BioJS-MSA doesn't use galaxy prefix

[hexylena]

If galaxy is running with a prefix like /galaxy/, BioJS-MSA is not aware of this.

[saketkc]

cc @greenify

[wilzbach]

Last time I asked whether there is a variable or configuration from which the MSA can get the browser path to itself.

I would be happy to change that if Galaxy can give the visualization plugins the absolute url to the them...

[hexylena]

Yes, it can. We've done this with our IPython Viz plugin though I'll have to dig into the code to figure out how we did it. I was seconds away from submitting this issue on biojs2galaxy.

[hexylena]

You've already done it in a couple places, you're just missing some of the others. In galaxy.mako, you have root which will correctly determine the correct root, you just need to use that for url and jsonURL on L43-44

[wilzbach]

Oh sry, I was replying too fast - I was referring to the plugin path which is hard-coded to plugins/visualizations in biojs2galaxy.

thanks to @erasche I updated biojs2galaxy with the correct root url :)

[hexylena]

Oh, yeah, it would be nice if there was a method that'd get the full URL for a viz plugin. Anyway, great, thanks so much for getting this fixed in upstream!