Conda/mamba

It is possible to customize your environment using anaconda and access that environment in your notebooks.

Configuring conda/mamba (only needed once)

From a terminal launcher, run mamba init. Then, write to .bash_profile in your home directory with the following content:

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
    . ~/.bashrc
fi

Using conda/mamba

Conda is well-documented at https://conda.io (its use is outside the scope of this documentation). You can safely substitute mamba for conda wherever it is listed; it is a faster reimplementation in C++ of conda.

Installing launchers

You must install the ipykernel package in order to make your custom environment available as a notebook kernel. After a minute or so, a new launcher should appear corresponding to your environment; it may be necessary to reload the web page.

Customizing conda with user scripts

For conda environments, you can add preamble scripts to ${CONDA_PREFIX}/etc/conda/activate.d; these will run before your notebook starts. For example, in the snowflakes conda environment example below, additional preamble scripts could be added to ~/.conda/env/snowflakes/etc/conda/activate.d.

Example: installing biopython in the snowflakes conda environment

The vanilla launcher screen shows the two default launchers: python, and python-safemode.

We then install a new environment named snowflakes, including the biopython package:

[burt@jupyter-burt-lpc ~]$ mamba create -q -y -n snowflakes biopython ipykernel
Package                            Version  Build                Channel                    Size
────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────────

+ _libgcc_mutex                        0.1  conda_forge          conda-forge/linux-64     Cached
+ _openmp_mutex                        4.5  2_gnu                conda-forge/linux-64     Cached
[ ... snipped for brevity ... ]
+ zeromq                             4.3.4  h9c3ff4c_1           conda-forge/linux-64     Cached

Summary:

Install: 66 packages

Total download: 3MB

────────────────────────────────────────────────────────────────────────────────────────────────────

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

The newer launcher now appears, with its full name visible via tooltip, indicating the name of the conda environment:

And the Bio module from biopython is available: