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Setting up your own computer for the course

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Windows computers:

MobaXterm is great program that combines a simple terminal capable doing ssh and scp and and X-server - that is - accessing remote computers, copying files to remote computers, and using the graphical interface that unix offers. Download here. You can choose to download a installation package or a portable program (for those with no rights to install programs) which could even be run from a USB-stick. When you run the program, Windows Firewall will block some features of MobaXterm and ask if they should be allowed. You can easily let the firewall continue to block, as it does not matter for the part of the program that you will be using. If really necessary you can unblock later.
When starting a ssh session to a remote server, you will be asked for the password again to use in a sftp session. You can cancel that if you don't want to transfer files back and forth between your computer and the remote server.
Here is a short downloadable instruction video for installing and using MobaXterm made by Daniel Edward Perez from Michigan State University.
You can also download "plugins" to MobaXterm, among those Perl, Python, Curl and Nedit. None of these are necessary the the PhD course, but they might be nice for use in the local terminal offered by MobaXterm.

If MobaXterm does not work for you you can try the old method described here - all the way down to the line.
SSH - Secure Shell - from For doing the exercises on our server you must be able to connect to the server using Secure Shell (SSH) and tunnel X through the connection.
If you use windows you can download a non-commercial version of ssh by clicking on the link above and do the following:

  • Make a standard install and start the SSH client.
  • Add a new profile - name it CBS.
  • Edit the profile. On the 'Connection' tab use '' as host name and your assigned user ID as user name. Compression should be set to 'None' and terminal answerback to 'Xterm', press OK.
  • Edit the profile again. This time choose the 'Tunneling' tab. Mark the checkbox 'Tunnel X11 connections' and press OK. Do not try to change both 'Connection' and 'Tunneling' tabs at the same time - it does not work. Tunneling should be checked in all profiles and the "quick connect".
  • Save your settings (the floppy).
  • Whenever you want to connect to the CBS server you just start the SSH client and choose the CBS profile and write your password. First time you connect you are asked to accept a server key - just do it.

You also need an X-server running to see the unix GUI (grafical interface). Any X-server running on your computer will do. If you don't have one, then Xming can be downloaded here.
It is freeware and quite good. You need Xming and Xming-fonts. The X-server must be running if you want to use X (clustalW, nedit, etc.) on the CBS server.
  • Do a standard install - yes to all :-).
  • When installing Xming Fonts, you will be told that there already is a Xming folder, and if you want to install on top of that. The correct answer is YES.
  • When you run the program use "Xming"
  • When you are running a small X will appear in your systray.

There are generally three errors.
  • When starting an X-program, like clustalW or nedit, you get the message: "X connection to localhost:21.0 broken (explicit kill or server shutdown)." This means that your X server (Xming) is not running.
  • When starting an X-program, you get the message: "Error: Can't open display:" This means that SSH is not tunneling X correctly. You must check your settings again.
  • When starting an X-program, you get the message: "Unable to load critical font" or similar message complaining about fonts. This means that you did not install Xming Fonts correctly. Look at the guide again.
  • Some people worry about the question from windows firewall asking to either allow or deny access to the internet from Xming. The answer does not matter, so say whatever you like.

Macintosh computers:

SSH - Secure Shell
If you're on a mac the ssh program is already installed (you can access it from the commandline in the "Terminal" application). You log on using
"ssh -Y" (without the quotes). XXXXXX is your user ID (we will provide you with this before the first exercise).

  • X-Server
    This depends on your version of Mac OSX:
    • OSX version 10.8: Download and install XQuartz
    • OSX version 10.5 - 10.7: the X11 application is already installed by default.
    • OSX version 10.3 - 10.4: X11 is either on your install disk or you will have to download it from Apple and install it. Check this page for instructions.

    UNIX/Linux computers:

    Not only do you already have ssh and X11 installed and running, you probably even understand what they do!