1. The Bash Shell
   Bash is a commonly-used shell or command line that gives you the power to do simple tasks more quickly.
   • Download the Git for Windows installer.
   • Run the installer and follow the steps bellow:
     • Welcome to the Git Setup Wizard -- Click on "Next".
     • Information -- Click on "Next".
     • Select destination location -- Click on "Next".
     • Select components -- Click on "Next".
     • Select start menu folder --Click on "Next".
     • Adjusting your PATH environment -- Select "Use Git from the Windows Command Prompt" and Click on "Next". If you forgot to do this you might have some installation problems. This can be fixed by reruning the installer and selecting the appropriate option.
     • Configuring the line ending conversions -- Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
     • Configuring the terminal emulator to use with Git Bash -- Select "Use Windows' default console window" and Click on "Next".
     • Configuring experimental performance tweaks -- Click on "Next".
     • Completing the Git Setup Wizard -- Click on "Finish".
   • This will provide you with both Git and Bash in the Git Bash program.
2. R
   In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
   • Download R from here
   • Run the .exe file that was just downloaded
   • Go to the RStudio Download page
   • Under Installers select RStudio 0.99.896 - Windows XP/Vista/7/8
   • Double click the file to install it
   • Once it's installed, open RStudio to make sure it works and you don't get any error messages.
   • Optional: if you can find the "Console" in RStudio copy this bit of code install.packages("ggplot2"). It will download the Graphics package that we will use in the workshop.

1. R

In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
• Go to CRAN and click on Download R for (Mac) OS X
• Select the .pkg file for the version of OS X that you have and the file will download.
• Double click on the file that was downloaded and R will install
• Go to the RStudio Download page
• Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) to download it.
• Once it's downloaded, double click the file to install it
• Once it's installed, open RStudio to make sure it works and you don't get any error messages.
• Optional: if you can find the "Console" in RStudio copy this bit of code install.packages("ggplot2"). It will download the Graphics package that we will use in the workshop.

1. R
   In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
   • Follow the instructions for your distribution from CRAN. For most distributions, you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora run sudo yum install R) but make sure that you have at least R 3.2.2 (as pre-packaged versions might be out of date).
   • To install RStudio, go to the RStudio Download page
   • Under Installers select the version for your distribution.
   • Once it's downloaded, double click the file to install it (or sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
   • Once it's installed, open RStudio to make sure it works and you don't get any error messages.
   • Optional: if you can find the "Console" in RStudio copy this bit of code install.packages("ggplot2"). It will download the Graphics package that we will use in the workshop.

1. Download the version of VirtualBox that is appropriate for your operating system from https://www.virtualbox.org/wiki/Downloads and install it.
2. Next download the OVA (Open Virtualization Archive) file to your desktop from http://environmentalomics.org/bio-linux- download/.*Important: Right click on the link below where it says "OVA file for use with VirtualBox/VMWare" and choose "Save link as" from the drop down menu.

VirtualBox setup:
• Ensure you have at least 40GB free disk space.
• Start the VirtualBox and select Import Appliance from the File menu and import the .ova file (don't worry that it says you need an OVF file) and select "next"
• When importing the appliance, select the option to reinitialize the MAC addresses of network cards which is in small print below the larger menu. (This step takes a few minutes.)
• Start the virtual machine (VM) and if you see a log-in screen, log in as user manager with password manager.
• Once this is working, you can delete the .ova file to save space.
• See the VirtualBox docs for more details including how to share folders and hardware. You will also want to adjust hardware settings such as CPU, RAM and video acceleration settings to suit your hardware.

You should treat the VM as a real machine for security purposes and apply all system security updates in a timely manner. The default manager password is, clearly, not secure. This might not be a problem because by default nobody can access the Linux VM unless they have direct access to your computer, but if you open up the network settings (eg. by adding port forwarding rules) then you must secure the account with a strong password or else take other steps to limit remote access. Ideally enforce key-only access via SSH.