Frequently Asked Questions

Why am I getting the error libmamba Could not solve for environment specs?

This indicates that micromamba was unable to find a set of packages which met all the constraints that were set for the environment.

This can happen if you forgot to include a channel that is the source for a required package.

This error sometimes occurs when moving from one CPU architecture to another, such as when moving from x86 to ARM-based CPUs (such as Apple M1 and M2 CPUs). Some conda repositories do a good job of supporting multiple architectures (such as Conda Forge), but others only support x86 CPUs (Bioconda). You can work around this by forcing docker build ... to emulate another CPU architecture by appending --platform=linux/amd64 to the FROM line of your Dockerfile. However, emulation can result in significantly slower builds.

Why do I get errors when building the example Dockerfiles?

Docker Desktop has a configuration setting for how much disk space to use. When this limit is reached, the error messages thrown by the container may not seem related to disk space. For example:

  • micromamba install ... may give the error libmamba Non-writable cache error``

  • apt-get install ... may give the error At least one invalid signature was encountered.

To free up some of the disk space allocated to Docker, execute docker system prune --all. Then attempt the docker build ... command again.

Why am I getting the error critical libmamba Subprocess call failed. Aborting.?

docker had a change in how ulimit values are set within containers starting in docker v22.10. By passing docker build or docker run the flag --ulimit nofile=65536:65536 you can increase the nofile limit within the container.

How do I install software using apt/apt-get/apk?

The default user in mambaorg/micromamba does not have root-level permissions. Therefore you need to switch to user root before installing software using the system package manager. After installing the software you should switch back to $MAMBA_USER:

Dockerfile
FROM mambaorg/micromamba:2.8.1

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

USER root
RUN apt-get update && apt-get install -y --no-install-recommends \
    bluetooth \
    && rm -rf /var/lib/apt/lists/*
USER $MAMBA_USER

How can I stop micromamba from hanging when emulating a different CPU architecture?

A bug in QEMU can cause micromamba install ... to hang when emulating a different CPU. In particular, this has been observed when emulating x86 on ARM-based CPUs (such as Apple M1 and M2 CPUs). To work around this, you can configure micromamba to use only one thread for extracting packages:

micromamba config set extract_threads 1 \
&& micromamba install ...

For more information see issue #349,

How can I use a mambaorg/micromamba based image in a GitHub Action?

GitHub Actions override the two methods our images use to automatically activate environments. First, the ENTRYPOINT script is disabled and second, the ~/.bashrc file is not sourced becuase the location of the home directory is modified.

To enable automatic activation of environments, you can use the _entrypoint.sh script as the shell command in your GitHub Action.

jobs:
  my_job:
    runs-on: ubuntu-latest
    container:
      image: mambaorg/micromamba:latest
      options: --user=root
    steps:
    - uses: actions/checkout@master
    - shell: _entrypoint.sh /bin/bash --noprofile --norc -eo pipefail {0}
      run: |
        micromamba info
        which micromamba

If you are using the actions/checkout action, you will need to add the --user=root option to the container section of your GitHub Action. This is because the actions/checkout action creates a directory in the container that is owned by root.

How can I use a mambaorg/micromamba based image with apptainer?

There are three apptainer/singularity sub-commands that can be used to execute a container:

  1. apptainer run will execute the entrypoint script and automatically activate the base environment.

  2. apptainer exec does not execute the entrypoint script and therefore does not automatically activate the base environment. By prepending /usr/local/bin/_entrypoint.sh to the command you want to execute within the container, you can activate the base environment. For example:

    apptainer exec /usr/local/bin/_entrypoint.sh micromamba info

  3. apptainer shell does not execute the entrypoint script and therefore does not automatically activate the base environment. By supplying the --shell /usr/local/bin/_apptainer_shell.sh option to apptainer exec, you can activate the base environment. This option can alternatively be supplied via the APPTAINER_SHELL environment variable.