RADCamp ICCB Brisbane 2025 - Day 1
Overview of the morning activities:
- Intro to ipyrad resources
- Software setup
- RADseq data quality control (QC)
- ipyrad assembly of simulated data Part I
Intro ipyrad Resources
- ipyrad documentation (detailed explanations and tutorials)
- ipyrad gitter channel (a chat room for getting help)
- ipyrad github repository (reporting issues)
Accessing Cloud Computing Resources
For this workshop we will use a cloud server hosted by the Eaton Lab at Columbia University. To log in you will need a gmail account. Open a browser window and go to:
You will see a login screen prompting you to log in with gmail. Click this button, and you might need to confirm an authorization to verify your identity.
The default view is the ‘Classic’ jupyter notebook view, but I prefer the newer JupyterLab view because it keeps everything in one place. Open JuptyerLab by going to View->Open JupyterLab
Once logged in you’ll see the JupyterHub File Browser and Launcher panes.
Note: These cloud resources will not persist past he workshop. The Eaton lab JupyterHub server is only accessible for your account for the duration of this workshop. After the workshop we will delete user accounts and restrict access permissions, so don’t save anything valuable here!
Installing ipyrad
To start the terminal on the jupyter dashboard, click “Terminal” in the Launcher.
ipyrad uses conda, which is a package manager for python. We downloaded
the minconda installer
and saved it in the work directory, so you can run the installer from there.
bash ./work/BlackRockData2/Miniconda3-latest-Linux-x86_64.sh
During the miniconda installation push the space bar until prompted and then:
- Type ‘yes’ to acknowledge the license agreement
- Push ‘enter’ to confirm the install location (
/home/jovyan/miniconda3) - Type ‘yes’ to initialize conda
After it’s finished type ‘exit’ and then open another terminal. Your prompt should now look like this:
(base) jovyan@493222dbc32d:~$
Now you can install ipyrad (and a few of the other necessary packages we’ll be using) with conda like this (it will take 1-2 minutes):
conda install -c conda-forge -c bioconda ipyrad fastqc -y