All variables that are set in your environment can be found by using

env

The variable that is most important to us is PATH. The PATH is where the computer is looking for the commands. To see the contents of the variable type:

echo $PATH

In the sbatch files we have been adding the full path to the commands. Another option is to add the full path of the command you want to use to the variable PATH. This is what module load essentially does.

For example the following two commands are equivalent.

export PATH=/export/apps/samtools/0.1.19/bin:$PATH

module load samtools