Installing Anaconda

Linux Anaconda installation

  1. Open https://www.anaconda.com/download with your web browser.
  2. Download the Python 3 64-bit installer for Linux.
  3. Open a terminal window.
  4. Type bash Anaconda3- and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with: cd ~/Downloads. Then, try again.
  5. Press [Enter]. You will follow the text-only prompts. To move through the text, press the [space] key. Type yes and press [Enter] to approve the license. Press [Enter] to approve the default location for the files. Type yes and press [Enter] to prepend Anaconda to your ${PATH} (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.

macOS Anaconda installation

  1. Open https://www.anaconda.com/download with your web browser.
  2. Download and run the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Windows Anaconda installation

  1. Open https://www.anaconda.com/download with your web browser.
  2. Download and run the Python 3 installer for Windows.
  3. Install using defaults for installation except
    • make sure to check Add Anaconda to my PATH environment variable (this is required to work with git bash)
    • make sure to check Register Anaconda as my default Python 3.6.
    • you can skip installation of VSCode (though it is a very nice tool)

Warning

You must select the Register Anaconda as my default Python 3.6 option on Windows.

Post-installation

We need to add some Anaconda channels, which is done by issuing the following commands in the terminal [1]:

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Note

On Windows, you can install these channels using the Anaconda Navigator, a graphical tool provided through your Start Menu on that platform.

Starting the Anaconda prompt (Windows-only)

Once Anaconda has been installed, you can start a terminal that “sees” the Anaconda Python installation as follows:

  1. Click on the Start/Windows menu
  2. Go to Anaconda
  3. Scroll down (if necessary) to Anaconda Prompt
  4. Click on Anaconda Prompt

This will give you a terminal window where you can run the commands to install Python modules and create conda environments.

Note

We will not be using the Anaconda Prompt as our terminal in this workshop as it does not, by default, understand the Bash commands we will be using to navigate the system.

[1]The terminal means either your bash terminal (macOS/Linux), or the git bash terminal (Windows)