Conda / Mamba

Overview

Conda is a cross-platform package and environment manager widely used in bioinformatics. Mamba is a drop-in replacement that resolves dependencies in C++ and is significantly faster. Together with the Bioconda channel they provide pre-built packages for thousands of bioinformatics tools.

This page covers installation, environment management, and best practices for reproducible analyses.

Installation

Install Miniforge, a minimal Conda distribution that bundles Mamba and defaults to conda-forge.

# Install Miniforge (includes mamba)
curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh

Note

On macOS, replace Linux-x86_64 with MacOSX-x86_64 (Intel) or MacOSX-arm64 (Apple Silicon).

After the installer finishes, restart your shell so that the mamba and conda commands are available.

Basic Usage

Creating an environment

Always create a dedicated environment per project and pin package versions.

# Create an environment for an RNA-seq project
mamba create -n rnaseq -c conda-forge -c bioconda \
  fastqc=0.12.1 fastp=0.23.4 star=2.7.11b \
  subread=2.0.6 samtools=1.19 multiqc=1.21

Activating and deactivating

# Activate the environment
mamba activate rnaseq

# When finished
mamba deactivate

Exporting and sharing

# Export the environment for reproducibility
mamba env export > environment.yml

A collaborator recreates the same environment with:

mamba env create -f environment.yml

Listing environments and packages

# List all environments
mamba env list

# List packages in the active environment
mamba list

Removing an environment

mamba env remove -n rnaseq

Key Parameters

mamba create

Flag

Description

-n

Name of the new environment.

-c

Channel to search (repeat for multiple channels).

--override-channels

Ignore default channels; use only those given with -c.

--strict-channel-priority

Resolve from channels in order (recommended to avoid mixed builds).

mamba install

Flag

Description

-n

Install into a named environment (instead of the active one).

--update-deps

Also update existing dependencies as needed.

--dry-run

Show what would be installed without making changes.

Best practices

  • Pin versions – samtools=1.19 ensures everyone gets the same build.

  • One environment per project – avoids dependency conflicts across unrelated tools.

  • Prefer Mamba – identical syntax to conda but 10–100x faster dependency solving.

  • Keep base clean – never install analysis tools into the base environment.

Expected Output

After creating and activating the rnaseq environment:

which fastqc
# ~/miniforge3/envs/rnaseq/bin/fastqc

fastqc --version
# FastQC v0.12.1

samtools --version | head -1
# samtools 1.19

See Also