mkatari-bioinformatics-august-2013-introlinuxnotes
This is an old revision of the document!
Manny's Bioinformaics Workshop
Some useful information about linux
Environment variables and PATH
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
mkatari-bioinformatics-august-2013-introlinuxnotes.1376409597.txt.gz · Last modified: 2013/08/13 15:59 by mkatari