Micromamba Apptainer

This small definition file can be used to create a conda environment in an apptainer / singularity container.

Givent environment.yml is combined with the micromamba_apptainer.def definition file to create a SIF-image:

  graph TD;
      E[environment.yml]-->S[my_environment.sif];
      D[micromamba_apptainer.def]-->S[my_environment.sif];

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Example

Create a environment.yml file with all needed channels and dependencies present. Name the environment base. This is important as all packages will be installed to the base environment.

name: base
channels:
  - conda-forge
dependencies:
  - python
  - numpy

Create an apptainer image with the bootstrapping definition.

For apptainer:

apptainer build my_environment.sif micromamba_apptainer.def

You can run python from the the image with apptainer run:

apptainer run my_environment.sif python -c 'import numpy as np; print(np.__version__)'

apptainer run automatically activates the base-environment.

Singularity usage

If you're using singularity, just swap apptainer to singularity in all commands.