In this tutorial, you will learn how to create and run a notebook in JupyterLab on the platform, download data from the notebook, and upload results to the platform.
First, launch DXJupyterLab in the project of your choice, as described in the Running DxJupyterLab guide.
Once your JupyterLab session is running, click on the
DNAnexus tab on the left sidebar to see all the files and folders in the project.
To create a new empty notebook in the DNAnexus project, select
New Notebook from the top menu.
ipynb file will be created and viewable in the DNAnexus project browser, which refreshes every few seconds.
You can rename your file by right-clicking on its name and selecting
You can open and edit the newly created notebook directly from the project (accessible from the
DNAnexus tab in the left sidebar). To save your changes, simply hit
Ctrl/Command + S or click on the
save icon in the Toolbar (an area just below the tab bar at the top). A new notebook version will land in the project, and you should see in the "Last modified" column that the file was created recently.
Since DNAnexus files are immutable, whenever you save the notebook, the current version is uploaded to the project and replaces the previous version, i.e. the file of the same name. The previous version is moved to the
.Notebook_archive with a timestamp suffix added to its name. Saving notebooks directly in the project as new files ensures that your analyses won't be lost when the DXJupyterLab session ends.
To process your data in the notebook, the data must be available in the execution environment (as is the case with any DNAnexus app).
You can download input data from a project for your notebook using
dx download in a notebook cell:
%%bashdx download input_data/reads.fastq
You can also use the terminal to execute the
If your notebook generates any data you'd like to keep, you should upload it to the project before the session ends, i.e. before the worker in which the JupyterLab runs is terminated. You can do it directly in the notebook by running
dx upload from a notebook cell or from the terminal:
%%bashdx upload results.csv
NOTE: If you create a notebook from the Launcher or from the top menu (
Notebook), the notebook will not be created in the project but in the local execution environment. In order to move it to the project, you will have to upload it to the project manually. Make sure you upload your local notebooks to the project before the session expires, or work on your notebooks directly from the project, so as not to lose your work.
Check the References guide for tips on the most useful operations and features in the DNAnexus JupyterLab.