Cloud-SPAN Genomics Course: Setup


The software and data used for analysis during the course are hosted on an Amazon Web Services (AWS) virtual machine (VM) instance. A copy of such instance that requires no previous setup by you will be made available to you at no cost by the Cloud-SPAN team.

To accesss and use the resources in your AWS instance from your personal computer, you will use a command-line interface (CLI) program that is widely known as the shell or terminal. The shell is available by default for Linux and Mac users (so they don’t need to install any software).

Windows users will need to install Git for Windows on their computer as described below prior to the course. Git includes Git Bash which is a Windows version of the Unix Bash shell, the most widely used shell and the default shell in Linux systems.

You will need to use a laptop or desktop to take this course. Due to the need both to follow the instructor in zoom and to perform analyses, tablets and ipads are not suitable for using during this course. Having both an up to date browser and a stable internet connection is important.

Before the course you will receive via email the information that you will need to login to your AWS instance during the course.

Installing Git Bash in your Windows computer

The steps below correspond to the installation of Git for Windows version 2.33.1 from scratch. The installation of a more recent version, or updating a previously installed version, may show different wording in the screen messages mentioned below or may vary slightly in the number of steps to follow. Choose as many of the options below as possible.

Run Git Bash by double clicking on the Git Bash icon in your Desktop screen.

Git Bash launch icon

Exit Git Bash by pressing Ctrl-d – that is pressing the keys Ctrl and d simultaneously.

Bash stands for Bourne Again Shell. In addition to be a CLI, Bash shell is a powerful command programming language and has a long and interesting history which you can read in the Wikipedia entry for Bash shell.