I used the jruby zip executable to install 1.6.2, but it looks like they have released 1.6.4. How should I migrate from 1.6.2 to 1.6.4, should I have to re-install or is there a different command.
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Mostly all you need to do is reinstall gems on the newly-unpacked JRuby (recommended), or migrate your existing gem installs by copying the lib/ruby/gems/* over to the new location. There's no automated update tool for JRuby itself right now.

Charles Oliver Nutter
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Unpack new Jruby
export JRUBY_HOME=/path/to/jruby
export PATH=$PATH:$JRUBY_HOME/bin
Maybe even push the above to .bashrc
Add a list of required Gems to your Gemfile.
To reinstall Gems if needed the best way to do it is as follows
Jruby -S gem install bundler
Cd to /path/to/Gemfile
bundle install

tven
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On a Windows 10 machine I had to do similar, but had to use `setx /s COMPUTER JRUBY_HOME "/path/to/jruby"` instead of the `export` command. – chemturion Jan 18 '19 at 23:03