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Introduction to Bash Scripting and HPC Scheduler

This as an Introductory level workshop on Bash Scripting and HPC Job Scheduler, Slurm.



  • Familiarity with terminal and basic linux commands
  • Intermediate level knowledge on Molecular Biology and Genetics

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

  • Domain specific concepts in
    • Genetics, Genomics and DNA Sequencing
    • Variant Calling
    • RNA sequencing and data analysis


  1. Designing a Variant Calling Workflow
  2. Automating a Variant Calling Workflow
  3. RNA-seq Mapping And Count Data Workflow
  4. Introduction to HPC
  5. Working with Job Scheduler
  6. Supplementary #1
  7. Supplementary #2
  8. Supplementary #3


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