Installation¶
ViroConstrictor is only available on Linux (or Linux-based) operating systems. MacOS may also work but is not tested. ViroConstrictor will not work on Windows.
Installation with conda¶
ViroConstrictor releases are published on Bioconda to allow for easy installation.
If you already have Mamba installed then please use the command below:
mamba install -c conda-forge -c bioconda viroconstrictor
Click here if you don't have mamba installed in your system already
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 is to ensure there will be no conflicting dependencies.
You can create a dedicated environment and install viroconstrictor in it through a single command with both mamba and conda.
The following command will use mamba to create a new environment named 'pipeline_env' with viroconstrictor installed in it.
mamba create --name pipeline_env -c conda-forge -c bioconda viroconstrictor
You can change "mamba" for "conda" in the command above if you prefer to use conda or if mamba is not installed on your system.
Download and installation from source¶
First start by cloning 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 then please use the following command below where you replace {VERSION} with the version that you want.
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
Make a new Conda environment before continuing
If you have Conda installed on your system, please create and activate a new environment before continuing.
Use the following command to create and activate a new Conda environment named "ViroConstrictor" based on the environment-recipe we provide in the github-repository
conda env create -f env.yml; conda activate ViroConstrictor
Once the ViroConstrictor repository is downloaded and you've created a conda environment to work in then you can install the downloaded package with pip:
# Install the downloaded package with pip
pip install .
ViroConstrictor should now be installed!
You can verify if installation was successful by typing viroconstrictor --version on the command-line, this should show the installed ViroConstrictor version.