Jupyter notebook

Updated

To use Jupyter notebooks, you should be on the Bigelow network (either on site or connected to the VPN)

  1. Start an interactive session/job
    qsub -I -q route -l walltime=8:00:00 -l ncpus=2,mem=16G -N jupyter-interactive
  2. Navigate to your notebook directory and setup your environment
    module load anaconda3
    unset XDG_RUNTIME_DIR
  3. Determine the IP address of the current compute node
    hostname -I
  4. Start a jupyter notebook session
    jupyter notebook --no-browser --port=<port> --ip=<ip address>
    The port can be in the range of 8888-8988. The ip address is the IP found in the previous step.
  5. Copy and paste the URL from your notebook session into a web browser on your local computer

New method (beta)

  1. Start an interactive session/job
  2. Load the jupyter-notebook module
    module load jupyter-notebook
  3. Run run_jupyter to find the next available port and start a jupyter notebook session using it
    run_jupyter

Change theme

  1. Start an interactive session/job
  2. Load the jupyter-notebook module
    module load jupyter-notebook
  3. List available themes (screenshots available here)
    jt -l
  4. Set a theme
    jt -t <theme-name>
    e.g. jt -t oceans16
  5. Launch Jupyter Notebook (e.g. run-jupyter)


Still need help? Submit a ticket.

Conda environments

Prokka

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