Installation

ViromeXplore requires Nextflow and either Singularity (default) or Docker to run.

Conda Installation

If you do not have root privileges and only have access to conda, you can install both Nextflow and Singularity using the following command:

conda create -n ViromeXplore-env -c conda-forge -c bioconda singularity nextflow

This method allows ViromeXplore to run entirely within a conda environment.

System Installation

Alternatively, if you have root access, you can install Nextflow, Singularity, and Docker manually using system-level commands as shown below.

Install Nextflow

curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
nextflow -version

Install Docker

sudo apt-get update
sudo apt-get install -y \
  ca-certificates curl gnupg lsb-release

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg

echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] \
https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | \
sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

sudo apt-get update
sudo apt-get install docker-ce docker-ce-cli containerd.io
docker --version

Install Singularity

export VERSION=3.10.3
wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz
tar -xzf singularity-${VERSION}.tar.gz
cd singularity
./mconfig && make -C builddir && sudo make -C builddir install
singularity --version

Download the Github repository

git clone https://github.com/rhernandvel/ViromeXplore.git

cd ViromeXplore

ViromeXplore.nf is the main file which is needed to run the workflows as shown in the Running ViromeXplore section.

System Requirements

ViromeXplore has been validated on the following environment:

Ubuntu 22.04 LTS (x86_64 architecture)

The pipeline is expected to run successfully on other modern Linux distributions