Task 1: Brief introduction to basic Unix commands

This page briefly introduces Unix commands for HPC users without previous knowledge.

Pre-requisites:

Review this one-hour-long detailed introduction to VIM editor: Vim Tutorial
(optional) Familiarity with one unix text editors (for example Vi/Vim or Nano):
- VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; Editors (Vim))
- Nano (Basic tutorial for Nano users ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

Installing Putty and connecting to the HPC (Windows users; Mac users can directly use the available ‘terminal’ app)

Install Putty:

Installing PuTTY - QUT Media Hub

Connect to the HPC:

Connecting to the HPC with PuTTY - QUT MediaHub

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 team, for example type the following command and hit enter:

cd /work/trtp

Display list of files/directories 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

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

(Optional) Interactive session:

qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb

Create a folder to download data from ENA

mkdir myname/data

Move to the data folder:

cd mynam/data

Go to: Task 2: Download public RNA-seq data