Start by opening the Terminal application, which you can find using the Finder main menu in Go > Applications > Utilities. This will open a terminal running the bash shell (a shell is a program that interprets operating system control commands) on your desktop. Once installed, open Git BASH from the All Programs section of the start menu. Visit the Git for Windows web site, press the Download button, and install Git for Windows on your system. Instead, you will use the Git for Windows bash shell to send commands to the cluster and see the output generated. We will not actually use the “git” part of “Git for Windows”, although it is there in case you need it later. The program Git for Windows provides a terminal that will allow you to communicate with the cluster using a protocol known as SSH (Secure Shell). What programs you use depends upon whether you are going to be using Windows or MacOS. You will be using a couple of simple (and free) programs to communicate with the head node of the cluster.
Obtaining the necessary communications software I will let you know the password at the beginning of lab. from your laptop), check on their status, and download the results when your analysis is finished.
By now, you should have an account on the cluster, and today you will learn how to start analyses remotely (i.e. We will use the Xanadu computing cluster located at the UConn Health Center for most of the data crunching we will do in this course. The UConn Computational Biology Core is part of the Center for Genome Innovation (CGI).
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