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.
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
Docker is not currently installed by default on GridION devices. To install docker follow the instructions below.
A terminal window will open:
sudo apt update sudo apt install docker.io sudo usermod -aG docker <username>where
<username>should be replaced with your computer username.
docker run hello-world
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.
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:
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:
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.
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.
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
The EPI2MELabs Launcher is most easily installed:
sudo apt update sudo apt install ont-epi2melabs-launcher
In the event you wish to reinstall the Launcher on GridION and PromethION it is vital to run purge to remove the original version of the Launcher and its associated configuration files.
sudo apt purge ont-epi2melabs-launcher sudo apt autoremove
sudo apt update sudo apt install ont-epi2melabs-launcherThe first step removes the Launcher and any associated configuration files and dependencies that are only required by the Launcher. The second step reinstalls the labslauncher.
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.
The EPI2ME Labs launcher interface has all the functionality required for users to manage the EPI2ME Labs notebook server.
There are three options on the Start Server page:
Navigate the directory tree until the dialog is within your selected folder, then click Open.
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.
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.“:
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:
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.
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.