Command Line Introduction

Working from the command line gives computational biologists access to many analysis tools and enables the creation of reproducible scripts. This workshop will introduce commands for filesystem navigation, teach attendees how to create and edit scripts from the terminal with the text editor nano, and introduce utilities for interacting with our high-performance computer cluster, Quest.

A note on different shell interpreters

Working from the command line involves typing commands into a shell that interpretes it. Different operating systems have slightly different interpreters so we are going to log onto Quest, a Linux system, so that we are all using bash. But, you can work from the command line on your own laptop as well. If it is a Mac, it probably defaults to zsh which is almost identical to bash. And if you're on a Windows and using PowerShell, it is pwsh, which has a few more syntax differences.

Logging onto a remote host

You can use the command ssh to log onto a remote host, such as Northwestern's high performance computer cluster, Quest.

ssh [email protected]
# ssh followed by your username (netid for Quest) @ the host address

This will prompt you for a password, which is your netID password for Quest. It won't look like you are typing, but type it in an hit enter.

Filesystem navigation

Because you're working with only commands and no graphical user interface, it can take some getting used to moving around and accessing your files. A Linux filesystem starts with / as the base directory or folder, and all folders are organized from there.

You can see your current location in the filesystem with pwd. Try it out!

pwd

This is your home directory on Quest.

To list the contents of this folder, use the command ls. This will print out the files and folders in this directory. Generally, files will show up in white and folders will show up in blue.

Many commands can take additional arguments. Try the following:

ls -alh

If your home folder is relatively empty, the effect of these arguments may not be clear but they stand for "all", "long form" and "human-readable". Let's move to a different folder and try it again.

Changing directories is done with the command cd followed by the desired destination. Use the following command to move into the folder for this workshop series.

cd /projects/e32680

Now, repeat the list command with and without the arguments introduced above. What's the difference?

mkdir

touch

cp rm mv

Creating and editing scripts

Quest utilities