Installation Instructions for Nextflow, Docker, and Java JDK 17 LTS on Ubuntu

In this document, we provide instructions (with minimal assumptions of target hardware) required by a user to initiate testing of the pipeline.

If you need to install this pipeline on a cluster (HPC or K8s) then please refer the to the nf-core docs and community.

nf-core documentation

As the CholeraSeq pipeline uses nf-core template, the extensive documentation regarding installation, configuration and customization of the pipeline are applicable for CholeraSeq.

Prerequisites

Ubuntu Linux (18.04 or newer recommended)
curl and wget installed

1. Install Java JDK 17 LTS

Nextflow requires Java 17 or later. Here, we install OpenJDK 17 LTS:

sudo apt update
sudo apt install -y openjdk-17-jdk

The java version should NOT be an internal jdk release! You can check the release via java --version Notice the LTS next to OpenJDK line.


$ java -version
openjdk version "17.0.7" 2023-04-18 LTS
OpenJDK Runtime Environment (build 17.0.7+7-LTS)
OpenJDK 64-Bit Server VM (build 17.0.7+7-LTS, mixed mode, sharing)

2. Install Nextflow

# Download Nextflow
curl -s https://get.nextflow.io | bash

# Move Nextflow to a directory in your PATH
sudo mv nextflow /usr/local/bin/

Verify installation:

nextflow -v

nextflow run hello

Docker or Singularity

If your system administrator has setup Singularity or Apptainer for you, then please use the -profile singularity or -profile apptainer option. For Step-3 and Step-4 we assume that, you do have admin access for your machine and can install packages.

3. Install Docker

# Update package index
sudo apt update

# Install prerequisites
sudo apt install -y \
  ca-certificates \
  curl \
  gnupg

# 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

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

# Update package index again
sudo apt update

# Install Docker Engine
sudo apt install -y docker-ce docker-ce-cli containerd.io

Verify Docker installation:

sudo docker run hello-world

4. (Optional) Manage Docker as a Non-root User

sudo usermod -aG docker $USER
# Log out and log back in for group changes to take effect

You are now ready to use Nextflow with Docker and Java 17 on Ubuntu!

5. Run the test profile of CholeraSeq

This profile should download a small dataset and the relevant containers to initiate the pipeline execution.

# For users with access to docker containers
nextflow run CERI-KRISP/CholeraSeq -profile test,docker --outdir test_output


# For users with access to singularity containers
nextflow run CERI-KRISP/CholeraSeq -profile test,singularity --outdir test_output