Computational Techniques for Life Sciences

Environment Variables

On a Linux system, environment variables are variables that are defined in the current shell, and can be passed into processes that the shell spawns. They have many practical purposes, including but not limited to:

• Point to the locations of executables
• Point to the locations of libraries
• Point to other special locations in the shell
• Provide information about the user to the programs
• Provide other special information to programs

To print all of the environment variables currently defined in your shell, use the env command:

$ env

There are quite a few, many of which you will never need to use. There are some important ones, however. To filter the output, you can print the contents of a specific variable. Use the echo command to print the contents of an environment variable called PATH and you can pipe the output of env to the grep command (more on piping in the next section)::

$ echo $PATH
$ env | grep PATH

Note: The name of the variable is PATH; use $PATH to access the contents of the variable. You can also manually edit the content of environment variables using the export command:

$ echo BLAH                     # this is the variable itself
$ echo $BLAH                    # use $ to access the contents
$ export BLAH="some text here"
$ echo $BLAH

You can edit existing variables as well. The PATH variable, which defines which executables are available to you in your current shell, is often edited by users. We should be careful editing it because it stores the location of our very common commands like ls and cd. If we lose those paths, then it will be difficult to execute commands. Edit the beginning or the ending of the PATH variable as follows (contents at the beginning supersedes contents at the end):

$ export PATH=$PATH:/new/path/to/add
$ export PATH=/new/path/to/add:$PATH

Environment variables can be reset by logging out and in:

$ logout

Piping

Every program we run from the command line has three data streams associated with it:

1. STDIN (0) – Standard input, the data that is fed into the program
2. STDOUT (1) – Standard output, the data that is output by the program
3. STDERR (2) – Standard error, error messages from the program

With piping, we can direct these data streams from one program into another. A pipe uses the operator (|), and takes the output STDOUT from the program on the left, and uses that as the input STDIN for the program on the right.

$ env
$ env | head -n 4
$ env | tail -n 5
$ env | head -n 4 | tail -n 1

Pipes can be used to quickly chain together multiple applications into a pipeline.

Exercise

1. Print the contents of the PATH environment variable.
2. What files exist in some of the directories found in the PATH environment variable?
3. Find an environment variable that stores your username.
4. Store Webster’s dictionary in an environment variable called DICTIONARY.
5. Use a pipeline to search for every word that contains ‘ei’ in the DICTIONARY, and print the 5th word.

Click here for solution

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