Advanced Linux and Shell Scripting for biologists

March 20, 2020 - 12-4pm
Melbourne Bioinformatics Boardroom, Ground floor, 187 Grattan St, Carlton

Workshops

Advanced Linux and Shell Scripting for biologists

Overview

Presenter – Lev LaFayett, Research Computing Services

Job submission scripts in Slurm allocate resources and computation in batch mode. Job submissions can be made more powerful and flexible with a working knowledge of shell scripting and more advanced Slurm commands.

This workshop covers advanced Linux commands, regular expressions and regex tools, various shells, the use of variables, loops, conditional statements, the incorporation of shell scripting knowledge in job submission scripts, and autogenerating scripts with heredoc.

Learning objectives

By the end of this training, participants will understand:

• popular file compression and archiving tools.

• a range of extended redirection tools, metadata characteristics of files and filetypes, permissions and ownerships.

• the use of regular expressions and meta-characters with the searching capabilities of the grep utility.

• the concept of the shell environment and its relationship to the hardware and applications.

• the use of variables in the bash shell, how to incorporate these in shell scripts. Including loops and conditional statements.

• how to incorporate Linux commands and shell scripting knowledge in job submissions scripts

• and more…

Prerequisites and requirements

Knowledge of basic linux commands is required prior to attending this course, and participants are encouraged to attend the ‘Introduction to Linux and HPC for biologists’ workshop on March 19th if they have no prior linux experience.

This is a hands-on workshop and attendees must bring their own charged laptop to the workshop and have done the following:

  • aquired Access to Uniwireless/Eduroam
  • if you have an MS Windows machine, install the SSH client PuTTY. (Linux and Macs do not require any action.)
  • join ‘punim0001’ using your Spartan account: http://dashboard.unimelb.edu.au/karaage.