Advanced Usages¶

Pass list of packages to install within a Dockerfile RUN command¶

Dockerfile¶

FROM mambaorg/micromamba:1.5.8
RUN micromamba install -y -n base -c conda-forge \
       pyopenssl=20.0.1 \
       python=3.9.1 \
       requests=2.25.1 && \
    micromamba clean --all --yes

Using a lockfile¶

Pinning a package to a version string doesn’t guarantee the exact same package file is retrieved each time. A lockfile utilizes package hashes to ensure package selection is reproducible. A lockfile can be generated using conda-lock or micromamba:

docker run --rm -v "$(pwd):/tmp" \
   mambaorg/micromamba:1.5.8 /bin/bash -c "\
     micromamba create --yes --name new_env --file env.yaml \
     && micromamba env export --name new_env --explicit" > env.lock

The lockfile can then be used to install into the pre-existing base conda environment:

Dockerfile¶

FROM mambaorg/micromamba:1.5.8
COPY --chown=$MAMBA_USER:$MAMBA_USER env.lock /tmp/env.lock
RUN micromamba install --name base --yes --file /tmp/env.lock \
    && micromamba clean --all --yes

Or the lockfile can be used to create and populate a new conda environment:

Dockerfile¶

FROM mambaorg/micromamba:1.5.8
COPY --chown=$MAMBA_USER:$MAMBA_USER env.lock /tmp/env.lock
RUN micromamba create --name my_env_name --yes --file /tmp/env.lock \
    && micromamba clean --all --yes

When a lockfile is used to create an environment, the micromamba create ... command does not query the package channels or execute the solver. Therefore using a lockfile has the added benefit of reducing the time to create a conda environment.

Multiple environments¶

For most use cases you will only want a single conda environment within your derived image, but you can create multiple conda environments:

Dockerfile¶

FROM mambaorg/micromamba:1.5.8
COPY --chown=$MAMBA_USER:$MAMBA_USER env1.yaml /tmp/env1.yaml
COPY --chown=$MAMBA_USER:$MAMBA_USER env2.yaml /tmp/env2.yaml
RUN micromamba create -y -f /tmp/env1.yaml && \
    micromamba create -y -f /tmp/env2.yaml && \
    micromamba clean --all --yes

You can then set the active environment by passing the ENV_NAME environment variable like:

docker run -e ENV_NAME=env2 my_multi_conda_image

Changing the user id or name¶

The default username is stored in the environment variable MAMBA_USER, and is currently mambauser. (Before 2022-01-13 it was micromamba, and before 2021-06-30 it was root.) Micromamba-docker can be run with any UID/GID by passing the docker run ... command the --user=UID:GID parameters. Running with --user=root is supported.

There are two supported methods for changing the default username to something other than mambauser:

If rebuilding this image from scratch, the default username mambauser can be adjusted by passing --build-arg MAMBA_USER=new-username to the docker build command. User id and group id can be adjusted similarly by passing --build-arg MAMBA_USER_ID=new-id --build-arg MAMBA_USER_GID=new-gid

When building an image FROM an existing micromamba image,

Dockerfile¶

FROM mambaorg/micromamba:1.5.8
ARG NEW_MAMBA_USER=new-username
ARG NEW_MAMBA_USER_ID=57440
ARG NEW_MAMBA_USER_GID=57440
USER root

RUN if grep -q '^ID=alpine$' /etc/os-release; then \
      # alpine does not have usermod/groupmod
      apk add --no-cache --virtual temp-packages shadow; \
    fi && \
    usermod "--login=${NEW_MAMBA_USER}" "--home=/home/${NEW_MAMBA_USER}" \
        --move-home "-u ${NEW_MAMBA_USER_ID}" "${MAMBA_USER}" && \
    groupmod "--new-name=${NEW_MAMBA_USER}" \
        "-g ${NEW_MAMBA_USER_GID}" "${MAMBA_USER}" && \
    if grep -q '^ID=alpine$' /etc/os-release; then \
      # remove the packages that were only needed for usermod/groupmod
      apk del temp-packages; \
    fi && \
    # Update the expected value of MAMBA_USER for the
    # _entrypoint.sh consistency check.
    echo "${NEW_MAMBA_USER}" > "/etc/arg_mamba_user" && \
    :
ENV MAMBA_USER=$NEW_MAMBA_USER
USER $MAMBA_USER

Disabling automatic activation¶

It is assumed that users will want their environment automatically activated whenever running this container. This behavior can be disabled by setting the environment variable MAMBA_SKIP_ACTIVATE=1.

For example, to open an interactive bash shell without activating the environment:

docker run --rm -it -e MAMBA_SKIP_ACTIVATE=1 mambaorg/micromamba bash

Details about automatic activation¶

At container runtime, activation occurs by default at two possible points:

The end of the ~/.bashrc file, which is loaded by interactive non-login Bash shells.

