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Software Installation Guide

We need three software components: git, R and Python 3. The Python component also require two add-ons: Jupyter Notebook and NLTK.

Troubleshooting

If you run into problems, please:

  • Email the instructors. Note your OS (Windows? Mac?) and give us a description of how and where you are stuck. Screenshots work wonders.
  • On the workshop day, arrive early at 8:30am. The instructors will be ready to get hands-on with your laptop.

Git and GitHub

Git is an open-source version control system and runs locally on your machine. To install, head to https://git-scm.com/downloads. During installation, make sure to get certain settings right:

  • We don't need GUI clients: there is no need to install one.
  • Default editor: (Screenshot) You don't want to use Vim! Choose your favorite editor in the drop-down menu (Sublime Text, Notepad++, Atom, etc.) if you already have one installed. If you are not sure, pick Nano.
  • (Windows users only) Line ending conversions: (Screenshot) Choose the "Checkout as-is, commit Unix-style line endings" option.
  • For all other options, the default setting should work best for most users.

Signing up for a GitHub Account

GitHub accounts come in different levels. The free account allows you to create public repositories and collaborate with others; you can even have private repositories that only you and your collaborators can see (although you are limited to 3 collaborators).

  • Go to https://github.com
    • Create a username, supply an email (best to use .edu email) and password.
    • Choose the Free account and click Continue and then Submit
    • You now have a GitHub account

While at it, it's also a good idea to apply for "Educational Discount", available to faculty and students, which bumps you up to the "Pro" level access for free. Follow these steps to apply:

  • Go to https://education.github.com/
    • Click on Get benefits button in the upper right corner
    • Fill out the questions (select Individual account for question 2) and click Next
    • Then fill out your name, university issued email address, name of school, and a brief description of how you plan to use GitHub.
    • Click Submit request and GitHub will email instructions for the rest of the process.

Python 3

There are a LOT of Python distributions and therefore many ways to install Python. Two recommended options:

  • If you are completely new to Python, you should install Anaconda Python. It includes all necessary Python add-ons. (OPTION 1)
  • If you already have a working copy of Python 3 on your machine, you can install Jupyter Notebook and NLTK separately via pip. Recommended for advanced users. (OPTION 2)

OPTION 1: Install everything through Anaconda

Anaconda has the advantage of already including popular scientific libraries such as NLTK. It also includes the Jupyter Notebook interface.

  • Go to Anaconda Python's download page: http://www.anaconda.com/download/ Current version is 5.3.1.
  • Make sure you download and install the Python 3.7 version. Important!
  • 64-bit vs. 32-bit: if your system can handle it (most modern systems can), we recommend 64-bit.
  • Double-click the downloaded setup file to start the installation process. Details:
    • The setup file is 600MB; You will need 3GB of space on your hard drive.
    • Ignore away: a question about installing Visual Studio Code, a "Get the cheat sheet" dialog box popping up asking for your email, and a message about signing up for Anaconda Cloud.
    • The default settings and options should work fine for most of you.
  • Depending on your system, Anaconda may take a while to install. Once it finishes, check your installation:
    • Find Anaconda Navigator in your start menu (or Applications folder on Mac), launch it
    • Launch Jupyter Notebook
    • Jupyter opens up as a tab in your browser (Safari, Chrome, FireFox, etc.). You should be able to see your personal folders such as Desktop and Documents.

OPTION 2: Already have Python, add on components separately

If you already have a working copy of Python 3 on your machine (perhaps you installed python.org version of Python at some point), then you have a choice:

  1. Keep your existing Python copy, and install the Anaconda version separately. Both copies of Python will work independently. To go with this option, follow the Anaconda installation instructions above.
  2. Add NLTK and Jupyter Notebook to your existing Python 3. This is a sensible thing to do! Follow the instructions below. It assumes you are familiar with pip.
    • In your console window (cmd for Windows, Terminal for Mac), use pip3 to install the two add-on components:
    • Install NLTK: pip3 install nltk
    • Install Jupyter Notebook: pip3 install jupyter
    • If it did not work, pip3 is not in your system's path. Google for solutions or install Anaconda instead.
    • If installation went fine, verify your setup:
      • In your console, use the commandjupyter notebook to launch jupyter. It will open a tab in your default browser.
      • On the right-hand side, click on "New", choose "Python 3". Another tab will open up.
      • In the top cell, type in import nltk, and then hit the play ▶ button on top.
      • If there is no error message, your installation was successful.

R and R Studio

There are two options for installing R and RStudio.

  1. If you plan to install Python 3 with Anaconda, you can simply Install R and RStudio using Anaconda Navigator (Choose Option 1).

  2. However, if you don't plan to install Anaconda, it's quite simple to install R and RStudio (Choose Option 2).

OPTION 1: Install RStudio as a part of Anaconda

Anaconda doesn't install RStudio by default, so you need to install it. Luckily, it's quite simple.

  • In the Anaconda Navigator window, click Install RStudio (1.1.456 version)
  • It will take some time to install, there's a progress bar in the lower right corner to show it's working
  • You may also be asked to update Anaconda Navigator; it's okay to install and relaunch
  • Lauch RStudio and desktop app will open

OPTION 2: Install R and RStudio

R and RStudio are downloaded and installed separately.

  1. Download R from https://cran.r-project.org/
    • Select the appropriate version of R for your machine, which takes you to another page
    • Mac Users:
      • Under the heading Latest Release download R-3.5.1.pkg and run the installer
      • It is also a good idea to download and install XQuartz (https://www.xquartz.org/)
    • Windows Users:
      • Under the heading Subdirectories select base
      • Then, select Download R 3.5.1 for Windows and run the installer
  2. Download R Studio from https://www.rstudio.com/products/rstudio/download/
    • Select the free download and choose the appropriate installer for your machine
    • Run the installers
    • Mac Users simply drag the RStudio.app file into your Applications folder