Biocluster Jupyter

Jupyter

• There is an installation of Jupyter which is accessible at https://bioapps3.igb.illinois.edu/jupyter

Custom Conda Environment

• NOTE This must be done from the biologin nodes. It will fail on the compute nodes as they do not have access to the internet
• From Regular Command Line using SSH
• Load Anaconda Module

module load Anaconda3

• Create Conda Environment. Currently this doesn't work with a python version 3.11 or later

conda create -p $HOME/testenv python=3.10

• Activate Conda Environment

conda activate $HOME/testenv

• Install ipython conda package

conda install ipykernel

• Install custom ipykernel module. This will install the kernel file into $HOME/.local/share/jupyter/kernels. This can be seen by jupyterhub

ipython kernel install --user --name='testenv'

• Open Jupyterhub at https://bioapps3.igb.illinois.edu/jupyter and start a server.
• Your testenv kernel should be listed in the list of kernels