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Installation

NextITS was primarily developed for Linux. To run it from a command line on Windows, please use Windows Subsystem for Linux (WSL).

All pipeline dependencies were encapsulated in Singularity and Docker containers, which will be automatically downloaded with the first run of NextITS. Only the main dependencies must be installed manually. They include:

Nextflow

Nextflow is the workflow manager responsible for coordinating and executing all command line tools seamlessly.

Manual installation

Nextflow (>=23.04.0) requires Java 11 (or later, up to 20) to be installed.

To install Java, you may use your system's package manager.
If you're using Debian/Ubuntu, execute the following command:

sudo apt-get update
sudo apt-get install default-jdk

Alternatively, you may install Java using SDKMAN!:

curl -s "https://get.sdkman.io" | bash
sdk install java 17.0.6-amzn

Then, install Nextflow:

wget -qO- https://get.nextflow.io | bash
chmod +x ./nextflow
mkdir -p ~/bin & mv ./nextflow ~/bin/

Installation using conda

It is possible to install the basic dependencies using conda, a package and environment management system. Here, we will use mamba, which is a reimplementation of the conda package manager in C++ (it has a much faster dependency solver). 

mamba install -c bioconda nextflow

If you do not have conda and mamba, they may be installed running the following commands: 

## Install `miniconda`
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
bash /tmp/miniconda.sh -b -p $HOME/miniconda
~/miniconda/bin/conda init bash
source ~/.bashrc
rm /tmp/miniconda.sh

## Install `mamba`
conda install -c conda-forge mamba

Conda

For more details, see https://docs.conda.io/en/latest/miniconda.html

Container engines

NextITS integrates numerous bioinformatic tools, and managing their installations and updates can be quite intricate for users. To simplify this, all these tools are packaged within containers. This not only makes installations hassle-free but also ensures consistent software versions, guaranteeing reproducible results across different systems.

NextITS supports two container systems: Singularity and Docker.

Singularity is often the preferred choice for High-Performance Computing (HPC) environments due to its compatibility and security features. On the other hand, Docker might be a tad easier to set up on local systems, making it a popular choice for personal use.

Singularity

To install Singularity on Debian-based systems (including Ubuntu), run:

## Download dependencies
sudo apt update && sudo apt install -y \
    build-essential libssl-dev uuid-dev libgpgme11-dev libarchive-dev \
    libseccomp-dev wget pkg-config git cryptsetup dh-autoreconf squashfs-tools

## Download GO
export VERSION=1.18.1 OS=linux ARCH=amd64 && \
  wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
  sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
  rm go$VERSION.$OS-$ARCH.tar.gz

echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc && \
source ~/.bashrc

## Check Go installation
go env

## If conda points to wrong locations for Go, reassign environmental variables
export GOTOOLDIR="/usr/local/go/pkg/tool/linux_amd64"
export GOROOT="/usr/local/go"

## Download singularity
export VERSION=3.9.8 && \
  wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
  tar -xzf singularity-ce-${VERSION}.tar.gz && \
  cd singularity-ce-${VERSION}

## Compile and install Singularity
./mconfig && \
  make -C builddir && \
  sudo make -C builddir install

Singularity on HPC clusters

If you are working on an HPC cluster, your IT team probably installed Singularity as a Linux Environment Module.
You may check Singularity availability using
module avail singularity
If it is present on your system, you will need to load the module prior to running NextITS.
E.g., module load singularityce/3.9.1

Docker

To install Docker on Ubuntu, run the following commands.
For more details, see the Docker installation instructions. 

sudo apt-get install \
    apt-transport-https \
    ca-certificates \
    curl \
    gnupg-agent \
    software-properties-common

## Add Docker’s official GPG key:
sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
sudo chmod a+r /etc/apt/keyrings/docker.gpg

## Set up the repository
# Ubuntu
echo \
  "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
  "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

sudo apt update
sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

sudo groupadd docker
sudo usermod -aG docker $USER
newgrp docker

Databases

For ITS amplicons, you may use the following database for reference-based chimera removal:
https://owncloud.ut.ee/owncloud/s/iaQ3i862pjwYgdy.
This database originates from the most recent version of UNITE, version 9.

Test

Download the pipeline and test it on a minimal dataset with a single command

nextflow run vmikk/nextits -r main -profile test

Containers

Singularity

Download container from the Singularity library

singularity pull --arch amd64 library://vmiks/nextits/nextits:0-0-5

Build custom Singularity image

git clone https://github.com/vmikk/NextITS
sudo singularity build NextITS.sif ./NextITS/containerfiles/main_container.def

Docker

Download container from Docker Hub

docker pull vmikk/nextits

Build custom image

git clone https://github.com/vmikk/NextITS
docker build --tag nextits --file NextITS/containerfiles/NextITS.dockerfile .

Other container engines

Other container engines

In the future, we plan to add support for the other container engines (e.g., Podman, Shifter, or Charliecloud) in NextITS.