Adding micromamba to an existing Docker image failing to prefix error

[JaakkoAhola]

I have created a Docker image following adding-micromamba-to-an-existing-docker-image and the only difference is that I install python packages following the quick start.

So my Dockerfile is:

# bring in the micromamba image so we can copy files from it
FROM mambaorg/micromamba:1.5.0 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=mamba
ARG MAMBA_USER_ID=1000
ARG MAMBA_USER_GID=1000
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:
COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
RUN micromamba install -y -n base -f /tmp/env.yaml && \
    micromamba clean --all --yes

and the env.yaml is

name: base
channels:
  - conda-forge
dependencies:
  - pyopenssl=20.0.1
  - python=3.9.1
  - requests=2.25.1

the build goes without error but when I try to run a container similar to the quickstart:
docker run -it --rm mamba:existing python --version

I get error:
critical libmamba Cannot activate, prefix does not exist at: ''

What am I missing here or is there an underlying issue with any ot the .sh scripts related to the ENTRYPOINT or environment variabless?

[wholtz]

Hello @JaakkoAhola and thank you for the report.

It appears the behavior of micromamba activate "" changed from activating the default environment to throwing the error you were seeing. I have updated the _activate_current_env.sh script to substitute in the value of base when $ENV_NAME is not set -- #366.

You can add ENV ENV_NAME=base to your Dockerfile and it should work. Or you can wait a few minutes for the new images to finish building and then your Dockerfile should work as-is.

Please let us know if this resolves the issue for you.

[JaakkoAhola]

Thanks @wholtz now it works like a charm (I pulled new images).