Micromamba is a fast, lightweight version of the Mamba package manager. Unlike Miniconda, it comes as a single executable with no default Python installation or base environment, making it perfect for minimal installations.

Why Micromamba?

Traditional package managers like Conda can be slow and heavy. Micromamba offers:

• Fast installation and package resolution
• Minimal disk space usage
• No base environment overhead
• Full compatibility with Conda packages and channels

Installation

Linux and macOS

The recommended way to install Micromamba is using the automatic installation script:

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"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

For macOS users, you can alternatively use Homebrew:

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brew install micromamba

After installation, you’ll need to restart your shell or source your configuration file:

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source ~/.bashrc  # for bash
# or
source ~/.zshrc   # for zsh

Basic Usage

Setting up channels

First, let’s configure Micromamba to use conda-forge and bioconda channels:

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micromamba config append channels conda-forge
micromamba config append channels bioconda
micromamba config set channel_priority strict

Creating an Environment

Let’s create and activate a new environment called bioenv:

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micromamba create -n bioenv
micromamba activate bioenv

Installing Packages

Now let’s install seqfu from the bioconda channel:

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micromamba install -c bioconda seqfu

Common Commands

Here are some essential Micromamba commands:

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# List environments
micromamba env list

# Search for a package
micromamba search -c bioconda seqfu

# Update packages
micromamba update --all

# Remove a package
micromamba remove package_name

# Delete an environment
micromamba env remove -n bioenv

Updating Micromamba

You can update Micromamba itself using:

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micromamba self-update

Important Notes

• Micromamba uses MAMBA_ROOT_PREFIX to store environments (default is ~/micromamba)
• Unlike Conda, there’s no pre-configured base environment
• Micromamba is fully compatible with Conda packages and channels
• Configuration files (.condarc/.mambarc) are read if present but not shipped by default

Troubleshooting

If you encounter issues:

1. Ensure your MAMBA_ROOT_PREFIX is set correctly
2. Check if the channels are properly configured
3. Make sure you’ve activated the correct environment
4. Try running micromamba clean --all to clear the cache

Now you have a lightweight, fast package manager ready for your bioinformatics work. Happy computing!