Course materials for Spring 2021 term of Computational Genetics. Because of the auspicious timing of our class we have decided to focus on applying our developing computer programming chops to studying COVID and the evolution of the virus that causes the disease SARS-CoV-2.

Generally you will want to keep the your copy of the class materials that sits on the bio399cloud server up to date with what is on Github here. To do that you can follow these steps

If you want to download the material for the first time, or if you get in trouble somehow and want to start from the begining, use git clone to download. That is,

1. open a new terminal window on the server
2. type git clone https://github.com/andrewkern/bio399

If you have cloned the directory you have two choices: you could delete the entire thing and clone it again, or you could maintain you repo up to date with the remote one.

Warning: save your work If you want to just delete everything and start again you can, but be sure to save your own notebooks some place safe. perhaps download them to your own machine. Here are the steps to blast everything away and start afresh

1. open a new terminal window on the server
2. type rm -rf bio399/ -- this removes the directory
3. type git clone https://github.com/andrewkern/bio399

The other option is to keep things up to date with what's on the Github server without deleting anything. You can do this in the following way

1. open a new terminal window on the server
2. cd bio399/ -- move into the bio399 directory
3. type git pull . this may work, but it may complain about uncommitted changes and ask you to stash. don't do this. instead go to step 4
4. type git fetch origin
5. type git reset --hard origin/master

and that should keep you up to date!