Logging on to CBS system

Simon Rasmussen - June 2012

Overview

In this exercise we will prepare our computers to log on to the CBS system.

Student accounts

To be able to perform the exercises and project you will need an account to log in to the CBS computers. Open the google doc, select a student id and fill in your information. This will be your account that you must use for the rest of the course.

Databar computer

If you are using the terminal in the databar you need to do a couple of things before you can log on. First log in using your DTU login and password, this will take you to the desktop screen of the computer. Click "Start", "All Programs", "Installation of programs" (in the top of the menu) and a new window will open. Here Click on "Terminal" and install (double-click) "Xming" and when it is done installing, install "SSH Secure Shell".
Now in the "Start" and "All programs" menu there is now "Xming" and "SSH Secure Shell" icons, click on the "Xming" icon inside the "Xming" menu. Next hover mouse over "SSH Secure Shell" and open "Secure Shell Client". This will open the SSH terminal program that we need to use to connect to the server.

Click "Profiles" and "Add Profile", set the name of the profile to "Padawan" and press enter. Click "Profiles" again and chose "Edit profile". In the "Host name" field enter "padawan.cbs.dtu.dk" and you user name in "User name", it will be studXXX - remember to change studXXX to your number and click "OK". Open the profile again and click on the "Tunneling" tab, click "Tunnel X11 Connections" and press "OK". Now your computer should be set up for loggin in to CBS.

Now click "Profiles" again and chose "Padawan". Type in your CBS-password and press ok when it ask for your authentication response. Now you are logged in to the system.

Your own computer

You can either use a netcable from one of the databar computers, if it is not being used, and plug it into your own computer or use the wifi. Join the wifi "dtu" and fill in your DTU-login and password in the box that opens (Mac) or on the webpage you are taken to (Windows).

Go to Setting up your own computer for the course and follow the instructions there. This requires you to install "SSH - Secure Shell" and "Xming". Set up the SSH program as described in "Set up SSH client" above.

Open the "X11" and "Terminal" in the "Applications/Utilities" folder. You can close the window that the X11 program opens, but leave the program running in the background. In the terminal write "ssh -Y studXXX@padawan.cbs.dtu.dk" and enter your password when asked for it.

You probably already know how to log in to the system, but if you are not using the "studXXX" login you need to add a few lines to your ~/.cshrc file in order to have the program files in your path. Open ~/.cshrc with nedit and add the lines:

if ((`uname -n` == padawan)) then
   setenv PATH /home/local1/27626/bin/:${PATH}
   setenv LD_LIBRARY_PATH /home/local1/27626/lib/:${LD_LIBRARY_PATH}
endif

Going to work folder

When you log in you will be in your home, you need to go to the folder where we will do all exercises. This is done below using the change dir command (cd) and the make dir command (mkdir). NB you need to change the studXXX to your own number. When you are going to do any exercise you always have to change to this dir first. This can be done by "cd /home/local/ngs_course/studXXX" (again change studXXX to your number).

cd /home/local/ngs_course/
mkdir studXXX
cd studXXX

Try to run the command below. The output of the command should be "/home/local1/27626/bin//bwa". If not please contact a teaching assistant.

which bwa