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#General Notes on Bioinformatics  ##Command Line/Terminal Tutorial  This workflow is written assuming that the user is using a Mac or Linux. It is possible to perform much of this workflow in a Windows environment but would require details outside the scope of this project.  Some parts of this workflow require use of the UNIX command line. While potentially intimidating to the first-time user, we have attempted to provide all the information required to run scripts or software in this environment.  Here are a few simple commands needed for this workflow.  To access the command line on a Mac navigate to Applications > Utilities > Terminal  A terminal window will appear. In the terminal window, you can interact with your computer without using a mouse. Many of the popular  programs that are commonly used in common use  have a GUI (Graphical User Interface,) but many of the ones 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. 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. More information on the terminal  For more information on operating in the terminal, check out  this video:  http://comailab.genomecenter.ucdavis.edu/index.php/Video 
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http://www.ee.surrey.ac.uk/Teaching/Unix/  ##Summary of commands and terms  $ ls **ls**  lists files and directories (folders) in directory you are currently in $ cd use to change directories