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Fix contextual menu for blastview tracks #2621

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merged 1 commit into from Jun 1, 2021

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abretaud
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In recent version of Apollo, BlastView tracks (https://github.com/TAMU-CPT/blastview/) are broken: there's no contextual menu entry to "create new annotation" (and no drag and drop as it's a canvas track).
This patch fixes it

@hexylena
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hexylena commented May 28, 2021

I'm not sure that's broken though, it was never used by them to create annotations (only to inform human annotators) / never dragged and dropped

@abretaud
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I think the right click menu would show up in older apollo versions (before NeatCanvasFeature track type was added)
In the tutorial I was thinking I could show how to add a gene that is in the blast results, but was not spotted by augustus. I was thinking also to only look at the NCBI ref annotation at the end to tell: "look, by making changes with apollo you made the annotation look very close to the gold reference from ncbi (but in real life you won't have a gold ref)"

@hexylena
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Ok, that works then, that makes sense :) let's get that in then

@hexylena
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Not simple to get on EU (we were strictly off of the tagged releases with zero delta). I'll try and figure out how to do that.

@abretaud
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Ok thanks :) If it's too complicated I can always try to find other things to do in apollo

@rbuels
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rbuels commented May 28, 2021

@garrettjstevens could you have a look at this?

@garrettjstevens
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@abretaud I'm a bit wary of putting custom configuration for external plugins in the Apollo codebase (and please correct me if I'm understanding this wrong). Is there a way you can change the track config type when creating your BlastView track configurations?

@abretaud
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abretaud commented Jun 1, 2021

Yeah I see your point. The problem is that we generate single jbrowse data dirs to be used as a standalone jbrowse instance, or loaded into Apollo, so our config needs to work on both.
I don't really see a better solution than this patch, it's really a minimal reference to the external plugin from the apollo code

@garrettjstevens garrettjstevens merged commit 83a3b60 into GMOD:develop Jun 1, 2021
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4 participants