PATH from user account not used in notebook

I’m new to jupyterhub and have a confusing issue with PATHS. I’m running a The Littlest JupyterHub server for my college. I initially wrote a notebook to automate a physics simulation on a computer I owned. I started jupyterlab from tmux so it persists, then used the notebook. It served to replace a complicated bash script, I call commandline utilities like sed and the actual physics software with That all worked just fine.

I needed to make some changes to the dimensions and had to run everything again, but now I was going to do it using The Littlest JupyterHub server. I installed the physics software and can run it one simulation at a time on the terminal from the juppyterlab interface. The notebook I moved over does not use the same PATH as the terminal and does not find the required libraries and dependencies to actually run Geant4. If i copy past the code into IPython that I start from the terminal it works fine.

Why does my notebook not use the same path as set up by my .bashrc?