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

Prerequisites¶
- 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
Content¶
- Designing a Variant Calling Workflow
- Automating a Variant Calling Workflow
- RNA-seq Mapping And Count Data Workflow
- Introduction to HPC
- Working with Job Scheduler
- Supplementary #1
- Supplementary #2
- Supplementary #3
Setup¶
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