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Jupyter

The IFB Core Cluster integrates a JupyterHub service that let you spawn Jupyter servers over the cluster.

This service is accessible from a simple web browser by connecting with your IFB Core cluster account to https://jupyterhub.cluster.france-bioinformatique.fr

You need to have at least one active project on the cluster to be able to spawn Jupyter servers

Add custom environment to the JupyterLab

To add custom environment for JupyterLab you need first to open a ssh session to the cluster (see Logging in).

Add a user-defined Python environment

Create a conda environment:

module load conda
conda create -n <your-env-name> python=3.7 ipykernel

Install any specific Python librairies in this environment...

Register this new environment for Jupyter :

~/.conda/envs/<your-env-name>/bin/python -m ipykernel install --user --name '<your-env-name>' --display-name "My Python"

Add a user-defined R environment

Create a conda environment with R:

module load conda
conda create -n <your-env-name> r-base=3.6.3 r-irkernel jupyter_client

Install any specific R librairies in this environment...

Start R:

conda activate <your-env-name>
R

Register the R environment for Jupyter

IRkernel::installspec(name = '<your-env-name>', displayname = 'My R', user = TRUE)

Add any existing conda R environment

For example R 4.0.2 already installed on the cluster.

Start R:

module load r/4.0.2
R

Register the R environment for Jupyter

IRkernel::installspec(name = 'r-4.0.2', displayname = 'Cluster R 4',  user = TRUE)