This page provides a basic introduction to Unix commands to HPC users with no previous knowledge.
Pre-requisites:
Review this 1 hour long detailed introduction to VIM editor: https://www.youtube.com/watch?v=IiwGbcd8S7I
Log into the HPC
ssh userID@lyra.qut.edu.au
Brief basic Unix commands
Once you log into the HPC, you will land in your personal home space (i.e. /home/myStudentID/). This space is only accessible to you. To work in collaboration with others we use workspaces (i.e. /work/myProjectName/).
To go to a shared directory for your project named “kenna_team” type the following command and hit enter:
cd /work/trtp
Display list of files in a directory
ls -lh
Print working directory
pwd
Go to a sandpit folder
cd sandpit/
check available files and folders
ls -lhtr
Create a folder
mkdir myname mkdir myname/data
Enter new folder
cd myname/data #check working directory path pwd
Move back to the previous folder(s)
cd .. cd ../../
Make a backup copy of the file
cp launch_ENA_download.pbs ./myname/data #check that file has been copied ls -lh ./myname/data
View the content of a file (note hashtags # at the start of a line is used to provide information of the code underneath it - the commented lines are not executed)
#hash tags are used to add comments on what a command line does
#several commands can be used including cat, less, more, head and tail
cat myfile_copy.txt
#example: less -S allows to visualise very large (wide) files
less -S myfile_copy.txt
#stop viewing a file using the above command
--> Type “Control” and “c” at the same time.
Or “Control” and “d” at the same time.
#print the first 5 lines of a file
head -5 myfile_copy.txt
#print the last 5 lines of a file
tail -5 myfile_coy.txt
Go back to my personal space. Type 'cd' and hit enter. This will move you to /home/mystudentID/
cd
Interactive session:
qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb
Downloading public RNA-seq data from ENA
Go to the following directory
cd /work/trtp/sandpit/myname/data