EPI2MELabs Quick Start Guide

The following guide illustrates installation and use of the EPI2ME Labs notebook server.

EPI2ME Labs can also be run on Windows 10, macOS and Linux. For Windows and macOS platforms follow the instructions at Docker Desktop to install Docker. Docker installations through Docker Toolbox are not supported. Please also be sure to select the Hyper-V option during installation. The EPI2ME Labs Launcher application is available for these platforms from the Software Downloads page on the Nanopore Community or the GitHub release page. Please see also the Windows/MacOS Docker Install section below.

Installation

The EPI2ME Labs server runs in a Docker container in order to provide an isolated and resettable environment. It can be controlled using the EPI2ME Labs launcher application. The instructions below will install both of these tools onto your system

GridIon/PromethION Docker install

Docker is not currently installed by default on GridION devices. To install docker follow the instructions below.

  1. Click on the Search your computer button.

search computer 1

  1. Search for “terminal”, and click on the Terminal application:

search computer 2

A terminal window will open:

terminal window

  1. Run the Docker installation command (you can copy and paste this into the terminal window and press Enter):

    sudo apt update
    sudo apt install docker.io
    sudo usermod -aG docker <username>

    where <username> should be replaced with your computer username.

  2. Close your terminal window.
  3. Log out of your GridION and log back in again.
  4. Open a new terminal window.
  5. To test docker is working correctly, run docker run hello-world

docker hello

Windows and macOS Docker install

EPI2ME Labs is supported on Windows 10 Profession (and Enterprise) and macOS through Docker Desktop. Use of Docker Desktop on Windows 10 Home through the use of Windows Subsytem for Linux 2 (WSL2) is untested. For the most part, users should simply follow the installation instructions for their system on the Docker website.

Data shares

During installation users may be asked to allow Docker access to parts of their file system; users should grant access to any locations where data resides they wish to analyse with EPI2ME Labs. In particular users are likely to want to add the MinKNOW output directory as a share in Docker.

It is possible to allow data shares to Docker after installation by opening the Docker Desktop program and navigating to its settings page:

docker data share

On Windows 10 it may be possible to avoid having to add folders manually in the Docker Desktop program by checking that application notifications are enabled in the system Settings:

docker share permission

With notifications enabled, users may see pop-ups like the following when running the EPI2ME Labs launcher; users should click “Share it” in these instances.

docker share notify

Resource Limits

By default Docker Desktop sets fairly conservative resource limits for itself, you may wish to change these in the Docker Desktop settings pane. We recommend setting the Memory limit to at least 8Gb (some EPI2ME Labs tutorials may require more as indicated in their introductions) and the CPUs to one or two less than the maximum value for your system.

docker resource

Install the EPI2ME Labs launcher application

The EPI2ME Labs launcher application provides a convenient way to start, stop, and update the EPI2ME Labs notebook server. The source code for the application is available in our GitHub repository

Installing the Launcher on GridION and PromethION

The EPI2MELabs Launcher is most easily installed:

  1. Copy and paste the following into the terminal window and press Enter:

    sudo apt update
    sudo apt install ont-epi2melabs-launcher
  2. Click on the Search your computer icon, and search for “EPI2ME”. Then click on the EPI2ME-Labs Server Control icon. This will start the launcher.

Installing the Launcher on Windows 10 and macOS

We provide a Windows 10 installer and an macOS Application bundle on the Downloads page. Simply download and run these files to install the EPI2MELabs Launcher on these platforms.

Start EPI2ME Labs from the launcher

The EPI2ME Labs launcher interface has all the functionality required for users to manage the EPI2ME Labs notebook server.

  1. To start a notebook server click the Start button to reach the Start Server screen:

start screen

There are three options on the Start Server page:

  • Select path: the location on your computer which you want to be visible within the notebooks
  • token: a security token (password) to allow access to the notebook interface
  • port: network port to access the notebook server interface

option screen

  1. The data location is pre-filled with a default data path. To select a different folder, click Select path to show the selection dialog:

path select screen

  1. Navigate the directory tree until the dialog is within your selected folder, then click Open.
  2. We strongly encourage updating the token to a unique value. The token provides an authentication method that allows only trusted users access to the EPI2ME Labs server and is used as an additional security layer to help prevent other users on the network from running code and accessing data. This token will be used later in the workflow to connect Google Colaboratory to the server.
  3. Click Start on the main screen to start the notebook server.

The first time a server is started the server components must be downloaded. This will not happen on subsequent server starts.

When the server has successfully launched, there will be a message at the bottom of the launcher interface stating “Server status: running.“:

server running

Updating the server

The EPI2ME Labs launcher application automatically detects when updates are available to the notebok server. Oxford Nanopore Technologies’ may occassionally provide updates to provide new features or improved performance.

When an update is available attempting to start or restart the notebook server when an update is available will result in the following being displayed:

Update available

  1. To update the server, press the Update button on the main screen. The new server components will be downloaded:

Update download

Run a tutorial

  1. With the EPI2ME Labs notebook server running, click the Open EPI2MELabs link within the Launcher: Open EPI2MeLabs
  2. On the landing page select the notebook you wish to open. Opening a notebook template will create a copy of the file as a new document for you to edit. Notebook launch
  3. You can see all your data in the location you provided in the launcher by clicking /epi2melabs in the sidebar: epi2melabs mount
  4. To copy your own data into the tutorial, right-click on the data file and select Copy path. Copy filepaths
  5. Follow the guidance provided in the tutorial to perform data analysis.

Running code cells

Running code cells in JupyterLab requires clicking the play button in the navigation bar at the top of the screen (or to the right-hand side of a code cell). There is also a “Run” tab that can be used to run multiple cells.

Run code cells

Bookmarks and navigating notebooks

The JupyterLab environment provides a table of contents menu in the left-hand sidebar. These navigation prompts can also be used to fold content visibility in the notebook.

Bookmarks


Providing open bioinformatics resources for nanopore sequencing. Research use only. Follow us on twitter.