Using Mamba-forge to Manage Bioinformatics Software

The Problem: Software Installation in Bioinformatics

Bioinformatics pipelines often require many tools — and these tools frequently have conflicting dependencies. For example, one tool might require Python 3.8 while another needs Python 3.11, or two tools might each depend on different versions of the same library.

Installing everything system-wide quickly becomes a mess. The solution is to use isolated environments, where each project (or group of tools) gets its own set of packages that don’t interfere with each other.

What is Conda?

Conda is a package and environment manager. It lets you:

• Install tools (and all their dependencies) with a single command
• Create isolated environments that can be activated or deactivated
• Switch between different versions of the same tool without conflict

Conda is widely adopted in bioinformatics because most tools are available through two community channels:

• conda-forge — general-purpose packages
• bioconda — bioinformatics-specific tools

Installing Mambaforge

Mamba is a faster, drop-in replacement for the conda command. Mambaforge is a minimal installer that bundles Mamba with conda-forge as the default channel — making it the recommended starting point.

Download and run the installer

Here we show Linux (Intel) example, but see conda-forge download page for other platforms.

# Download the Mambaforge installer for Linux
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"

# Run the installer (follow the prompts)
bash Miniforge3-Linux-x86_64.sh

After installation, either open a new terminal or run:

source ~/.bashrc

You should now see (base) at the start of your prompt, indicating the base environment is active.

⚠ ️ Important: Configuring the Channel Mirror QIBC Users)

By default, Mamba fetches packages from Anaconda-hosted servers (anaconda.org). These are blocked on the HPC network.

To work around this, you need to redirect Mamba to an alternative mirror hosted by prefix.dev. This is done by editing (or creating) the ~/.condarc configuration file in your home directory.

# Add channel_alias line to Conda config file
echo 'channel_alias: https://repo.prefix.dev/' >> ~/.condarc

What each setting does:

You only need to do this once — the setting persists across all environments and sessions.

Basic Usage

Creating an environment

Rather than installing everything into base, create a dedicated environment per project or workflow:

# Create a new environment called "metax" with a few tools
mamba create -n metax \
  -c conda-forge -c bioconda \
  seqkit kraken2 bracken fastp multiqc

Activating and deactivating

# Activate the environment
conda activate metax

# Your prompt will change to (metax) — tools are now available
kraken2 --version

# Deactivate when done
conda deactivate

Installing additional tools into an active environment

# Make sure the environment is active first
conda activate metax

# Then install
mamba install -c bioconda seqfu

Listing your environments

conda env list

Quick Reference

• 💡 Tip: Always prefer mamba over conda for installing packages — it uses a faster dependency solver and is significantly quicker, especially for large environments.

• 💡 Tip: Avoid installing tools directly into base. Keep base clean and create a fresh environment for each project or analysis type.