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Some parts of this workflow require the user to provide text instructions for software programs by using a command line interface. While potentially intimidating to computer novices, the use of command line interfaces is sometimes necessary (_e.g._, some programs do not have graphical interfaces) and is also sometimes much more efficient. To access the command line on a Mac open the Terminal program (the default location for this program is in the "Utilities" folder under "Applications").  When this application is launched a new window will appear. This is known as a "terminal" or a "terminal window." In the terminal window, you can interact with your computer without using a mouse. Many popular programs have a GUI (Graphical User Interface) but some programs used in this workflow will not. So, instead of double-clicking to make a program run, you will type a command in the terminal window. Throughout this tutorial, we will instruct you to type commands, but copying and pasting them (when possible) will reduce the occurrence of typos.  We will walk you through how to run all of the programs required for this workflow, but you must first acquire a basic familiarity with how to interact with your computer through the terminal window. Below is a list of commands that will be required to use this workflow. There are many tutorials available to help you get started. For more information on operating in the terminal, check out  this informative video: https://www.youtube.com/watch?v=zRZT4nQP3sE