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Intermediate Shell for Bioinformatics

September 27, 2023 @ 10:00 am – 4:00 pm
Tyler McInnes

This online workshop is hosted by Genomics Aotearoa and NeSI, and is for New Zealand researchers interested in progressing their abilities with Shell.

This workshop will include:

  • An overview of the Shell, UNIX and Linux.
  • Downloading data from a remote source and checking data integrity.
  • Recap navigating files and directories, and commands used in routine tasks.
  • Inspecting and manipulating data, part 1 (the head, less, grep, and sed commands).
  • Inspecting and manipulating data, part 2 (using awk and bioawk to process text).
  • Automating file processing.
  • Challenges: solve example molecular biology problems using shell scripts.

This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:

  • Navigating files and directories.
  • An understanding of full versus relative paths.
  • Working with files and directories (examining files, creating, copying, moving and removing).
  • Use a command line-based text editor such as nano.

And have a basic understanding of:

  1. File/directory permission in Linux.
  2. For loops (preferred, not required).

If you lack the above skills, you can use these sites as a refresher – Introduction to Command Line Carpentries lesson

Setup: This is a fully online, hands-on workshop. The workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants one week prior to the workshop.

You can view the workshop material, including the objectives and content, here:

Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.

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