The PATH variable • uqsa

This is an explanation about the PATH variable and has a very distant relation to the uqsa package.

It is just generally true about shells (e.g. bash) and can be useful when troubleshooting the model-building procedures. Consult this text when a command is not found.

Locations of Applications

Most unix like systems (*BSD, GNU/Linux, macOS) have a way to find programs: the environment variable called PATH; a colon (:) separated string.

This is a possible value:

echo "$PATH"
#> /home/andrei/.juliaup/bin:/home/andrei/.local/bin:/home/andrei/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin

If you need to actually read it:

echo "$PATH" | tr ':' '\n'
#> /home/andrei/.juliaup/bin
#> /home/andrei/.local/bin
#> /home/andrei/bin
#> /usr/local/sbin
#> /usr/local/bin
#> /usr/sbin
#> /usr/bin
#> /sbin
#> /bin
#> /usr/games
#> /usr/local/games
#> /snap/bin
#> /snap/bin

The package manager of unix-like systems installs applications into places that are listed in the PATH variable. This way they can be found by name, rather than typing out the entire path.

(
cat<<EOF
#!/bin/sh
echo "Hello World"
EOF
) > test.sh
chmod 744 test.sh
[ -f test.sh ] && test.sh
./test.sh && rm test.sh
#> sh: 8: test.sh: not found
#> Hello World

This code-block creates a file (test.sh), makes it executable, and then tries to execute it. This doesn’t work, even though we are in the same directory as the file. But, typing out a relative path ./test.sh, using ., it is found.

Built-in commands

Some commands are shell built-ins (e.g.: echo, printf, pwd), they don’t need the PATH variable at all as they are an integral part of the shell itself (different shells can have slightly different built-ins).

Other commands are distinct, executable files that need to be found (e.g.: env, awk, perl). They can be symbolic links to such files as well.

Here is an example for awk:

type awk
which awk | xargs ls -gG
readlink -f `which awk`
#> awk is /usr/bin/awk
#> lrwxrwxrwx 1 21 Jul  1  2021 /usr/bin/awk -> /etc/alternatives/awk
#> /usr/bin/gawk

So, awk is not a built-in, but a file. The command which can find it, so it is in PATH. It is also a symbolic link, we can follow that link using readlink -f and find out that this particular system is using GNU awk (gawk).

When a program is not in one of the directories in the PATH variable, it can only be called by typing the entire path to it, or using a relative path.

Add locations to PATH

An interactive shell has a startup file:

~/.bashrc for bash
~/.zshrc for zsh (among others)

They also read ~/.profile, which often has something like this in it (if it doesn’t, you can add this yourself):

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/.local/bin" ] ; then
    PATH="$HOME/.local/bin:$PATH"
fi

So, if ~/.local/bin exists, it is appended to PATH, and you can definitely use that location to store shell scripts (just create it).

mkdir -p ~/.local/bin

There is a lot of fine detail related to the concepts of login shell or (non-) interactive shell and what shell reads which files in either of those cases (this is a bit complicated).

IFF still not in PATH

A new entry can be added from within the ~/*rc files, e.g.:

## for bash
[ "$SHELL" == "/bin/bash" ] && echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc
## for zsh
[ "$SHELL" == "/bin/zsh" ] && echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.zshrc