EPI2ME Labs Quick Start

EPI2ME Labs facilitates routine bioinformatics analyses by allowing users to run Nextflow) workflows in a desktop application with an easy-to-use graphical interface. The app has been designed with ease of installation in mind in order to make sequencing data analysis as accessible as possible. Find installers for all major operating systems on our Downloads page and click here for guidance on how to install.

EPI2ME Labs

Every time EPI2ME Labs is started, it checks if all dependencies required for running workflows are available. If one or more are missing, it will show a panel letting you know that some additional setup is required. Click on the panel and the app will guide you through installing whatever dependency is still lacking. You can also refer to the Installation page for extra information.

Installing workflows

Scroll down on the landing page to find the workflows available. Click on the card of one of the workflows you are interested in and confirm the download by clicking “Install workflow”. The workflow will then be downloaded and saved on your machine for later use.

Importing workflows

You can also import your own (or community-developed) workflows as long as they adhere to some design principles. Have a look at this post to see if the workflow in question needs tweaking before it can be imported. To import a workflow, navigate to the Workflows tab and click on the “Import workflow” button.

Running a workflow

Once you have installed one or more workflows, head to the Workflows tab and click on a workflow you would like to run. From the next view you can launch the workflow (with your own data or a demo dataset) or go to results of previous runs. You can also open the folder where the workflow files are stored or switch to a different version.

In order to run the workflow, click on the big button to open the launch wizard. Fill out the form (required parameter groups are marked with a red “X” which will turn to a green tick when filled out correctly) and press the “Launch workflow” button.

As soon as the run has started, the app will take you to a different view from where you can interrupt the workflow or view the logs.

You can go back to the workflow’s main page and then click “Workflow history” to see the run we just started.

Once the workflow finishes, we can have a look at the report.