PATH and export

In the previous lesson you saw that $PATH is the list of directories the shell searches when you type a command name. It is worth understanding properly, because "I installed it but the shell says command not found" is something you will hit again and again.

$ echo $PATH
/usr/local/bin:/usr/bin:/bin

When you type samtools, the shell looks in /usr/local/bin, then /usr/bin, then /bin, and runs the first match it finds. If it looks in all of them and finds nothing, you get command not found. The directory you are currently standing in is not on that list, which is why running your own script needs the ./ prefix.

Two commands tell you what is going on. which shows you which one the shell would actually run:

$ which samtools
/usr/local/bin/samtools

and type -a shows all the matches, in search order, which is how you diagnose the case where you have two versions installed and are getting the wrong one:

$ type -a python
python is /home/pete/miniconda3/bin/python
python is /usr/bin/python

The first line wins. Order matters: earlier directories in PATH shadow later ones.

To add a directory, assign a new value that includes the old one:

$ PATH=$HOME/bin:$PATH

Read that carefully. It puts $HOME/bin at the front, then a colon, then everything that was already there. Keeping the old $PATH is the whole trick. If you write PATH=$HOME/bin and forget the rest, you have just thrown away every directory the system needs, and almost nothing will work until you open a new shell.

Putting your directory first means yours wins over the system version. Putting it last, PATH=$PATH:$HOME/bin, means the system version wins. Choose deliberately.

Now, the export part. A plain assignment only affects your current shell. Programs you start do not see it:

$ MYVAR=hello
$ bash -c 'echo $MYVAR'

$ export MYVAR=hello
$ bash -c 'echo $MYVAR'
hello

export marks a variable to be passed on to any program the shell starts. Since PATH needs to be seen by everything, it is always exported:

$ export PATH=$HOME/bin:$PATH

There is still one thing missing. Everything above lasts only until you log out. To make it permanent, put the export line in a file bash reads when it starts. The usual choice is ~/.bashrc:

$ nano ~/.bashrc

and add at the end:

export PATH=$HOME/bin:$PATH

The file is only read when a shell starts, so your current shell will not notice. Either open a new one, or reread it now with source, which runs the file in the shell you are already sitting in:

$ source ~/.bashrc

Which file bash reads, though, is not as simple as that makes it sound, and getting it wrong is the usual reason a PATH change works now and is gone after a fresh ssh login. The next lesson is about those files: which one is read when, what else belongs in them, and how to avoid locking yourself out of your own account with a typo.