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Introduction to Bash Scripting and HPC Scheduler



  • Familiarity with terminal and basic linux commands
  • Some knowledge on shell environment variables and for loops
  • Ability to use a terminal based text editor such as nano
    • This is not much of an issue as we are using JupyterHub which has a more friendlier text editor.
  • Intermediate level knowledge on Molecular Biology and Genetics

Recommended but not required

Some of the things we won't cover in this workshop


Workshop material is designed to run on NeSI Mahuika cluster via Jupyter. Instructions on how to Set/Reset Authentication factors to access NeSI Services and Jupyter Login instructions can be found here


Lesson Overview
Background Objective of this workshop
1. Designing a Variant Calling Workflow Develop and test the steps involved in calling variants
2. Automating a Variant Calling Workflow Compile a script based on the above steps
3. RNA-Seq Mapping And Count Data Workflow Develop, test & compile a script for mapping reads and counting transcripts in a RNA-Seq data analysis pipeline
4. Introduction to HPC Introduction to High Performance Computing
5. Working with Job Scheduler Introduction to HPC Job Schedulers, Slurm Scheduler & life cycle of a Slurm job, Assessing resource utilisation and profiling
6. Supplementary #1
7. Supplementary #2
8. Supplementary #3