Excerpts from Hotz, Hans-Rudolf's message of 2011-11-01 09:42:38 +0000:
Well, I am not a linux system expert, but I don't see a reason, why you can't run Galaxy from an external drive as long as it is mounted correctly and you have all the read and write permissions.
Also, if you want galaxy to be installed under your home directory (for example) but have just the dataset files on an external drive, you can modify the "file_path" configuration option in universe_wsgi.ini. Importantly, note that the database and the file_path are interconnected, if you keep your existing database you will need to move files to the new location. The safest thing is to start with a clean Galaxy on the external drive. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University