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There is several ways of installing software on Linux. On this site I will cover install from repository, deb-packages, tar.gz-files and windows-setup-files.
Repositories are located on the web and contain prebuild-packages fore your linux distribution.
The most secure and stable packages are from the native debian.org (or its mirrors) repositories.
These are devided into 3 areas stable, contrib and non-free, which say something about the way they are licensed.
Stable = no problems.
contrib = depends on nonfree packages.
non-free = non-free (as in freedom - I think) - my opinion = no problem.
Appart from the native repositories there is third-party repositorys like "http://deb.playonlinux.com/". Packages from these repos are considered as unsecure. Be aware who you trust!
I use apt-get or synaptic to install packeges from the repositories. Which repositories to use is configured in /etc/apt/source.list. Se Install programs.
.deb-pakeges can be downloaded from several places like skype.com.:
-Download the packages
-Go to downloads
-Right-click and choose "open with.."
The command line way is to use dpkg. See $ man dpkg for futher info.
If it is possible choose the debian/wheezy version. Here again: Be aware who you trust!
Install "playonlinux" and use their wizards.