Installing something
from the repository means downloading it from the Ubuntu Software Center (or other APT utilities such as
apt-get,
aptitude, or
synaptic). If you add a PPA or other repository, such as
Medibuntu, the packages can be installed with your favorite package management utility (often
apt-get, although it could be others) just like packages included in Ubuntu by default, and is considered installed
from the repository.
Downloading
deb files directly from the Internet and installing them using
dpkg,
gdebi, or the Ubuntu Software Center (default in Ubuntu) is still installing the packages using APT, but
not from the repository. You still get some of the benefits of APT, such as automatic dependency resolution, but not others, such as automatic updates or reasonable assurance that the package's dependencies can be satisfied and the software will work well with your system. However, since APT knows about the package, it will likely make it through distribution upgrades and will be easy to remove at some point in the future, if necessary.
Downloading
run files (or any other form of Linux binary) from the Internet should almost always be avoided. Since APT doesn't know this software exists, you will need to install the dependencies yourself (which is often documented in the README that comes with the binary), and you are responsible for making sure you keep the software up-to-date and its dependencies remain installed through distribution upgrades. The recommend way to handle software that
must be installed this way is to install it to
/opt so that it is easier to manually manage and remove.
For example, I have
MATLAB (a piece of technical software often used by engineers for intensive mathematical computations and simulations) installed on my system in
/opt/MATLAB/R2008b (I know I have an older version, its expensive!). I then created a launcher (
/opt/MATLAB/R2008b/matlab.desktop) and soft-linked it to
/usr/share/applications/matlab.desktop so that it is displayed properly in my menu. Not only can I easily tell that I have MATLAB installed outside of the repository by listing the contents of
/opt, I can also remove it easily by deleting just one directory and one file:
/opt/MATLAB and
/usr/share/applications/matlab.desktop. However, that installation method is the exception not the rule. Use it as a last resort.
The order of preference for package installation should be
repository >
deb file >
binary installer.
Disclaimer: I made some generalizations to keep the explanation as simple as possible. However, my explanations are valid in
almost every case; there are merely some technicalities that I didn't cover for the sake of brevity.