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Jupyter Lab

1. Search a Jupyter Lab

First log-in CyVerse DE

After you login to DE, open the Apps window and search for Jupyter Lab with key word Jupyter or JupyterLab.

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2. Launch analysis

Launch the Jupyter Lab app by clicking launch analysis. Before you launch, you can either drag and drop or browse the files that you want to use with Jupyter. There is currently no restriction of how many files and size of the files that can be launched along with JupyterLab app.

Note

The input files and/or folders can be selected under the ‘Parameters’ tab.

Tip

If you have a working Jupyter workbook, you can import it into the app using input files and/or folder.

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4. Create Jupyter notebook

Jupyter notebooks are documents that combine live runnable code with narrative text (Markdown), equations (LaTeX), images, interactive visualizations and other rich output. Jupyter notebooks (.ipynb files) are fully supported in JupyterLab.

If you want to create a notebook, you can do so by clicking the + button in the file browser and then selecting a kernel in the new Launcher tab. Currently there are 3 different notebooks available - Python3, Julia and R. Click on Python 3 under Notebook section in the JupyterLab Interface, which will open a new Jupyter Notebook. A new file is created with a default name. Rename a file by right-clicking on its name in the file browser and selecting “Rename” from the context menu.

To know more about notebooks in JupyterLab click here

Tip

To open the classic Notebook from Jupyter Lab, select “Launch Classic Notebook” from the Help Menu.

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Note

There are plenty other cool stuff that you can do in Jupyter Lab such as using consoles, using terminal and using text editor.

5. Write your code

Once you open a new notebook, you can start writing your code, put markdown text, generate plots, save plots etc.

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6. Complete and Save Outputs

After finishing your analysis, you can save outputs to data store by clicking the Analysis window, then select the VICE analysis that you are running and select Complete and Save Outputs under the “Analyses” button.

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After you had done this, you can find the outputs that you generated (if any) using the same steps as before, but this time selecting ‘Go To Output Folder’.

Warning

Currently, VICE can run for 48 hrs beyond which the apps will be terminated. If you have opted for email notifications from DE, then you’ll get a notification 1 day before and 1 hour before the app gets terminated. If you want to extend the time, you need to login to http://cyverse.run, find your analysis and then click the hour glass which automatically extends the app run time to 3 more days.

Fix or improve this documentation

7. Jupyter-lab with SQL

Now you can run SQL queries inside a notebook. Here is a quick launch


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