Detecting selective sweeps in population genomic data

Detecting selective sweeps in population genomic data

Derek Setter, June 2022

How to run this activity

The activity on sweep detection will be run through Jupyter Notebooks. So, just as in the introductory tutorial on Python and Jupyter Notebooks by Hannes Svardal, you will first need to start a Jupyter Notebook on your AWS instance and connect to it.

Connect to the instance using SSH. Use “wpsg” as the username and the usual password. You can do that either through Guacamole in your web browser:

• http://ec2-XXX-XXX-XXX-XXX.compute-1.amazonaws.com:8080/guacamole where XXX-XXX-XXX-XXX is replaced by the Amazon instance IP address assigned to you.

Or you can use SSH from your terminal:

• ssh [email protected] (replace XXX with your Amazon instance IP address)

Once connected through SSH:

• Navigate into the tutorial directory: cd ~/workshop_materials/a10_sweep_detection
• Start a screen session by typing: screen
• Confirm with the “Return” key
• Start the conda virtual environment: conda activate sweeps-env
• Start the notebook server: jupyter notebook --no-browser --port=8889
• The command blocks the terminal. That is normal. Keep it running. You can detach from the screen and get back to a functional terminal by typing “Ctrl + a, d” (first “Ctrl + a”, then “d”)
• In your local browser, navigate to the web address: http://ec2-XXX-XXX-XXX-XXX.compute-1.amazonaws.com:8889 (replace XXX with your Amazon instance IP address
• Then you should see the contents of the folder in which your instance is running.

 
Open the jupyter notebook sweep_workshop_no_solutions.ipynb. All instructions and background information about the activity will be given in the Jupyter Notebook.