From Conda to Docker

Miniconda environments are an easy to use and flexible way of organising dependencies, and to ensure reproducibility as each environment can be shared as a YAML file.

In this short note, we will see how to generate an environment to be used to generate a Docker container.

Generating the environment

We will use mamba to quickly generate a new environment with the tools we need (see Miniconda tutorial).

For this example we will use a set of tools from bioconda. If needed, we can specify the exact version, or a version range (e. g. samtools>=1.14).

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mamba env create -n MyEnv -c conda-forge -c bioconda -y \
  fastp  bwa "seqfu>1.9" "samtools=1.14"

Save the environment as a file

A handy feature of Miniconda is the possibility of saving the current environment to a YAML file.

Adding --no-builds will skip the build specification from the YAML file.

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# Activate the generated environment first
conda activate MyEnv

# Export the environment, removing the first and last line
# that specify the environment name and prefix (path)
conda env export | head -n -1 | tail -n +2 > environment.yaml

Dockerfile

Micromamba is a striped-down version of conda, based on mamba, and is available as a docker image, that we can use to make a Dockerfile.

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FROM mambaorg/micromamba:0.19.1
RUN mkdir /home/mambauser/eggnog
COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yaml /tmp/env.yaml
ARG MAMBA_DOCKERFILE_ACTIVATE=1
RUN micromamba install -y --file env.yaml && \
     micromamba clean --all --yes

To build the image:

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docker build -t imagename .

By default, Docker will run as a root (thus requiring sudo). To allow your user to run sudo-less docker commands:

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sudo groupadd docker
sudo usermod -aG docker $USER
newgrp docker

Singularity

If you push your docker container to a hub, from there you can pull the image as a singularity container. If using Docker Hub, for example:

1. docker login with your username and password (required once)
2. Build the image tagging it as username/imagename:version
3. Push the image to the repository with docker push username/imagename:version

To generate the Singularity image:

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singularity pull docker://username/imagename:version