where do you want to me put this VIS? Here? IUC? galaxytools next to the protein VIS? Or do you expect a different kind of visualization?

peterjc commented 9 years ago

That looks very slick. I'm happy for it to join the galaxy_blast repository, but https://github.com/galaxyproject/tools-iuc would work too.

[Long term, we could end up forking peterjc/galaxy_blast to galaxyproject/galaxy_blast, or even merged into https://github.com/galaxyproject/tools-iuc for IUC administration?]

hexylena commented 9 years ago

Commenting on this as I've done work in a related direction...

screenshot from 2015-05-20 18 33 23

Not technically a viz plugin (it's a tool) though.

bgruening commented 9 years ago

Just to collect a few more: http://brig.sourceforge.net/ (is not maintained anymore, as it seems)

hexylena commented 9 years ago

I tried to use that and nearly wrapped it for Galaxy, but ended up deciding it wasn't all that useful. Happy to wrap if need be.