Dockerfile
Some tips-and-tricks for creating a Dockerfile for the submission to this challenge. The Dockerfile Reference can be found here: https://docs.docker.com/engine/reference/builder/ and the best practices here: https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/.
FROM
Pick a suitable base image for your container. Search on Docker Hub for your preferred operating system, for example CentOS or Ubuntu. Optionally, specify a version tag (eg centos:7), because the :latest tag (default when not specifying a tag) might change between your submission and our evaluation.
You can also search on Google or Github for base images that already contain the default tools you need. There is a high chance that your favourite neuroimaging tools have already been containerized.
If you want to use a GPU, be sure to pick a nvidia/cuda base image. Have a look at all the available tags to find your favourite OS.
You can also search on Google or Github for base images that already contain the default tools you need. There is a high chance that your favourite neuroimaging tools have already been containerized.
If you want to use a GPU, be sure to pick a nvidia/cuda base image. Have a look at all the available tags to find your favourite OS.
RUN
Limit the number of RUN commands, by combining them into a single RUN. Each command in a Dockerfile creates a layer in your container, increasing the total container size. So in stead of this:
RUN apt-get update
RUN apt-get install -y aufs-tools
RUN apt-get install -y automake
RUN apt-get install -y build-essential
RUN apt-get install -y libsqlite3-dev
RUN apt-get install -y s3cmd=1.1.*
RUN rm -rf /var/lib/apt/lists/*
RUN apt-get install -y aufs-tools
RUN apt-get install -y automake
RUN apt-get install -y build-essential
RUN apt-get install -y libsqlite3-dev
RUN apt-get install -y s3cmd=1.1.*
RUN rm -rf /var/lib/apt/lists/*
Do this:
RUN apt-get update && apt-get install -y \
aufs-tools \
automake \
build-essential \
libsqlite3-dev \
s3cmd=1.1.* \
&& rm -rf /var/lib/apt/lists/*
Be sure to do the clean-up within the same command! Otherwise the clean-up happens in a new layer and does not have any effect on the previous layers.
ENTRYPOINT
If your base image contains a non-default ENTRYPOINT (or USER, CMD, WORKDIR), you can reset this with:
ENTRYPOINT ["bash"] CMD [] USER 0 WORKDIR /
For example, the jupyter docker-stacks with python base images start a notebook server, which is probably not needed for this challenge.
