Installation

Overview

All tools in this book are installed through Conda and Mamba, the standard package managers for bioinformatics. Miniforge is the recommended Conda distribution because it ships with Mamba (a fast, C++ drop-in replacement for conda) and defaults to the conda-forge channel.

This page walks you through installing Miniforge, creating isolated environments for your projects, and exporting them for reproducibility.

Installation

Download and run the Miniforge installer for your platform.

# 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

Follow the prompts and allow the installer to initialise your shell. Restart your terminal once installation finishes.

Note

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

Basic Usage

Creating an environment

Create a dedicated environment for each analysis project. Pin every package version so that results stay reproducible.

# 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 an environment

# Activate the environment
mamba activate rnaseq

All tools listed above are now on your $PATH. Deactivate with mamba deactivate when you are done.

Key Parameters

Flag / option

Description

-n

Name the new environment.

-c

Add a channel (use conda-forge and bioconda).

--override-channels

Ignore channels in .condarc and use only those on the command line.

--strict-channel-priority

Resolve packages from channels in the order listed (recommended).

Exporting for Reproducibility

Lock your environment so collaborators can recreate it exactly.

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

Share environment.yml alongside your analysis code. A collaborator recreates the environment with:

mamba env create -f environment.yml

Expected Output

After running mamba activate rnaseq, verify that tools are available:

fastqc --version    # FastQC v0.12.1
samtools --version   # samtools 1.19
multiqc --version    # multiqc, version 1.21

See Also