Mastering Python for Bioinformatics

Appendix B. Understanding $PATH and Installing Command-Line Programs

PATH is an environment variable that defines the directories that will be searched for a given command. That is, if I type foo and there’s no built-in command, shell function, command alias, or program anywhere in my PATH that the shell can execute as foo, I’ll be told this command cannot be found:

$ foo
-bash: foo: command not found

In Windows PowerShell, I can inspect the PATH with echo $env:Path, whereas on Unix platforms I use the command echo $PATH. Both paths are printed as a long string with no spaces, listing all the directory names separated by semicolons on Windows or by colons on Unix. If the operating system didn’t have some concept of a path, it would have to search every directory on the machine for a given command. This could take minutes to hours, so it makes sense to restrict the searching to just a few directories.

Following is my path on my Macintosh. Note that I have to put a dollar sign ($) in front of the name to tell my shell (bash) that this is a variable and not the literal string PATH. To make this more readable, I’ll use Perl to replace the colons with newlines. Note that this command will only work on a Unix command line where Perl is installed:

$ echo $PATH | perl -pe 's/:/\n/g' 
/Users/kyclark/.local/bin 
/Library/Frameworks/Python.framework/Versions/3.9/bin  /usr/local/bin ...