Introduction To Shell/Unix
Many software don't have a graphical user interface (or GUI) that users can use to run a pipeline. Instead many of these tools are only available through the command line interface. To use the command line interface you will need to know shell commands - which is exactly what we will cover here!
Learning Objectives
Getting To the Terminal
Getting to a shell terminal will be different based on whether or not you have a Mac or a Windows machine:
- Mac: Click the Terminal icon on your application bar at the bottom of your screen to open a shell terminal
- Windows: I recommend using a program like MobaXterm. MobaXterm is an enhanced terminal for Windows machines that allows you to use Unix commands. This is useful because many bioinformatics programs are written for Unix shells!
What is a Command?
When working with command line you will need to use "commands" to perform tasks. You can think of a command as the same thing as a click using a mouse - you can open a file/folder, move between folders, edit a file, etc.. However, commands on command line are far more powerful and can automate all this clicking. A command has the following structure:
command [options] [arguments]
Explanation of Terms
commandname of the command you'd like to use[options]options you can input to modify the original command[arguments]the inputs you'd like the command to work with
Data For Today's Tutorial
To get started let's copy some data to get started! So in command line enter the following code to copy data to your computer:
wget https://github.com/BioNomad/omicsTrain/blob/main/docs/programming_languages_tools/unix/unix_tutorial.zip
The wget command can be used to pull most files from the internet! However this file is compressed (ends in either .zip,.tar, or .tar.gz), meaning we can't access the files yet. To uncompress our data let's use the unzip command:
unzip unix_tutorial.zip