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JBrowse-in-Galaxy v0.4 #507
It's finally here! Just in time for the new year :) Opening for review of the tool (under WIP) while I fix the installation recipe.
TODO before out of WIP
(This is apparently not a happy subject for some, but) we're almost at feature parity with trackster. v0.5 will likely be a minor update which adds support for
The other last real feature on the roadmap before I hit 1.0 is support for protein sequences. I have work in various places but this will necessitate patches to upstream.
Please comment on #508 if you have other features you'd like to see
Say you have four gff3 files from four different gene callers, and wish to plot them all under a single group. You can do that with the added
There are a couple different "colour score scaling" methods built in and automatically used. Here we see a blast XML dataset that's automatically been processed into a GFF3 representation. It takes advantage of the "blast" scoring mechanism which writes a horrifically complex JBrowse config that automatically calculates opacity in relation to the e-value of the hit.
Here we see the "linear" scoring mechanism with a manually specified min/max of 0/1000. The min/max values can be automatically detected from the GFF3 file, or specified in the configuration
Lastly BigWig files are more easily configurable. You can specify the colour pivot points, the positive/negative colours, or you can let them automatically be determined. The below plots showcase features like custom min/maxes, custom pivot points, etc.
Would produce the following:
So I decided it was best if JBrowse had the ability to produce both a "standalone" and the data dir without JBrowse. What I really wanted was that all of JBrowses outputs could be just the data directory rather than making a full copy of JBrowse every time you want to produce a visualization, but I didn't see any technical solutions to that problem which didn't involve really unpleasant things. E.g. hacking JBrowse into a visualization plugin which would require splitting out static resources and an index.html template that would require some really, really ugly hacks and a separate viz plugin to install just for JBrowse and a special JBrowse datatype which means people would have to be on 16.01, rather than 15.05 or so.
@bgruening not a problem. I'm really hoping there's a better solution in the future, but I just haven't found anything I'm happy with yet. The data dir is a stopgap solution until we get to the point where datatypes, viz plugins, and tools are all easy to install and depend upon.
I'm almost done writing the help text, and then it should be good to go :)