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: 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/ )

Log into the HPC

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:

Display list of files/directories in a directory

Print working directory

Go to a sandpit folder

check available files and folders

Create a folder

Enter new folder

Move back to the previous folder(s)

Make a backup copy of the file

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)

Go back to my personal space. Type 'cd' and hit enter. This will move you to /home/mystudentID/

(Optional) Interactive session:

Create a folder to download data from ENA

Move to the data folder:

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