UNIX Shell Half Day Workshop

Who: Titus Brown (instructor), Catalina Anghel (TA)

When: November 29th, 2016

Times: 9:15am-12:15pm

Where: 1043 Valley Hall, UC Davis campus

Cost: there is no fee.

Contact the instructor with any questions.

This workshop is open to everyone, including graduate students, postdocs, staff, faculty, and community members. We have extra space for UC Davis VetMed affiliates; contact the lead instructor if you are an SVM affiliate.

In-class Etherpad


This half day workshop will provide an introduction to the bash shell. The shell is a very powerful tool for using scientific software and working with large data sets. It is primarily used to manage files and run programs, and it allows for automation of repetitive tasks.

Topics overview

  • Introduction to the UNIX shell
  • Navigating the filesystem
  • Managing and manipulating files
  • Scripts


  • 9am-10:30a: Introduction, navigation, file manipulation
  • 10:30a: Coffee break
  • 10:45a-12:15p: Scripts

Installation instructions

The Bash Shell


  1. Download the Git for Windows installer here.

  2. Follow install instructions.

    • Click “next”
    • Click “next”
    • Click “next”
    • Click “next”
    • Click “next”
    • Select “Use Git from the Windows Command Prompt” and click on “next”. If you forget to do this, re-run the installer and select the correct option.
    • Click “next”, keep “Checkout Windows-style, commit Unix-style line endings” selected.
    • Select “Use Windows’ default console window” and click on “next”
    • Click on “next”
    • Click on “finish”

There is a video tutorial under “The Bash shell - Windows” on this page if you run into trouble.

Mac OS X: nothing needs to be installed.

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.