Using Conda in Apptainer

Important Notes

We will preface this tutorial on how to use Conda inside a container with the following important notes:

Even inside a container, Conda should not be your preferred solution. Priority should always be given to using modules from our software stack, and wheels from our Python wheelhouse. These are optimized for our systems and we are better equipped to provide support if you use them. Please contact us if you need a module or a Python package that is not currently available on our systems.
This tutorial will use the micromamba package manager instead of Conda. If you choose to use Conda instead, keep in mind that its use is subject to Anaconda's Terms of Service and might require a commercial license.
This tutorial shows how to create a read-only image, i.e., a one-off .sif file containing a Conda environment that has everything you need to run your application. We strongly discourage installing software interactively with Conda inside a container and will not show how to do this here.

Creating an Apptainer image and using Conda to install software inside it is a 3-step process. The first step is to create a .yml file describing the Conda environment we wish to create inside the container. In the example that follows, we create the file environment.yml. This file is where we give our environment a name, then give Conda a list of packages that must be installed and the channels where to look for them. For more information see here.

environment.yml

name: base
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - python
  - pip
  - star
  - bwa
  - multiqc

Second, we create an Apptainer image definition file. This file, here called image.def, describes what are the steps Apptainer should take to create our image. These steps are: 1. Pull a Docker image from DockerHub that has the micromamba package manager pre-installed. 2. Create a copy of the Conda environment definition file environment.yml inside the container. 3. Call micromamba and have it configure the environment defined in environment.yml.

image.def

Bootstrap: docker
From: mambaorg/micromamba:latest

%files
    environment.yml /environment.yml

%post
    micromamba install -n base --file environment.yml && \
        micromamba clean --all --yes

The last step is to build the Apptainer image using the definition file above:

module load apptainer
APPTAINER_BIND=' ' apptainer build image.sif image.def

You can test that your image provides multiqc, for example, like this:

apptainer run image.sif multiqc --help

```text title="Expected Output"

/// MultiQC 🎃 v1.25.1

Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY] ...