First of all install debian (squeeze was used for the first version of this document, changes for wheezy are mentioned where appropriate) in a standard Installation including the packages
 
ssh
sudo
 
Bring everything you need for a basic system to work (Networking, DNS, hostname etc.). Check that IP and DNS are working properly.
After changes to the hostname (edit the file /etc/hostname accordingly), issue the command:

hostname `cat /etc/hostname`

The symbols used in the command above are somteimes called "backticks" or "backquotes", don't confuse with the regular quote symbols. The command within the backticks is executed and the result pasted into the command line!

If you work behind an internet proxy, enter the configuration into the current user's bashrc and into the root user's bashrc.

echo http_proxy=http://yourproxy.yourdomain:proxyport >> .bashrc

Login again to make this setting active or issue the command

export http_proxy=http://yourproxy.yourdomain:port

in the command shell.
 
Edit the appropriate apt configuration file to allow use of the proxy (e.g. /etc/apt/apt.conf)

Acquire::http::Proxy http://yourproxy.yourdomain:proxyport;

To distiguish system installation and ILIAS data, ist is advisable to use separate disks or partitions. The actual layout of your server depends on hardware layout or other system requirements. This installation assumes that the system resides on the first hard disk (sda1) and Ilias data is stored in directories below /srv. /srv is the mountpoint for a single partition od a second virtual harddrive, sdb1
This requires an entry in the /etc/fstab file, reading

/dev/sdb1      /srv   auto   defaults  0  0

If the disk was mounted before, unmount it and issue the command

mount -a

If this is successful, the disk is mounted in the right place and the command ensures, that the disk will be mounted correctly after a system reboot

Update the Installation (apt-get update and apt-get upgrade). You may want to disable installation from the cdrom/dvd by editing the apt entries in /etc/apt.
 
If working in a virtual machine, consider to install the virtualisation guest tools.

To prepare for growth of data-areas, consider using LVM for the server data.