Skip to main content

Software Installation

The necessary software must be installed prior to the workshop. Workshop instructors will NOT be available to help you during the workshop.

Software installation instructions are below. If you need assistance, there will be a software installation clinic on the Evanston campus on Friday, June 22nd in the Research Computing Offices in Mudd Hall, Suite 2220, 12-2pm (on the hallway that runs between Tech and Cook behind the library). If you need assistance and cannot make that time, please contact us for options.

The folks at Data Science Nights can also help you get the software you need installed. Upcoming Data Science Nights are on June 25th and July 30th.

If you do not have administrative rights on your computer (for example, some medical school computers), you may need assistance from your local IT department to install software. Alternatively, web-based options that do not require any software to be installed locally are also available for some workshops.

Python

All Python workshops require Python 3.6 run through Jupyter Notebook. If you’re unfamiliar with Jupyter Notebooks, and you’re not taking the Introduction to Programming with Python workshop, see the Resources page for links to help you get started.

In addition to the instructions below, you may be asked to install additional packages during the workshop.

For Introduction to Programming with Python, you will also need an Integrated Development Environment (IDE). This is an application that allows you to write and run scripts. We’ll be using Spyder, which comes as part of the Anaconda distribution (see below), in the workshop. If you can’t install Anaconda, you can still install Spyder separately as a package (ask an instructor).

Option 1: Install on your laptop

If you already have a different version of Python (for example, 2.7) installed with Anaconda, then installing Python 3.6 and making it available through Jupyter Notebooks isn’t as simple as installing a new version of Anaconda. See Adding Python 3 to Jupyter Notebook. If you have another version of Python installed, but don’t have Anaconda installed, you can follow the instructions below.

We recommend the Anaconda distribution of Python, as it comes with Jupyter Notebooks and many commonly used packages needed in the workshops. Download Anaconda for Python 3.6.

After installing, launch Anaconda Navigator from your Applications folder or Start Menu. Then open Jupyter Notebooks from the Anaconda Navigator menu. This will open a web browser window and a terminal window (or Anaconda prompt). You may need an access code that appears in the terminal (or Anaconda prompt) window to start the program in the web browser window. Once Jupyter Notebooks is open, you’ll see a Jupyter logo at the top of the page and a list of folders on your computer on the page. Click the New button in the upper right and make sure there’s a Python 3 option listed in the New Menu.

Option 2: Use Google Colaboratory Online

Google Colaboratory lets you create and run Jupyter-like Python notebooks online. You can save notebooks to Google Drive and open Jupyter notebooks from Google Drive. See an overview of the system for more details.

This is recommended only as a backup if you’re unable to successfully install Python on your laptop. For the Intro to Programming with Python workshop, you need to have Anaconda installed on your laptop (option 1 above).

R

For all R workshops, you need access to R and RStudio. You may be asked to install additional packages during the workshop.

If you know how to use R, the tidyverse set of packages is needed for several workshops. It takes a while to install, so it’s good to install ahead of time. You can install it from the Packages tab in the bottom right window of RStudio or with the R command:

install.packages(“tidyverse”, repos=”http://ftp.ussg.iu.edu”)

We’ll cover how to install packages in the R: Introduction and R: Refresher workshops, so if you’re new to R, don’t worry about installing any packages ahead of time.

Option 1: Install on your laptop

If you already have R installed, as long as you have a recent version of R with the version number starting with 3.4 or 3.5, you should be fine. For RStudio, we recommend you use a recent version with the version number starting with 1.1.

If starting from scratch, you should install R first, and then install RStudio.

R: Install R

RStudio: Install RStudio Desktop (free)

After installation is complete, open RStudio to confirm your installation.

Option 2: RStudio Cloud

RStudio offers RStudio Cloud to use R and RStudio for free through your web browser. Once you create an account and log in, you’ll need to make a new project to see RStudio. RStudio Cloud is still in alpha release, which means there may be occasional errors or bugs. However, it should be sufficient for the summer workshops. See the Guide for more information on using the service. Note that you can create new Projects from GitHub repositories.

Option 3: Quest

R and RStudio are available as part of the Quest Analytics Nodes. You need a Quest allocation (account) to access the Analytics Nodes; a Research I allocation is where you want to start if you don’t already have a Quest allocation.

Quest allocation requests can take several days to be processed, so you’ll need to apply for an allocation at least a week before your first workshop. You should log into RStudio on the Quest Analytics Nodes before the workshop to ensure you’re able to.

Note that Quest will be offline the week of June 25th for annual maintenance, so you won’t be able to use the Quest Analytics Nodes for the R: Introduction workshop.

Command Line

For this workshop, you need access to a terminal program running a Bash shell.

If you have a Mac, there’s no need to install anything for the workshop. The built-in Terminal program in Applications > Utilities will suffice.

If you have a Windows laptop, we recommend you install and use Git Bash. This gives you access to the Bash commands you’ll use in the workshop, and it will install Git (used for version control) as well.

Databases and SQL

You need three things for this workshop:

  1. An SSH client to connect to a remote server.
    • Mac Users: The Terminal program in Applications > Utilities works, so you don’t need to install a special program
    • Windows Users: If you don’t already have an SSH client, download and install PuTTY
  2. DataGrip: this is a program that makes working with databases easier. It has a free 30 day trial, or you can apply for a free license that gives you access to many JetBrains products.
  3. If you want to connect to a database from R or Python, you will need to install a package to connect to a PostgreSQL database.
    • R: install RPostgreSQL
    • Python: install psycopg2

GIS

Laptops will be provided with the required software for this workshop. Workshop participants who want to install GIS software on their own computers will receive instructions by email.