ruby installation issues on linux? about phylogenerator2 HOT 3 CLOSED

from phylogenerator2.

If a program called raxml is in your $PATH (this is the case if you've apt install mafft for MAFFT, then it will all be fine.

It sounds like this is something quite profound going wrong with your ruby installation. At the risk of sounding a bit difficult, I would suggest making sure you've got that installed cleanly. As a quick test, what happens if you start Ruby interactively (irb) and then type into the console require "bio"?

I would also try sudo apt install ruby-dev and then re-running sudo gem install bio. Something very peculiar is going on, but hopefully re-running those with the dev tools will fix this. Have you used Ruby before? It sounds like you might have done something with your runtime environment (http://stackoverflow.com/questions/38797458/ignoring-gem-because-its-extensions-are-not-built)

I've sent you an email with a more detailed installation guide that I used in a session I ran recently, in case that's useful. Thanks again for looking at this Ross.

from phylogenerator2.

Got the simple plants demo working :)

FYI, I think it required gem install bio NOT sudo gem install bio for my installation.

Perhaps RVM might be an idea? I know NVM saves my ass with similar node package issues
http://stackoverflow.com/questions/2119064/sudo-gem-install-or-gem-install-and-gem-locations

from phylogenerator2.