Introduction to Bash

Course Homepage
April 2019

This project is maintained by UofABioinformaticsHub

Important

If you are running a University administered machine, you will hopefully have pre-configured your machine. The following installations will only be able to be performed if you have Administration privileges on your computer. If you have not pre-configured your machine, we will provide you with an USB containing a live install of Ubuntu for you to use.

Installing Bash on Windows

  1. Download and install git bash by going to the following site: https://git-for-windows.github.io/ and selecting the Git-2.xx.x-(32|64)-bit.exe file as is appropriate for your computer. If you’re unsure if you have a 32 or 64 bit computer, follow these instructions
  2. Please install to C:\Program Files\Git (the default). If you do install elsewhere please change any file paths below accordingly.
  3. Accept all defaults until you see the following screen. Please use the drop-down menu to select nano as the default editor instead of vim.

  1. When presented with this screen during installation, select the first option

  1. Accept defaults for all other options, especially the following:

Installing Notepad++

Although we may not use this much today, an excellent alternative editor for scripts on the Windows OS is Notepad++. A key difference between Windows and Linux/OSX systems is the hidden characters used to denote end-of-line (EOL). Most editors such as Wordpad, MS Word etc will change these without you knowing and scripts will not be able to be run if edited using these programs. Notepad++ does not do this and using this software will allow you to edit scripts conveniently without breaking them.

Notepad++ can be obtained from here

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