Free

Advanced Linux and Shell Scripting for Biologists

Event Information

Share this event

Date and Time

Location

Location

Melbourne Bioinformatics Boardroom

187 Grattan st

Ground floor

Parkville, VIC 3010

Australia

View Map

Event description
Want to take it to the next level?

About this Event

Overview

Presenter - Lev LaFayette

Workshop offered by 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

Most workshops are FREE for all researchers and students from the University of Melbourne and its affiliated research institutes. For details of charges for external participants please see the Melbourne Bioinformatics Training page.

Building Access

Please note that the venue for the workshop, 187 Grattan St (Building 257), does not have an accessible entrance. There are a number of steps leading from street level up to the ground floor entrance and there are no accessible toilets available in the building.

If you have any access requirements in order to participate in this workshop, please contact the workshop organiser (bioinformatics-training@unimelb.edu.au) as soon as possible to discuss your requirements further.

Share with friends

Date and Time

Location

Melbourne Bioinformatics Boardroom

187 Grattan st

Ground floor

Parkville, VIC 3010

Australia

View Map

Save This Event

Event Saved