Conda and Bioconda Tutorial: Install Bioinformatics Tools in Environments

Chapter 2 of 5: Installing Miniforge and setting up Bioconda

What you need

• A Linux or macOS terminal. On Windows, use WSL2 with Ubuntu (Bioconda does not build packages for native Windows). The Linux tutorial in this path shows how to set up WSL2.
• About 3–5 GB of free disk space for Miniforge and a few environments. Big environments (R with Bioconductor, deep learning) need more.
• An internet connection. No admin (sudo) rights are needed.
• Basic Linux commands: cd, ls, cat. If these are new, do the Linux Command Line for Bioinformatics tutorial first.

Step 1: Download and run the Miniforge installer

Why: Miniforge gives you conda and mamba, already pointing to conda-forge, with no licence questions. You install it once, in your home folder.

Open your terminal (on Windows, open Ubuntu from WSL2) and run these two commands. The first downloads the right installer for your system; the second runs it.

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

• curl -L -O: download a file; -L follows the GitHub redirect, -O keeps the original file name.
• $(uname): prints your system name (Linux or Darwin for macOS), so the right installer is picked.
• $(uname -m): prints your CPU type (x86_64, aarch64 or arm64).
• bash Miniforge3-….sh: runs the installer script.

The installer asks three things. The exact wording changes between versions, but the answers do not:

1. Licence: press Enter, scroll with Space or press q, then type yes.
2. Install location: press Enter to accept ~/miniforge3 (inside your home folder).
3. Initialize conda for your shell? Type yes. This adds a few lines to your ~/.bashrc (or ~/.zshrc on macOS) so the conda command works in every new terminal.

Installation takes about 1–3 minutes. Now close the terminal and open a new one. You should see (base) at the start of your prompt.

Step 2: Check that conda works

conda --version
conda info

Look for three things: the platform (it should match your machine), the channel URLs (conda-forge, not repo.anaconda.com), and the envs directories (where your environments will live).

If you see conda: command not found, you answered “no” to the initialize question. Run this once, then open a new terminal:

~/miniforge3/bin/conda init bash

On macOS, replace bash with zsh.

Step 3: Add the Bioconda channels (run once)

Why: conda needs to know where to find bioinformatics tools and in which order to search the channels. These three commands come from the official Bioconda documentation. Run them exactly in this order.

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

• conda config: changes your conda settings, saved in the file ~/.condarc.
• --add channels bioconda: adds Bioconda to the top of your channel list.
• --add channels conda-forge: adds conda-forge above Bioconda. --add always puts the new channel at the top, so you add the lowest-priority channel first.
• --set channel_priority strict: tells conda to take each package only from the highest-priority channel that has it.

Now check the result:

conda config --show channels
conda config --show channel_priority

conda-forge must be first and bioconda second. If you also see defaults in the list (common if you used Anaconda or Miniconda before), remove it:

conda config --remove channels defaults

# Strict channel priority (simplified)
for each package NAME the solver needs:
    for CHANNEL in channels, from highest to lowest priority:
        if CHANNEL has any build of NAME:
            candidates = builds of NAME in CHANNEL only
            stop searching lower channels for NAME
    pick the best candidate that satisfies all constraints
    (newest version first, then highest build number)

# Flexible priority: candidates come from ALL channels;
# higher channels are preferred, but a lower channel's build
# is used when it is needed to satisfy the other constraints.

No permission to change your settings? On a shared machine you can pass the same choices on every command instead. On the command line, channels are listed from highest to lowest priority, the opposite of conda config --add:

conda create -n qc fastqc multiqc --channel conda-forge --channel bioconda --strict-channel-priority

Step 4 (optional): Stop base from activating in every terminal

Why: base is where conda itself lives. If it is always active, you may install tools into it by accident. A small, clean base is the most common advice in the conda and Bioconda documentation.

conda config --set auto_activate false

Older conda versions call this setting auto_activate_base. If conda says the key is unknown, run conda config --set auto_activate_base false instead. You can still type conda activate to enter base when you need it.

Defaults are from the conda documentation and change only rarely. Check yours with conda config --show.

CONDA_SUBDIR=osx-64 conda create -n oldtool sometool
conda activate oldtool
conda config --env --set subdir osx-64