Introduction

We described the mission of Dockstore on our about page, but now it’s time to learn how to actually use it as a contributor.

This “Getting Started” series is an introduction to everything required to properly use Dockstore as a contributor of workflows or tools. It is designed to be somewhat modular, so if you wish to jump into any individual topics, you may do so. But if you follow it in order, you’ll learn an overview of how Docker and workflow languages like CWL, WDL, Nextflow, and Galaxy are changing how scientists use and create tools via a series of tutorials which goes through the whole process of:

• Creating a Docker image that an analysis will run within

• Describing a simple analysis with a descriptor file written in one the following languages: CWL, WDL, Nextflow, or Galaxy

• Creating a Dockstore account

• Registering a tool or a workflow on Dockstore

The tool we will be using throughout this tutorial is BAMStats. It is a tool for summarising Next Generation Sequencing alignments. It accepts a BAM file as input and produces a ZIP file containing an HTML report on the alignment.

Assumptions

Note that this tutorial series assumes you are running on a system that can run Docker. This isn’t the case for all users, especially HPC users. Read our notes on Docker alternatives for more details. But if you cannot run Docker, that does not mean you cannot use Dockstore – you can still search for tools and workflows written by other people, and import workflows to our cloud compute partners.

This tutorial was designed with Linux (specifically Ubuntu) in mind, but will work almost exactly the same for Mac users. If you are a Mac user and run into errors, make note of this FAQ entry.