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
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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/).
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Print working directory
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pwd |
Go to a sandpit folder
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cd sandpit/ |
check available files and folders
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ls -lhtr |
Create a folder
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mkdir myname mkdir myname/data |
Enter new folder
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cd myname/data
#check working directory path
pwd |
Move back to the previous folder(s)
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cd ..
cd ../../ |
Make a backup copy of the file
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cp myfile.txt myfile_copy.txt |
Move a copy of a file to a newly created folder - note it is recommended to make a copy of important files prior to modifying or executing commands on them.
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mv myfile_copy.txt myfolder/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)
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#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 505 lines of a file
head -505 myfile_copy.txt
#print the last 205 lines of a file
tail -205 myfile_coy.txt |
Go back to my personal space. Type 'cd' and hit enter. This will move you to /home/mystudentID/
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qsub -I -S /bin/bash -l walltime=10:00:00 -l select=1:ncpus=2:mem=4gb |
Downloading public RNA-seq data from ENA
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Go to the following directory
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cd /work/trtp/sandpit/myname/data |