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Introduction to software management using Conda

steps to install software management tool
Bioinformatics tools often have complicated dependencies depending on the Operating System

Conda, an open-source package manager, helps to curb these limitations. The link below gives a detailed description of Conda as a package manager.

A condensed version of the Conda package management is known as Miniconda. Miniconda is an easy option for users who prefer a lighter installation of Conda than the complete Anaconda distribution. It is specifically created to give this lightweight and minimalistic installation.

Installing Miniconda

Download Miniconda for your specific OS to your home directory



screenshot of the result of running the wget command

macOS Intel x86:

curl -O

screenshot of the result of running the curl command



screenshot of the result of running file on linux


screenshot of the result of running file on Mac

  • Follow all the prompts: if unsure, accept the defaults
  • Close and re-open your terminal
  • If the installation is successful, you should see a list of installed packages with
conda list 

If the command cannot be found, you can add the Anaconda bin to the path using:

export PATH=~/miniconda3/bin:$PATH

screenshot of the result of running export PATH command

Importing conda environment with all required tools for the course

a. Import conda environment from yml file. Please download and unzip the attached yml file before installing the environment.

conda env create -n MOOC --file MOOC.yml

b. To activate the conda environment

conda activate MOOC

Installing tools on macOS with M1 or M2 chips

Conda does not work on macOS with M1 or M2 chips. Use brew to install the required tools. “brew” refers to the primary command-line tool used to interact with the Homebrew package manager. It is the command you use to install, manage, and update software packages on macOS and Linux systems. The name “brew” is short for “Homebrew.”

A detailed description of Homebrew can be found here:

Installing brew:

Step 1:

mkdir homebrew && curl -L | tar xz --strip 1 -C homebrew

screenshot of a listing that appears upon running the mkdir commands from previous sentence

Step 2:

eval "$(homebrew/bin/brew shellenv)"

brew update --force --quiet

chmod -R go-w "$(brew --prefix)/share/zsh"

screenshot of the listing upon running the previous commands

To install the tools using brew, run the following command:

brew install FastQC BWA Samtools BCFtools Freebayes sratoolkit

screenshot of the listing upon running the previous brew command

MultiQC is not available on Homebrew but can be installed using pip:

pip3 install multiqc

screenshot of the listing upon running the previous pip3 command

© Wellcome Connecting Science
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Bioinformatics for Biologists: Analysing and Interpreting Genomics Datasets

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