Introduction to Unix

This is meant to provide the resources needed to learn how to use the basic unix command line interface.

What is Unix?

Unix is a basic operating system that is the foundations for many modern computer systems. Most high performance servers run on a particular flavour of linux which relies on unix. In addition, MacOS is built upon Unix. Windows does have a command line interface but it is different from Unix.

The majority of bioinformatic programs do not come with a nice point and click interface, but instead require the typing of commands into a basic computer terminal. This will likely seem archaic and difficult at first, but basic unix interface is very powerful. The basic unix commands will allow you to read files, browse directories, and run programs by typing commands instead of clicking on things.

Getting started

First you need to know how to get to the unix command line, which depends on the type of operating system your computer is running.

For Macs

• There is a program already installed on your system called "Terminal". Simply go to the "Launchpad", search for terminal, and click on the the app.

For Windows

• You can install a unix emulator called https://gitforwindows.org/
• The direct download installed for that program is here: https://github.com/git-for-windows/git/releases/download/v2.40.1.windows.1/Git-2.40.1-64-bit.exe

Logging into a server with ssh

• Within your terminal window you will type 'ssh', followed by your 'username@servername' followed by the server name. So for example if your username was joe and the server was hank.is.cool.ca , you would type:

  ssh [email protected]

• Hit enter, and then you will likely be asked about authenticity of host and whether you want to continue connecting. Hit enter again. Then you will be prompted for your password. Type in your password carefully followed by enter. Note that when typing your password the cursor will not move (it looks like nothing is happening), but be assured whatever your type is being entered.

• If successful, you will have a new prompt and you will from now on be working on the remote server. If this is your first time logging in with a temporary password, you can change that by entering the command "passwd" followed by enter.

  passwd

Tutorials

Ok, once you know how to get to the unix command line you will need to learn the basic commands.

There are several tutorials out there (Google is your friend). For example you could start with this one: https://github.com/KorfLab/unix_and_perl/blob/main/bootcamp.md