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Basics

What is PATH?

PATH comes up frequently in documentation describing Linux administration tasks, troubleshooting threads, etc. PATH is an environmental variable that describes where executable files (software) might be located in a system, so that when you type mkdir into the bash shell, the system knows where to look to find the program mkdir.

You can see your PATH at any time by using $ echo $PATH. The output is a list of directories that contain executable files separated (delimited) by a colon ':'.

Module usage on HCC primarily relies on PATH modification. For example, when you first log on, your PATH might look like this:

/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:
/util/opt/bin:/opt/puppetlabs/bin:/home/biocore/your_user_name/bin

Then, when you load a module, additions are made to your path:

$ module load qiime2/2019.10
$ echo $PATH
/util/opt/anaconda/deployed-conda-envs/packages/qiime2/envs/qiime2-2019.10/bin:
/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:
/sbin:/util/opt/bin:/opt/puppetlabs/bin:/home/biocore/your_user_name/bin

Important Notes

  • Within this wiki, any time that you see a $ at the beginning of a line of a code block, this indicates that the line is meant to be run in a bash shell under a non-root user account. Any time that you see a # at the beginning of a line of a code block, this indicates that the line is meant to be run in a bash shell as root (or as a user using sudo).