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There are multiple ways.
First, install a linux-like system (ex. Cygwin). Cygwin is a collection of tools which provide a Linux look and feel environment for Windows. Visit Cygwin, download it, and use Cygwin terminal like you used in TACC's lonestar server. But Cygwin is not a way to run native Linux apps on Windows. Cygwin is a linxLinux-like system is not linux per se. You may need to install additional modules and commands on Cygwin in order to complete certain jobs.
Second option is to install a virtual machine (VM) and linux. VM is a completely isolated guest operating system installation within a normal host operating system. VM allows you to have two or more OSs OS in one physical PC machine. You can install linux, OS X, Windows Vista, Windows 98 on a VM. Which VM and linux is the best? Actually, there is no best choice because everyone has own taste. In terms of popularity, Oracle VM Virtual Box and Ubuntu is a pretty nice choice. More importantly, they are free! I won't explain how to install VM and Ubuntu on your Windows because you can easily find wonderful instruction instructions by googling. Google "virtual box ubuntu". Here is one easy and useful guide.
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Ubuntu inside VB and Windows work like two different computers in one physical PC. When you generate beautiful graphs and awesome tables on Ubuntu for your labmeeting on Ubuntu, you can't open it with MS office on Windows. Don't send them to yourself via email. Shared Folders functionality makes multiple OS to share some space in the hard drive. You can run NGS utilities on your Ubuntu and spit out the output into the shared folder. Then, open it with MS office on your Windows. Oh! before you set up Shared Folders, you should install the Guest Additions on your VM. Here is how to install Guest Additions and how to share folders
In summary,
- Install VM on your Windows
- Install Ubuntu on your VM
- Install Guest Additions if the VM is Oracle VB
- Share folders with your Windows