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Installation

ViroConstrictor is available only on Linux (or Linux-based) operating systems. MacOS may also work, but it has not been tested. ViroConstrictor will not work on Windows.

Prerequisites

ViroConstrictor requires the following software to be installed on your system:

Installation with Conda

ViroConstrictor releases are published on Bioconda to allow for easy installation.

# Recommended: Install with Mamba (faster)
mamba install -c conda-forge -c bioconda viroconstrictor

# Alternative: Install with Conda
conda install -c conda-forge -c bioconda viroconstrictor

Installation through Mamba/Conda is the recommended method for installing ViroConstrictor.

Use a Dedicated Conda Environment for ViroConstrictor

It is recommended to install and use ViroConstrictor in a dedicated Conda environment. This will help ensure that there are no conflicting dependencies.

You can create a dedicated environment and install ViroConstrictor in it using a single command with either Mamba or Conda.

The following command will use Mamba to create a new environment named viroconstrictor with ViroConstrictor installed: 

mamba create --name viroconstrictor -c conda-forge -c bioconda viroconstrictor
mamba activate viroconstrictor

You can replace "mamba" with "conda" in the command above if you prefer to use Conda or if Mamba is not installed on your system.

Apptainer (formerly Singularity) runs bioinformatics tools in containers, which helps avoid software conflicts between different tool versions. ViroConstrictor can use its pre-built containers for its analysis tools when Apptainer is available. This reduces the need to install individual tools on your system.

Download and installation from source

First, clone the repository and make sure you're on the latest released version of ViroConstrictor:

Download a specific version

If you want to download a specific version of ViroConstrictor, use the following command, replacing {VERSION} with your desired version.

git clone -b {VERSION} --depth 1 https://github.com/RIVM-bioinformatics/ViroConstrictor.git; cd ViroConstrictor

# Clone the repository from GitHub and switch to the latest released version
git clone https://github.com/RIVM-bioinformatics/ViroConstrictor.git; cd ViroConstrictor; git checkout tags/$(git tag --sort=committerdate | tail -1) >> /dev/null

Create a New Conda Environment Before Continuing

Use the following command to create and activate a new Conda environment named ViroConstrictor based on the environment recipe provided in the GitHub repository:

conda env create -f env.yml; conda activate ViroConstrictor
The "ViroConstrictor" Conda environment should now be active

Once you have downloaded the ViroConstrictor repository and created a Conda environment to work in, install the package with pip:

# Install the downloaded package with pip
pip install .

Verify the installation

You can verify if the installation was successful by typing viroconstrictor --version on the command line; this should display the installed ViroConstrictor version.