Data Science in Omics Introduction

An OMICS Course Part 1: Shell, Organizing and Genomics

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Computer Setup

BIOC 6820 students will need their own laptops or desktops set up with Git Bash before the course begins, R and RStudio need to be installed later. You will need an account on the “Pete” HPC at Oklahoma State, and a personal (free) account on GitHub

Shell (most important)

Windows users must download the software Git for Windows which includes a Shell called “GitBash” (The instructions are shown below under GitHub). GitBash is called an ‘emulator’ because it simulates a Linux environment, and all the linux commands we will be using are available inside the GitBash terminal window. As a bonus, it installs “Git” which is a command-line interface you will need later in the course when using GitHub for your data. THis course was developed, maintained, and exists on GitHub.

Mac users are fortunate because they only need to use their “Terminal” program for all “windows” or “shells” we use in this class.

Special Note:

Data Carpentry Genomics Workshop

Part of this course is designed to follow the Data Carpentry Genomics Workshop, which was FIRST previewed in June 2019. In 2022 and beyond, we will not be using the Amazon Cloud Services. Instead, we will be using the Oklahoma State University “Pete” supercomputer from the OSU HPCC. If you have a powerful enough personal computer*, you can follow the instructions at Data Carpentry Option B to install all the necessary software. However, Windows OS users may not be able to use a single linux emulator (e.g. GitBash, Cygwin) but also need to use the Windows 10 (build 14393 or later) Subsystem for Unix-based Applications, to install “Bash on Ubuntu on Windows10”.

* A 4-8 core processor at > 3.0GHz, at least 16Gb of RAM, at least 500Gb of free disk space on an SSD drive (1 Tb recommended).

R

Download and install the most recent 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. Email your username to your instructor.
  3. Once your instructor adds you to the course’s GitHub organization you will receive an email asking you to accept the invitation. Click on the link to accept.
  4. To confirm you are part of the class:
    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

For Windows

  1. Download the latest 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 don’t do this, 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. Open RStudio
    2. File -> New Project -> Version Control -> Git
    3. If you reach a page called Clone Git Repository with some fields to fill out everything is working

For 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.

For 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. Open RStudio
    2. File -> New Project -> Version Control -> Git
    3. If you reach a page called Clone Git Repository with some fields to fill out, everything is working

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, it will not show up in your /Applications folder, because 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