Getting Setup for the Workshop

Computer Setup

The workshop is hands-on data analysis, and in an effort to make the class entirely portable and reproducible, we are providing a Virtual Machine to run the workshop on. A virtual machine is like a small, simplified Operating System that operates within your existing computer and allows for a controlled computing environment.

Alternatively, if you’re comfortable with R and GitHub, you can likely get this analysis to easily work on your existing computer. We’ll provide instructions for setup using both methods below.

Option 1- Installing the virtual machine (Recommended)

First, you need to install the program VirtualBox (it’s free and available at https://www.virtualbox.org/wiki/Downloads). Once the software is installed, please download our virtual machine from this link.

If you’re a MacOS user with newer Apple Silicon Processors (eg. M1 or M2), you’ll need a developmental version of VirtualBox. See here

You can then import the virtual machine following these instructions: 1. Open VirtualBox 2. Click File → Import Appliance
3. Select the file “EOGW_Linux.ova” that you downloaded from Google Drive

After the machine is up and running, please open terminal and type the following commands:

cd 2024_NACE_GenomicsWorkshop/Workshop
git pull

Then you should open RStudio from the menu button by typing rstudio in the search bar

Option 2-

If you have your own RStudio working environment and access to GitHub, you can setup your own computer to perform the analyses that are part of this workshop. You also need to install the program Plink, and make sure to get version 2.

Open Rstudio and type the following in your Console:

install.packages(c("ggplot2", "vcfR", "reshape2", "adegenet", "hierfstat", "pcadapt", "tidyr","rmarkdown", "knitr"))

Clone the course repository to your computer:

git clone https://github.com/MarineEvoEcoLab/NACE_MAS_Genomics_Workshop.git

Now, you’re ready to go!