Getting started

Setting up infrastructure

Depending on whether you plan to run the OpenPipelines workflows locally or in the cloud

Starting workflows locally

If you want to start workflows locally, you will need to install Nextflow.

Install Docker (optional)

Docker is a containerization platform that allows you to package your application and all its dependencies into a single image. It is used to run the analysis pipelines.

If you are planning on running the workflows locally, you will need to install Docker. You do not need to install Docker if the workflows will be run in the cloud using AWS Batch, Azure Batch, Google Cloud Batch, or other cloud-based compute environments.

To install Docker, follow the instructions here.

Install Java

Nextflow requires Java 11 or later. To check if Java is installed on your system, run:

java -version

If Java is not installed, you can download it from here.

Install Nextflow

Nextflow is distributed as a single executable file. To install it, run:

curl -s | bash

This command will download the latest version of Nextflow and store it in the current directory.

To install Nextflow system-wide, move the downloaded file to a directory in your $PATH, e.g.:

mv nextflow /usr/local/bin

Test the installation

To test the installation, run:

nextflow run hello -with-docker

Using Nextflow Tower

Nextflow Tower is a web-based user interface for running and monitoring Nextflow pipelines. If you are planning on using Nextflow Tower, a compute environment will need to be set up.