Data Science with R for the Life Sciences

Computer Setup

WIS 6934 students will need their own laptops set up with R by week 2, Git by week 10, and SQL by week 13.

R

Download and install the R base system and RStudio. Both are needed. Installing RStudio will not automatically install R.

GitHub

  1. Create an account on GitHub (https://github.com) using the Sign up for GitHub form on the right side of the page.
  2. Send your username to your instructor.
  3. Once your instructor adds you to the course GitHub organization you will receive an email asking you to accept the invitation. Click on the link to accept.
  4. Check if this worked
    1. Go to https://github.com.
    2. Sign in if necessary.
    3. In the upper left corner click on the drop down with your name.
    4. Confirm that the name name of the course GitHub organization is present

Git

Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on “Next”.
    2. Click on “Next”.
    3. Keep “Use Git from the Windows Command Prompt” selected and click on “Next”. If you forgot to do the integration with R will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on “Next”.
    5. Keep “Checkout Windows-style, commit Unix-style line endings” selected and click on “Next”.
    6. Keep “Use Windows’ default console window” selected and click on “Next”.
    7. Click on “Install”.
    8. Click on “Finish”.
  3. Check if the installation is working:
    1. Send your username to your instructor. Once you have received a GitHub invite to the class organization accept it and only then proceed.
    2. Open RStudio
    3. File -> New Project -> Version Control -> Git
    4. On the page called Clone Git Repository paste https://github.com/dcsemester/install-test.git into the “Repository URL:” box.
    5. Click “Create Project”
    6. Enter your GitHub username and password when prompted
    7. If you see no errors and a file named SUCCESS.txt in your Files tab then everything is setup correctly.

If git and RStudio aren’t talking to each other (i.e., you don’t get the expected result from when you check the installation), try the following:

  1. Open RStudio
  2. Select the Tools menu -> Global Options -> Git/SVN
  3. Next to Git executable click Browse
  4. Navigate to C:\Program Files\Git\bin\ and double click on git (this should change the value in Git executable to C:\Program Files\Git\bin\git)
  5. Click OK

Do not change the git executable to C:\Program Files\Git\mingwXX\bin\git as this will fail on some systems with an error message including “rpostback-askpass”.

Mac OS X

  1. Open up the Terminal, type in “git” and press enter.
  2. This should cause a pop-up window to appear. It will have several options; click on “Install” (not “Get Xcode”).
  3. Click “Agree”.
  4. When the install is finished, click “Done”.
  5. To make sure this worked, type in “git” in the Terminal and press enter. Some information will come up, including a list of common commands. If this doesn’t work see additional instructions below.
  6. Check if git and RStudio are talking to each other:
    1. Send your username to your instructor. Once you have received a GitHub invite to the class organization accept it and only then proceed.
    2. Open RStudio
    3. File -> New Project -> Version Control -> Git
    4. On the page called Clone Git Repository paste https://github.com/dcsemester/install-test.git into the “Repository URL:” box.
    5. Click “Create Project”
    6. Enter your GitHub username and password when prompted
    7. If you see no errors and a file named SUCCESS.txt in your Files tab then everything is setup correctly.

If the git installation didn’t work (i.e., you don’t get the expect result from Step 5), try the following:

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent “mavericks” installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled “snow-leopard” available here

If git and RStudio aren’t talking to each other (i.e., you don’t get the expect result from Step 6), try the following:

  1. Open RStudio
  2. Select the Tools menu -> Global Options -> Git/SVN
  3. Next to Git executable click Browse
  4. Navigate to usr/local/bin/ and double click on git (this should change the value in Git executable from /usr/bin/git to /usr/local/bin/git)
  5. Click OK

Linux

Git is probably already installed. If it is not already available install it via your distro’s package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

SQL

Download and install DB Browser for SQLite

Python

Python installation is not required for WIS 6934. Python materials on this site are no longer under active development.

Download and install the Anaconda Scientific Python Distribution. I recommend you use a special editor like the Wing Intelligent Development Environment - 101.