This is an old revision of the document!
Back to Manny's Bioinformatics Workshop Home
What is Linux ?
It is a free and open source operating system released in 1991 under the GNU GPL license.GPL allows anyone to use, modify and redistribute with the requirement that they pass it on with the same license.
It is the leading operating system of choice for servers such as supercomputers. More than 90% of the top 500 fastest computers are based on Linux.
MAC computers are related to Linux because they are also based on UNIX
Depending on the purpose of the Linux machine, it may or may not have a Desktop environment that we are familiar with on our personal computers. Linux uses X Window System to provide the Desktop environment.
A popular distribution of Linux operating system is called Ubuntu.
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