Setup

To participate in a this workshop, you will need access to UF Hipergator and the software described below.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the FAQ page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other bioinformatics workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have three windows open at the same time, one for the command line shell (powershell/terminal), one for the website (to copy commands), and one window for the Zoom video conference client. In order to see all three at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have your terminal and website up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the terminal and the website.
Divide your screen: If you only have one device and one screen, practice having three windows (the zoom window, a terminal/powershell and the website) open together. How can you best fit both on your screen? Try it out in advance to decide what will work best for you.

Connecting to Gatorlink VPN

Gatorlink VPN is required to access University if Florida Research Computing OnDemand service, which will provide access to HiperGator cluster.

Visit UF VPN webpage (vpn.ufl.edu).
Login using the username and password that was emailed to you.
In the next page, download Cisco Anyconnect software and install it.
Once installed, run Cisco Anyconnect and click Connect.
Enter the username and password provided and click OK. You should now be connected to Gatorlink VPN.

Connecting to HiperGator

Make sure you are connected to Gatorlink VPN before the following steps.

In you web browser, navigate to UFRC OnDemand (ood.rc.ufl.edu).
Login using provided username and password. You will be redirected to UFRC OnDemand homepage.
To connect to remote shell, click on Clusters in navbar and click Hipergator Shell Access. Note that the shell will open in new tab.
To view and transfer your files, click on Files in navbar in UFRC OnDemand homepage and click /blue/general_workshop. Double click on directory named as your username to find your files.

To view instructions for connection using terminal, click here. Note that this method does not work with guest accounts in Hipergator.

(Recommended) Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. Installation of one of the suggested text editors is recommended but not necessary.

You can use Notepad++ or Sublime Text to edit the code. You can access download page by clicking the the name above.

You can use BBedit or Sublime Text to edit the code. You can access download page by clicking the the name above.

You can use one of the following text editors in linux.

Gedit
```
sudo apt-get install gedit
```
Kate
```
sudo apt-get install kate
```
Sublime Text
```
sudo apt-get install sublime-text
```

You can access download page by clicking the the name above or install using command line from respective commands.

(Optional) Figtree for tree visualization

We will generate a tree in Newick format. You can download a tree viewing software such as Figtree to visualize the tree. Figtree is available for download for Windows, MacOS and Linux from its github repository.