What is a shell script?

Understanding how to build pipelines in Unix scripts will help you with consistency and documentation. Bash scripts can string together many processing steps in simple or complex ways. For example, neuroimaging software like FSL and AFNI provide command line tools that can be called from a shell script. Like true programs, shell scripts use variables and control structures, and can take arguments. In fact, if you've played bashcrawl, you've seen what Bash shell scripts can do!
Because you already have experience with Unix commands and configuration, shell scripts are not a big leap.

The shell script should be in your search path: Often, you will put your shell scripts in the bin directory in your home area, and make sure that ~/bin is added to your search path. (Remember, the ~ stands for your home directory).
The shell script is a simple text file that will be interpreted by the operating system. It can even contain a list of unix commands you want to run, just as you would type them at the command line.
Tom Hicks discusses Unix shell scripting concepts in this 6-minute video.

Bash Scripts 1 (5 pts)