Remove vg msga

[faithokamoto]

Changelog Entry

To be copied to the draft changelog by merger:

• vg msga is removed

Description

Messed with a lot of test stuff, but it doesn't rely in vg msga any more. You know what does rely on it, though? The wiki.

• https://github.com/vgteam/vg/wiki/Complex-graph-visualization
• https://github.com/vgteam/vg/wiki/RDF%3A-for-VG
• https://github.com/vgteam/vg/wiki/VG-RDF%2C-the-Ensembl-bacteria-E.-coli-genome-hack-attack

I'm not entirely sure what to do about those buggers. I guess for the first two I could just run the command and save the output? But the last one is that sort of broken page that I would now be breaking even further.

@adamnovak since you asked for it :)

[faithokamoto]

It failed some doc job /builds/vgteam/vg/doc/../README.md that I have no idea where it is. Looks like we'd just need to delete some line that tests msga.

[faithokamoto]

Oh, silly. That means the repo base level README.

[adamnovak]

For the last one (https://github.com/vgteam/vg/wiki/VG-RDF%2C-the-Ensembl-bacteria-E.-coli-genome-hack-attack) we could try vg map or vg giraffe, if they work on such long inputs, to get a GAM, and then vg augment to add the GAM to the graph.

[faithokamoto]

I think the last one is begging for me to actually try to rerun the entire example. I'll put it back on the wiki update list...

[faithokamoto]

Reworked the tutorial to not use vg msga: https://github.com/vgteam/vg/wiki/Graph-&-annotations-for-two-E.-coli-strains

Will plug it into everywhere relevant tomorrow, I'm about to go watch Project Hail Mary again :)

[faithokamoto]

@adamnovak anything else we might need to worry about before this gets merged in?

[adamnovak]

I think that's probably it.