Peter
Assuming you can SSH into your Ubuntu server, and have Drush installed on it (take a look at https://www.drupal.org/node/1248790 for installation instructions), you get to a command line, generally inside the site you want to work with (otherwise you need to have set up aliases), and the Drush commands should work. I always start with “drush status” to see if it is the site/database I am expecting.
I have not tried using a command line on my desktop with an alias pointing to a remote server that requires using a proxy, but I am pretty sure it could be done (we have discovered ways to do a lot of things via proxies that aren’t always as well documented as they could be).
We use Drush on our servers for some things like setting up new users and getting around a nasty issue we have with database compatibility in a Drupal 6 site we maintain.
Gregg Marshall
Consultant/Contractor, Drupal Development
NYS ITS Web Services
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