Conda Environments

Adding a conda environment to a container may be easily done using cotainr.

As an example, consider the following conda environment file, my_conda_env.yml:

Base image requirement

In order to include a conda environment in your container, you must use a base image in which bash is installed.

my_conda_env.yml

channels:
  - conda-forge
dependencies:
  - python=3.11.0
  - numpy=1.23.5

A container based on the official Ubuntu 22.04 DockerHub image, containing this conda environment, may be built using:

$ cotainr build my_conda_env_container.sif --base-image=docker://ubuntu:22.04 --conda-env=my_conda_env.yml

The conda environment is automatically activated when the container is run, allowing for directly using the Python and NumPy versions installed in the conda environment, e.g.

$ singularity exec my_conda_env_container.sif python --version
Python 3.11.0
$ singularity exec my_conda_env_container.sif python -c "import numpy; print(numpy.__version__)"
1.23.5

Pip packages

cotainr does not support creating a container directly from a pip requirements.txt file. However, pip packages may be included in a conda environment, e.g. updating my_conda_env.yml to

my_conda_env.yml

channels:
  - conda-forge
dependencies:
  - python=3.11.0
  - numpy=1.23.5
  - pip:
    - scipy==1.9.3

allows for installing SciPy via pip.