Page Comparison

This page provides a basic introduction to briefly introduces Unix commands to for HPC users with no without previous knowledge.

Pre-requisites:

• Review this

...

• one-hour-long detailed introduction to VIM editor: https://www.youtube.com/watch?v=IiwGbcd8S7I

• (optional) Familiarity with one unix text editors (for example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; 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 project named “kenna_team” team, for example type the following command and hit enter:

cd /work/trtp

Display list of files/directories in a directory

ls -lh

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Create a folder

mkdir myname
mkdir myname/data

Enter new folder

cd myname/data

#check working directory path
pwd

...

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

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Create a folder to download data from ENA

...

mkdir myname/data

Move to the following directorydata folder:

cd /work/trtp/sandpit/myname/mynam/data

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