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setup.Rmd

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@@ -18,9 +18,9 @@ By the end of the chapter, readers will be able to:
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## Installing software on your own computer
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In this section we will provide instructions for installing the software
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required by this book on our own computer.
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Given that installation instructions can vary widely based on the computer setup
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This section will provide instructions for installing the software required by
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this book on our own computers.
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Given that installation instructions can vary widely based on the computer setup,
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we have created instructions for multiple operating systems.
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In particular, the installation instructions below have been verified to work
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on a computer that:
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**For macOS users only:** Apple recently changed the default shell in the terminal to Zsh.
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However, the programs we need work better with the Bash shell. Thus, we recommend you change
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the default shell to Bash by opening the terminal
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([how to video](https://youtu.be/5AJbWEWwnbY)) and typing:
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([how-to video](https://youtu.be/5AJbWEWwnbY)) and typing:
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```
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chsh -s /bin/bash
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controlling your projects, as well as sharing your work with others.
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**Windows:** To install
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Git on Windows go to <https://git-scm.com/download/win> and download the windows
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version of git. Once the download has finished, run the installer and accept
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Git on Windows, go to <https://git-scm.com/download/win> and download the Windows
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version of Git. Once the download has finished, run the installer and accept
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the default configuration for all pages.
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**MacOS:** To install Git on Mac OS open the terminal and type the following command:
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**MacOS:** To install Git on Mac OS, open the terminal and type the following command:
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```
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xcode-select --install
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```
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**Ubuntu:** To install Git on Ubuntu open the terminal and type the following commands:
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**Ubuntu:** To install Git on Ubuntu, open the terminal and type the following commands:
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```
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sudo apt update
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### Miniconda
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To run Jupyter notebooks on our computers we will need to install a program
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To run Jupyter notebooks on our computers, we will need to install a program
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similar to the one we used as our web-based platform. One such program is
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JupyterLab. But JupyterLab relies on Python; we can install this via
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the [miniconda Python package distribution](https://docs.conda.io/en/latest/miniconda.html).
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Once the download has finished, run the installer and accept the default
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configuration for all pages. After installation, you can open the Anaconda Prompt
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by opening the Start Menu and searching for the program called
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"Anaconda Prompt (miniconda3)". When this opens you will see a prompt similar to
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"Anaconda Prompt (miniconda3)". When this opens, you will see a prompt similar to
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`(base) C:\Users\your_name`.
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**MacOS:** To install miniconda on MacOS, download
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bash path/to/Miniconda3-latest-Linux-x86_64.sh
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```
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> Note: most often this file is downloaded to the Downloads directory, and thus the command will look like this:
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> Note: most often, this file is downloaded to the Downloads directory, and thus the command will look like this:
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> ```
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> bash Downloads/Miniconda3-latest-Linux-x86_64.sh
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> ```
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The instructions for the installation will then appear:
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(1) Press Enter.
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(2) Once the licence agreement shows, you can press space scroll down, or press `q` to skip reading it.
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(2) Once the licence agreement shows, you can press space scroll down or press `q` to skip reading it.
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(3) Type `yes` and press enter to accept the licence agreement.
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(4) Press enter to accept the default installation location.
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(5) Type `yes` and press enter to instruct the installer to run `conda init`, which makes `conda` available from the terminal/shell.
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This section will help you
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save your work from the JupyterHub web-based platform to your own computer.
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First in JupyterHub, open a terminal by clicking "terminal" in the Launcher tab.
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First, in JupyterHub, open a terminal by clicking "terminal" in the Launcher tab.
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Next, type the following in the terminal to create a
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compressed `.zip` archive for the work you are interested in downloading:
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