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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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strange NeatHTMLFeatures track rendering #2039

Closed trstickland closed 5 years ago

trstickland commented 5 years ago

I am seeing strange rendering of introns with apollo 2.3.0, which may be related to making NeatHTMLFeatures the new default. A quick screen grab...

screengrab of track rendering

So the intron "hats" are there, but there's also the grey background with the blue arrows. Does this indicate that the styling of NeatHTMLFeatures and another styling (HTMLFeatures???) are applied?

We have the NeatHTMLFeatures plugin included in the apollo.groovy config file, but there's no track type config in the track config (trackList.json). This is the same configuration that we were using with apollo 2.1.0 & jbrowse 1.12.5, which rendered introns as expected with (only) the "hats".

FWIW, I saw this previously with apollo 2.2.0, when explicitly setting NeatHTMLFeatures in the track type config in trackList.json files. Removing the track type config (i.e. reverting to the default) resulted in the "grey with blue arrow" styling -- I wasn't sure if this was right, but the 2.30 release appeared before I could figure it out.

I also tried the latest master branch version (at time of writing, d36d5be) which behaves the same.

nathandunn commented 5 years ago

@trstickland Its generally because the JBrowse CSS changes require a slight change in the definitions.

Can you post the CSS for those transcript and I can suggest how to fix them?

I'll try to update docs and make an announcement to help others with that.

Basically, you'll want to remove a lot of the external styling. I removed this (which was needed before):

    "style" : {
        "className" : "feature"
     },

And it worked for me.

nathandunn commented 5 years ago

@trstickland Were you able to confirm that this works?

trstickland commented 5 years ago

@nathandunn Sorry, I've been working on other things today, will have a go tomorrow hopefully.

trstickland commented 5 years ago

That's it -- just removing that in the trackList.json file fixes it.

Thanks for pointing me in this direction: I would never have spotted this, as that particular configuration hasn't changed since our previous build in which the rendering was fine :-/

Please feel free to close.

nathandunn commented 5 years ago

Awesome. I'll make a brief announcement.