Common Uses

Create locally and use remotely

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Working with Data

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Jupyter Notebook

This example demonstrates how to build and run an image with Jupyter Notebook.

Note

When you exit a Docker image, any files you created in that image are lost. So if you create Jupyter Notebooks while in a Docker image, remember to save them to a mounted directory. Otherwise, the notebooks will be deleted (and unrecoverable) after you exit the Docker image.

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

# Build the image.
docker build --tag notebook --file notebook.Dockerfile .

# Run the image. The current directory is mounted to the working directory of the
# Docker image, so our notebooks are saved to the current directory.
docker run --rm -it --publish 8888:8888 --volume $(pwd):/work notebook \
    jupyter-notebook --no-browser --ip 0.0.0.0

Multiple Conda Environments

This example demonstrates how to create a Docker image with multiple conda environments.

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:buster-slim \
    --miniconda \
        version=latest \
        env_name=envA \
        env_exists=false \
        conda_install=pandas \
    --miniconda \
        version=latest \
        installed=true \
        env_name=envB \
        env_exists=false \
        conda_install=scipy \
> multi-conda-env.Dockerfile

docker build --tag multi-conda-env --file multi-conda-env.Dockerfile .

One can use the image in the following way:

docker run --rm -it multi-conda-env bash
# Pandas is installed in envA.
conda activate envA
python -c "import pandas"
# Scipy is installed in envB.
conda activate envB
python -c "import scipy"