Cloud Workstation
Learn about the Cloud Workstation app, which lets you explore and manipulate data on the DNAnexus Platform, as you would on a local Linux machine.
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Learn about the Cloud Workstation app, which lets you explore and manipulate data on the DNAnexus Platform, as you would on a local Linux machine.
Last updated
Was this helpful?
sets up a virtual workstation that lets you access and work with data stored on the DNAnexus Platform, just as you would on a local Linux machine, but without having to download files to your computer.
You can configure this workstation to use any of the . You can easily save files or analysis results from your workstation session, to the project within which you launched it. You can also create a snapshot of the session, if you want to pick up work at a later date.
You'll need the dx command-line client to access the virtual workstation. if you haven't already done so.
You'll also need to if you haven't already done so.
From the command line, use the dx client to you'd like to work in.
Next, use dx run to launch Cloud Workstation, taking care to add the --ssh flag:
Once the app launches, you'll see a list of optional parameters:
Once you've either set or skipped the optional parameters, you'll be connected to the worker running Cloud Workstation. You'll see the following in your terminal:
To access a file within your virtual workstation, you must download it from a Platform project to the workstation. If you want to save a file from your workstation session, you must upload it to the workstation's parent project.
In order to do either, you must prepare your workstation by running the following two commands:
Your virtual workstation is now ready to use.
This includes files stored in the workstation's parent project.
You can download any file from any project to which you have access.
To download a file named my-file.txt from the parent project, use the command:
When downloading a file or files from a project other than the parent project, you might want to avoid having to enter the project ID. To do this, start by getting a list of projects to which you have access. Then choose a project:
Now you can download a file to your virtual workstation, by entering only the filename:
Your virtual workstation has network access, so you can download and use any tool you need during your session, just as you would on a Linux workstation.
Use the following commands to perform a test upload:
You should see the contents of your project change, with the new file test_file_from_workstation.txt appearing in the file list, between the first and second invocations of dx ls.
You can also shut down the workstation by finding the job in the UI's Monitor page, and clicking the Terminate button at the right end of the row displaying info on the job.
By default, your virtual workstation will launch on a mem1_ssd1_v2_x8 instance type, which has 8 cores, 16 GB of memory, and 180 GB of storage. To run the app on a different instance type, use the --instance-type flag with dx run, as in:
The Cloud Workstation app is set up to use Ubuntu 24.04.
When connecting to the execution environment, you are using the job's credentials to interact with the DNAnexus API. The job has a limited subset of your Platform user permissions. By default, a job running the Cloud Workstation app has VIEW permissions to all projects to which you have VIEW or greater permissions.
The Cloud Workstation app provides the minimum functionality necessary to support an interactive workstation.
Possible customizations include:
Specifying different inputs
Prepackaging external utilities for use within the worker
Changing the instance type of the worker
Changing access permissions
See the .
The first command unsets an environment variable that's set when the workstation is launched. This allows you to navigate from within the workstation to any of the projects to which you have access. The second command invokes to change your workstation's working directory, to that of the parent project.
For more information about these and other environment variables used within the execution environment, see this .
To access a file within your virtual workstation, you must download it to the workstation, using the command.
To download a set of reads from the SRR100022 exome from the public :
If you would like a tool or tools to be available within your workstation when it launches, you can .
If you want to save any files from your workstation session, you must upload these files to the workstation's parent project, using .
Note that if you changed project context as you downloaded files to your virtual workstation, you must use the --path flag with , to ensure you upload files to the correct project:
By default, your virtual workstation will automatically shut down once the maximum session length is reached. If you want to shut it down earlier, use the command, taking care to use $DX_JOB_ID to include the workstation's job ID:
See the for a full list of available instance types.
By default, the command hides projects to which you have only VIEW permissions. To see a list of those projects, use the command dx select --level=VIEW.
To make your own version with enhanced functionality, you can create a custom applet, based on the Cloud Workstation app. To get the original source code for the the Cloud Workstation app, run dx get app-cloud_workstation. See to learn how to build a custom applet that incorporates an existing executable.