The ENTRYPOINT script, which is automatically prepended to docker run commands.

The activation in ~/.bashrc ensures that the environment is activated in interactive terminal sessions, even when switching between users.

The ENTRYPOINT script ensures that the environment is also activated for one-off commands when Docker is used non-interactively.

Setting MAMBA_SKIP_ACTIVATE=1 disables both of these automatic activation methods.

Adding micromamba to an existing Docker image¶

Adding micromamba functionality to an existing Docker image can be accomplished like this:

Dockerfile¶

# bring in the micromamba image so we can copy files from it
FROM mambaorg/micromamba:1.5.8 as micromamba

# This is the image we are going add micromaba to:
FROM tomcat:9-jdk17-temurin-focal

USER root

# if your image defaults to a non-root user, then you may want to make the
# next 3 ARG commands match the values in your image. You can get the values
# by running: docker run --rm -it my/image id -a
ARG MAMBA_USER=mambauser
ARG MAMBA_USER_ID=57439
ARG MAMBA_USER_GID=57439
ENV MAMBA_USER=$MAMBA_USER
ENV MAMBA_ROOT_PREFIX="/opt/conda"
ENV MAMBA_EXE="/bin/micromamba"

COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE"
COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh
COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh
COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh

RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \
    /usr/local/bin/_dockerfile_setup_root_prefix.sh

USER $MAMBA_USER

SHELL ["/usr/local/bin/_dockerfile_shell.sh"]

ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
# Optional: if you want to customize the ENTRYPOINT and have a conda
# environment activated, then do this:
# ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "my_entrypoint_program"]

# You can modify the CMD statement as needed....
CMD ["/bin/bash"]

# Optional: you can now populate a conda environment:
RUN micromamba install --yes --name base --channel conda-forge \
      jq && \
    micromamba clean --all --yes

On `docker exec ...`¶

Your experience using docker exec ... may not match your expectations for automatic environment activation ( #128, #233) docker exec ... <command> executes <command> directly, without an entrypoint or login/interactive shell. There is no known way to automatically (and correctly) trigger conda environment activation for a command run through docker exec ....

The recommended method to explicitly activate your environment when using docker exec ... is:

docker exec <container> micromamba run -n <environment_name> <command>

If you want to use the base environment, you can omit -n <environment_name>.

An alternative method to trigger activation is to explicitly run your command within an interactive bash shell with -i:

docker exec <container> bash -i -c "<command>"

Finally, you can modify the PATH at build-time to approximate an activated environment during docker exec:

Dockerfile¶

ENV PATH "$MAMBA_ROOT_PREFIX/bin:$PATH"  # Not a preferred method!

Warning

Modifying PATH will not work in all cases, such as multiple conda environments within a single image.

Use of the `ENTRYPOINT` command within a Dockerfile¶

The mambaorg/micromaba Dockerfile makes use of the ENTRYPOINT command:

Dockerfile¶

ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]

Warning

If a derived image overrides this ENTRYPOINT configuration, then some of the automatic conda environment activation functionality will break.

If you wish to modify the entrypoint for a derived image while retaining automatic conda environment activation, then append your command to the end of the ENTRYPOINT list:

Dockerfile¶

ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "new-addition.sh"]

Use of the `SHELL` command within a Dockerfile¶

The mambaorg/micromaba Dockerfile makes use of the SHELL command:

Dockerfile¶

SHELL ["/usr/local/bin/_dockerfile_shell.sh"]

Warning

If a derived image overrides this SHELL configuration, then some of the automatic conda environment activation functionality will break.

Advanced Usages¶

Pass list of packages to install within a Dockerfile RUN command¶

Using a lockfile¶

Multiple environments¶

Changing the user id or name¶

Disabling automatic activation¶

Details about automatic activation¶

Adding micromamba to an existing Docker image¶

On `docker exec ...`¶

Use of the `ENTRYPOINT` command within a Dockerfile¶

Use of the `SHELL` command within a Dockerfile¶

micromamba-docker

Navigation

Related Topics

Advanced Usages¶

Pass list of packages to install within a Dockerfile RUN command¶

Using a lockfile¶

Multiple environments¶

Changing the user id or name¶

Disabling automatic activation¶

Details about automatic activation¶

Adding micromamba to an existing Docker image¶

On docker exec ...¶

Use of the ENTRYPOINT command within a Dockerfile¶

Use of the SHELL command within a Dockerfile¶

On `docker exec ...`¶

Use of the `ENTRYPOINT` command within a Dockerfile¶

Use of the `SHELL` command within a Dockerfile¶