Creating nipype_tutorial using Neurodocker

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1

I’m using nipype as a starting point to familiarize myself with Docker image creation. The end goal is to create images for a workshop I’m running this summer.

I’m going through the documentation on repronim, and a lot of things aren’t working. Maybe I can contribute at some point by submitting pull requests or something. In the mean time, I’m just trying something fairly basic to start with.

neurodocker generate docker \
    --pkg-manager apt \
    --base debian:buster-slim \
    --miniconda \
		create_env=jupyter \
        version=latest \
        conda_install="matplotlib notebook numpy pandas seaborn" \
    --user nonroot \
    --workdir /work \
> notebook.Dockerfile

One problem was that --base-image is now --base. Got that.

According to docker scan, there are lots of vulnerabilities with buster, but rolling with that now to simplify.

Now --miniconda wants either create_env or use_env. I went with create_env, and named it jupyter.
When I build the image, it seems to install everything in that environment as expected.

docker build --tag notebook --file notebook.Dockerfile .

However, using that environment when trying to run Jupyter Notebook has me stumped. Just for completeness, here’s my run command line.

docker run --rm -it --workdir /work --volume $PWD:/work --publish 8888:8888  --ip 0.0.0.0 notebook jupyter-notebook

If I run a bash shell in the container, I can’t activate the environment because .bashrc hasn’t been set up. So I conda init bash, then source /home/nonroot/.bashrc, then I can conda activate jupyter and it will run.

So the problem is, how do I conda init bash when creating the image, then conda activate jupyter when the image is run?

I’ve tried this in the first RUN in the Dockerfile:

    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
	&&   echo 'conda init bash' >> "$ND_ENTRYPOINT" \            # added this
	&&   echo 'source $HOME/.bashrc' >> "$ND_ENTRYPOINT" \       # added this
	&&   echo 'conda activate jupyter' >> "$ND_ENTRYPOINT" \     # added this
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \

Since I’m posting here, you probably suspect this doesn’t work, and you would be right.
It looks like the conda init bash runs, as I see that /home/nonroot/.bashrc has been modified, but when activate runs, it says the shell has not been initialized.

Questions:

  • Am I missing an updated procedure somewhere?
  • Can I use neurodebian:bullseye which seems to be more secure?
  • How can I create, conda init and conda activate an environment?
  • Can I use the same procedures (whatever those might be) to create the full nipype image as is done here?

Thanks!

2

just wanted to check this first before moving to the other issues. the current unreleased version does use --base-image (see here. could it be you are using an older version? can you try to install directly from github for now? i’m checking to see if we can make a new release.

3

Both installation methods from the github README (via the Neurodocker docker image or pip) install version 0.7.0, which seems to allow --base only.

4

ah i meant something like:

pip install https://github.com/ReproNim/neurodocker/archive/refs/heads/master.zip
5

Thanks @satra , that got me started on the solution.

Here’s a gist of what I wound up doing, in case any Future People™ are looking for a solution.

GitHub unhelpfully sorts the files alphabetically.

  • Install neurodocker first using install_neurodocker.sh
  • Download the nipype_tutorial files and create the docker using build_docker_image.sh
  • Change the paths in run_nipype_tutorial_docker.sh and give it a try.

Caveat emptor. Void where prohibited. Valid in 49 US states, sorry Tennessee.

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