Running DXJupyterLab

The DNAnexus platform provides an interface for starting and managing DXJupyterLab sessions. In this guide, we will show you how to start DXJupyterlab both from the UI and the CLI.

Note: A license is required to access DXJupyterLab. Please contact sales@dnanexus.com for more information.

Running from the UI

1. Select Tools > JupyterLab from the top main menu to start DXJupyterLab

If you have used DXJupyterLab before, the page will display a list of your previous sessions run across different projects.

2. Click on the New JupyterLab button in the top right corner

This will open a window from which you can start a new JupyterLab environment. In this window, you can configure your session, e.g. specify its name, select an instance type, and choose the project in which JupyterLab should be started.

If a snapshot file is provided, a DXJupyterLab environment saved previously will be loaded from that file. A snapshot tarball file can be created when running a JupyterLab session.

You can adjust the duration of the session, after which the environment will automatically shut down. Based on this duration and the instance type, the estimation of the price will be shown in the bottom-left corner (if you have access to the billing information for the selected project).

If you select Enable Spark Cluster, a JupyterLab environment with a standalone Spark cluster will be started. With this option, you can also set the number of nodes in the cluster. This number includes the master (one node) and the worker nodes.

3. Initiate the session by clicking Start Environment

First, the JupyterLab will be in an Initializing state, where it waits for the worker to spin up and for the JupyterLab server to be up and running. Clicking on the row corresponding to your session and the i icon in the top right corner will display more information corresponding to the JupyterLab job.

4. Open a JupyterLab environment in your browser when the state is set to Ready

Once the JupyterLab server is running, the session state will change to Ready and the name of the session will turn into a link. By clicking this link, you can open a JupyterLab environment page in your browser. You can access your job via the URL https://job-xxxx.dnanexus.cloud, where job-xxxx is the ID of the DXJupyterLab's job.

Running DXJupyterLab from the CLI

You can start the JupyterLab environment directly from the command line by running the app:

$ dx run app-dxjupyterlab

Once the app starts, you may check if the JupyterLab server is ready to server connections, which will be indicated by the job's property httpsAppState set to running. Once it is running, you can open your browser and go to:

https://job-xxxx.dnanexus.cloud

where job-xxxx is the ID of the job running the app.

In order to run the Spark version of the app, use the command:

$ dx run app-dxjupyterlab_spark_cluster

You can check the optional input parameters for the apps on the DNAnexus platform (platform login required to access the links):

From the CLI, you can learn more about dx run with the following command:

$ dx run -h APP_NAME

where APP_NAME is either app-dxjupyterlab or app-dxjupyterlab_spark_cluster.

Next steps