Containers 8: Extra material

Containers can be large and complicated, but once you start using them regularly you’ll find that you start understand these complexities. There are lots of different things you can do with images and containers in general, especially when it comes to optimising build time or final image size. Here is some small tips and tricks that you can be inspired from!

If you want to read more about containers in general you can check out these resources:

• A “Get started with Docker” at docker.com Links to an external site..
• An early paper Links to an external site. on the subject of using Docker for reproducible research.

A base image with Conda

We’ve used Conda throughout this container tutorial, and we did it by installing Conda inside the image when we built it. Wouldn’t it be nice if we didn’t have to do this particular step? After all, installing Conda is just busy-work, compared to installing the actual environment that we want to use for the analyses. Luckily, there are already container images out there that have Conda (and Mamba) installed, such as the ones over at condaforge/mambaforge! What follows is a Dockerfile that you could use instead of the ones described above to install things using a Conda environment.yml file, without having to install Conda in the Docker image when building it!

FROM condaforge/mambaforge:4.10.1-0
LABEL description = "Image description"
MAINTAINER "Firstname Lastname" firstname.lastname@gmail.se

# Use bash as shell
SHELL ["/bin/bash", "-c"]

# Set working directory
WORKDIR /project

# Copy and install the Conda environment
COPY environment.yml ./
RUN conda config --set channel_priority strict \
    && mamba env update --name base --file environment.yml \
    && mamba clean --all --force-pkgs-dirs --yes

# Start Bash shell by default
CMD /bin/bash