Biostat Kubuntu User's Guide

The Biostatistics IT team supports the Kubuntu/Linux Desktop for all faculty and staff. We provide around the clock (well almost) email support through biostat-it@list.vanderbilt.edu. We also support more immediate responses as well. Just email us or come by any of our offices between the hours of 8am to 5pm Monday thru Friday to see if we're available. Our IT team includes DalePlummer, JeffreyHorner, ColeBeck, CharlesDupont, JeremyStephens, and ZhouwenLiu.

How do I know I'm running Kubuntu?

Click on "K menu -> Help" and look for the Kubuntu Docs link:

If you don't see Kubuntu anywhere in the document list, then contact Biostat IT.

Keeping your Kubuntu System Up To Date

Your computer will automatically notify you that new upgrades are available by displaying a Yield sign in the lower right corner of your screen on your Panel.

By clicking on that icon, you will start the upgrade process, but it will prompt you to enter your password to get into administrator mode first. Once you've entered your password, you should see a screen like this:

Click on the "Fetch List of Updates" button to update your computer's package database with the central server database:

And then click on the "Apply Updates" button to update your computer:

Once that's done you should see a window like this:

If you encounter an error anytime during this process, please contact Biostat IT.

Installing packages

Using Kubuntu, you can install (or remove) packages without the need of an administrator. The tool used to do this is called 'Adept Manager'. You can run it from your K menu:

It'll ask you for your password. After that, you'll see this:

Let's say you wanted to install the fortune program so that you can read groovy quotes. Just type "fortune" into the search bar, and you'll get a list of candidate packages.

Then click the package you want, and it will expand to show a bit more information. Click the 'Request Install' button.

After that you can click the 'Apply Changes' button at the top to install the package.

After installation finishes, you can read fortunes to your heart's content.

Using Sudo

The sudo command lets you run programs as the superuser, giving you full access to your computer. For example, if you wanted to run R as the superuser so you could install a new package, you would run sudo R from the command line. sudo would then ask you for your user password before running R (NOTE: the password you enter for sudo is the same one that you use to login to your workstation).

sudo is not something you want to use lightly. Since it gives you superuser privileges, be extra cautious of any command you run. A good rule of thumb is to only use sudo when you have to, and then when you're done, exit the program. If you need to install an R package, for example, run sudo R, install the package, and exit. Restart R without sudo and use it normally.

There's a KDE counterpart for sudo called kdesu. You can use kdesu to run KDE programs that you want to have superuser privileges. Open the K menu, located on the left side of your Panel, and select the "Run Command" action like so:

Or you can type Alt+F2 to bring up "Run Command"

kdesu will then ask you for your password:

Konqueror and getting to files on the Network.

Use Konqueror to connect via SSH to your UNIX/Linux accounts on other servers:

How to add an application button to the Kicker panel

Kicker is the application launcher panel of the K Desktop Environment:

Besides the K Menu, where you can start applications, Kicker is also capable of running docked applets like the pager, the taskbar, or the clock. Kicker usually resides on the bottom of the desktop, but it can also be moved to any other border. You can get help and instructions for the Kicker panel by typing "help:/kicker" into the location bar of Konqueror.

It is convenient to have icons on the Kicker panel for the applications we use most oftern. There are a number of ways to add an application to the Kicker panel:

• Drag and Drop - Drag any file from Konqueror into Kicker and it's there. Dragging also works from the K Menu with any entry. You can change the attributes like optional command line parameters or the icon by clicking it with the right mouse button and choosing Configure applicationname Button... from the context menu. For example, many of us have Firefox installed and use it as our preferred web browser. In most cases it is installed as a Kubuntu package and because of that an icon for the program is placed in the K Menu. One might want to have a Firefox icon on the Kicker panel, too. This is easy to accomplish - navigate to the Firefox icon in the K Menu and drag the icon from the K menu to the Kicker panel.
• Using the context menu to add a KDE application - Click the right mouse button on any free space in Kicker and choose Add Application to Panel. There you can choose an application which will then be added to Kicker.
• Using the context menu to add a non-KDE-application (for example SAS).

Playing quicktime videos in Kubuntu

This codocs that are used to play ATI VCR-2 video, Cinepak video, DivX ;-), Indeo Video, Intel 263 video, Microsoft MPEG-4 video, Morgan Multimedia Motion JPEG video, QuickTime, RealAudio, RealVideo 8, RealVideo 9, and Windows Media Video 9 movies using the Mplayer movie player.

• First you must add the 'Medibuntu' repository to the source list. The easiest way to do this is the run the following command. This can be done by either using the 'Run Command' item on the K menu or by using a terminal. To use the 'Run Command' in its window press the button labeled '_O_ptions >>. Then check the box labeled 'Run in _t_erminal window'. Then press the 'Run' button to execute the command.
  

  sudo wget http://www.medibuntu.org/sources.list.d/gutsy.list -O /etc/apt/sources.list.d/medibuntu.list
  

• Next the GPG key must be added to the apt keyring. Run the following command in a terminal using 'Run Command'.
  

  wget -q http://packages.medibuntu.org/medibuntu-key.gpg -O- | sudo apt-key add -
  

• Then follow the instructions as given in Installing Packages for launching Adept package manager. Follow those instructions until the screen looks like this

• Push the Fetch Updates button as illustrated in the following picture.

• Adept will then proceed to update the lists of available packages.
• Use the search box to check that the 'mplayer' package is installed. If it is not installed then request it to be installed.
• Use the search box to find the 'w32codecs' package and request it to be installed.
• Finally press the 'Apply Changes' button the complete the install.

What else?