In addition to what Bret said ... two things ...
you've not mentioned if you plan to upgrade the OS ... 9.0.4 of Ubuntu is very old. Would cloning it to a virtual and then doing the 'Moodle March' make any sense? Eventually, one will need newer versions of not only MySQL but PHP + updates to operating system as well.
Think it might be wise to install a fresh Ubuntu long term support version (server), get the latest apache/mysql/php working, then backup the 1.9.7 site (DB, datadir, and code directory) and restore to the new server.
Since you are on linux may as well enjoy 'git'. One could use git to do the first step in the moodle march ... that of 1.9.7 to 1.9.19+.
http://docs.moodle.org/24/en/Git_for_Administrators
Using git will mean command line, but it's more efficient than browser installs/upgrades and one doesn't have apache/browser issues. Plus one can do the moodle march rather quickly AND one is prepared to make the jump to the next version when released.
'spirit of sharing', Ken