Introduction to the command line interface (shell/bash/Unix/Linux)

Audience Computational skills required Duration
Biologists None 3-session online workshop (~7.5 hours of trainer-led time)

Description

This repository has teaching materials for a 1-day Introduction to shell workshop. This workshop focuses on teaching basic skills to use the command line interface, specifically bash, the lessons include for loops, shell scripting, positional parameters. This workshop is a prerequisite to a workshop on RNA-seq analysis.

Note for Trainers: Please note that the schedule linked below assumes that learners will spend between 3-4 hours on reading through, and completing exercises from selected lessons between classes. The online component of the workshop focuses on more exercises and discussion/Q & A.

These materials were developed for a trainer-led workshop, but are also amenable to self-guided learning.

Learning Objectives

  1. Navigate around the command line interface (bash/shell)
  2. Create and manipulate text files
  3. Submit jobs to a high-performance computing cluster

Lessons

Installation Requirements

Mac users: No installation requirements.
Windows users: GitBash

Dataset

Introduction to Shell: Dataset

Citation

To cite material from this course in your publications, please use:

Jihe Liu, William J. Gammerdinger, Meeta Mistry, Mary E. Piper, & Radhika S. Khetani. (2022, January 6). hbctraining/Intro-to-shell-flipped: Shell and HPC Lessons from HCBC (first release). Zenodo. https://doi.org/10.5281/zenodo.5826091

A lot of time and effort went into the preparation of these materials. Citations help us understand the needs of the community, gain recognition for our work, and attract further funding to support our teaching activities. Thank you for citing this material if it helped you in your data analysis.

These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.