Creating custom envs on conda for Jupyter Notebook

You might limited by the packages inside the default environment, so you can create new envs and add your own packages like so:

Inside /arc/project/<allocation>/jupyter/jupyter-datascience.sif is an image that defines an environment (essentially another OS/docker image) that contains the necessary files to Jupyter Notebook.

We will modify it using this command:

First run:

module load gcc
module load apptainer

apptainer shell --home /scratch/<allocation>/<CWL>>/my_jupyter/ --env XDG_CACHE_HOME=/scratch/<allocation>/<CWL>/my_jupyter /arc/project/<allocation>/jupyter/jupyter-datascience.sif

Once you run this, you should see a prompt like so:

Apptainer>

Inside the prompt, run:

 conda create --prefix /arc/project/<allocation>/jupyter/<your_environment_name>

And then run:

conda install -y ipykernel --prefix /arc/project/<allocation>/jupyter/<your_environment_name>

and for the R kernel:

conda install -c conda-forge r-irkernel /arc/project/<allocation>/jupyter/<your_environment_name>

To install packages:

WARNING: All R packages must be installed using conda-forge. Fortunately, almost every package can be installed this way. Do not try installing using install.packages(). You will break things.

Activate the conda environment we created in a previous step with:

source activate /arc/project/<allocation>/jupyter/<your_environment_name>

Then use conda and pip as normal.

Once you are satisfied with the packages you installed, package your environment into a kernel image like so:

python -m ipykernel install --user --name <your_environment_name>

If you installed R and related R packages:

Initialize the R kernel using:

R

IRkernel::installspec(name = "my_r_env", displayname = "R (My Environment)")

Once you're done, run exit in the shell, and then go to Initializing a Jupyter Notebook Instance