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#General Notes on Bioinformatics  Command ##Command  Line/Terminal Tutorial 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. 
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Summary ##Summary  of commands and terms $ ls lists files and directories (folders) in directory you are currently in  $ cd use to change directories 
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$ less file_name view a file  command line – the command line is where you type commands in a terminal window  script – a computer program. Usually computer programs are called scripts when they perform relatively simple functions that are limited in scope. Scripts are typically only run from the command line  directory – a folder  Software ##Software  updates Software packages are updated with varying frequencies. Some software updates will render the instructions offered here obsolete. When this occurs, you should consult with the software manual for help, or an internet search with a description of the problem you are having can prove helpful. Another option is to email the software developer; many are remarkably responsive. As a last resort, consult with a colleague who is more comfortable with bioinformatics. It is customary to offer a small favor or gift. Most software updates will require only minor modifications. For example, we might provide you with instructions to type:  ./software_1.2.0/software.py