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JupyterLab

Systems Available

JupyterLab default version is available on these systems:

  • deNBI-Cloud
  • JSC-Cloud

Files in /home/jovyan are stored persistently. Everything else will be lost after a restart.

Environment

The default environment for JupyterLab is based on the official jupyter/minimal-notebook.

Kernel customization

To use your own environment and packages it is recommended to use the Repo2Docker option, as this provides way more options and is easier to use.
To install a new kernel in your running JupyterLab simply run:

python -m ipykernel install --user --name mykernel --display-name "MyKernel"

This will create a kernelspec file at /home/jovyan/.local/share/jupyter/kernels/mykernel/kernel.json. You can update this, to use any environment you like to use.

Use own virtualenv

1. python3 -m venv /home/jovyan/.local/share/jupyter/kernels/venv_mykernel
2. /home/jovyan/.local/share/jupyter/kernels/venv_mykernel/bin/pip install ipykernel  # ipykernel is required in each environment
3. # Replace "/opt/conda/bin/python" in /home/jovyan/.local/share/jupyter/kernels/mykernel/kernel.json with "/home/jovyan/.local/share/jupyter/kernels/venv_mykernel/bin/python"
4. Using "MyKernel" will then use the newly created python environment