Uploading Data from your Local Computer

Warning

Uploading to DNAnexus from your laptop should not be done over the VPN — ensure you are disconnected before continuing with this guide!

DNAnexus provides a command line utility, dx, to enable users to upload input data, download results, and run workflows in the cloud. Click here to learn about all of the commands included in dx.

The dx command line tool is written in Python. It can be installed onto your computer using pip install dxpy. However, many computers ship with multiple versions of Python, and that can lead to many really strange errors (e.g. one version of Python trying to load libraries from a different version of Python). Thus, we highly recommend the use of conda environments to create an isolated Python environment and install dx there.

Tip

If you are interested in learning more about the features provided by conda, their getting started guide is quite good. This is not strictly necessary for continuing with this guide.

Installing via conda

To install conda and start creating isolated Python environments, you can visit the conda download documentation and complete the install instructions for your operating system. Be sure to select "Python 3.X version" when choosing which version to download. Once you complete installation, you should be able to use the conda command in your terminal.

conda can be used to create multiple, independent Python environments. To leverage it to use dx, you'll need to do two things:

  • a one-time creation of a Python 3 environment with dx installed.
  • an environment activation step for every new terminal you open. Note that the environment we create will not be accessible without this explicit activation step.

To create an isolated Python 3 environment with dxpy installed, use the following command (you can give your environment any name, here we name it dx-env).

# conda create -n [environment-name] python=3 dxpy -y
conda create -n dx-env python=3 dxpy -y

Once you the environment is created, you can run this command each time you open a new terminal to ensure that environment is active.

# conda activate [environment-name]
conda activate dx-env

You should now be able to use the dx command line tool in your terminal.

dx --help

Authenticating

Next, you'll need to configure the dx command line tool with access to your St. Jude Cloud account. Rather than exposing your username and password, best practice is to generate an authentication token that lives for a short period of time instead. You can do so by following this guide on how to generate a DNAnexus authentication token.

Replace <auth-token> with your own token in the example below.

dx login --token <auth-token> --noprojects

Upload and download files

With DNAnexus toolkit installed and configured, files can be transferred between St. Jude Cloud and your local computer by running dx upload and dx download. To get acquainted with the command, you can view the relevant help messages.

dx upload -h
dx download -h

To upload a file sample.1.bam to the /test/ folder in the project-alpha cloud project, you could use the following command:

dx upload sample.1.bam --destination "project-alpha:/test/"

To download all files in the /results/ folder in the project-alpha cloud project to the current working directory, you could use the following command:

dx download -r "project-alpha:/results/"

The dx command line utility and its upload/download subcommands have many options you can configure based on your use case. We recommend you view the help messages or reach out to us on the St. Jude Cloud helpdesk Slack channel for more information.