The lab uses Mac workstations running Mac OS X, which come pre-configured to University standards by IT systems. We established a setup procedure to standardise the work environment in the lab and streamline know-how sharing.

Upon receiving your machine, you should go through the setup procedure before working on your projects.

Update Mac OS X

Make sure that you are running latest Mac OS X version before installing any tool. To do that, go to: System Preferences > Software Update. The system will automatically check the presence of new updates and, if so, download and install them by pressing the Update Now button.

Install Developer Tools

Developers Tools is a package including the basic tools for development on Mac OS X, including gcc, python and git. To install Developer Tools, open a Terminal and run the following command:

xcode-select --install

press the Install button and agree to the license terms.

Install Visual Studio Code

Visual Studio Code (VSC) is a powerful open-source IDE, which provides excellent tools for code development, including autocomplete, online debug, and Latex live compilation.

To install VSC, download the installer from: Move the application from the Downloads folder to the Applications folder, which you can find in the Finder.

Recommended plugins to install:

  • Better comments
  • Code spell checker
  • Docker
  • Git Graph
  • EditorConfig for VSCode
  • Git History
  • Latex workshop
  • Nextflow
  • Remote containers
  • Remote - SSH
  • Rewrap
  • Todo Tree

Install Docker

The lab uses Docker containers as the underpinning execution system for the projects. You can install the latest release from

Install Nextflow

Nextflow is the default workflow orchestration system. You can install Nextflow from the command line by running:

curl -s | bash

Install miniconda

You should use miniconda to install any software you might need, since it allows user-level installations of most common Unix software. If you cannot find your software in the default channel, please check also the conda-forge and bioconda channels.

To install miniconda, download the installer in your home directory as follows:


Then, run the installer as follows:


and answer 'yes' to each question including the default location. Finally, activate your installation by running:

source ~/.bashrc

Install Pipx

Many tools we use are written in Python and, depending on how your system and projects are configured, they might create unwanted problems, which can be easily avoided by using Pipx.

To install Pipx, open a Terminal and run the following command:

python3 -m pip install --user pipx
python3 -m pipx ensurepath

Install cookiecutter

cookiecutter is a command-line utility that creates folder structures from a template. We use cookiecutters to bootstrap all our projects.

To install cookiecutter, open a Terminal and run the following command:

pipx install cookiecutter

Install bump2version

We manage semantic versioning using bump2version, which can be installed by opening a Terminal and run the following command:

pipx install bump2version