10x Genomics Cloud CLI Reference

The 10x Genomics Cloud CLI is a command line interface (CLI) that allows you to upload FASTQ files to projects in your 10x Genomics account, create projects from the command line, and manage other tasks related to your 10x Genomics account.

It is an executable that can be run directly and requires no compilation or installation.


Downloading and unpacking

Download the 10x Genomics Cloud CLI for your operating system and unpack it to a convenient location. Make sure you download the 10x Genomics Cloud CLI for the operating system where your data lives. Your home directory is a good default location.

Linux

If you’re using a Linux system, use the command below to download:

curl -f -o txg-linux-v1.0.1.tar.gz https://cf.10xgenomics.com/cloud-cli/1.0.1/txg-linux-v1.0.1.tar.gz

and then to unpack:

tar -zxvf txg-linux-v1.0.1.tar.gz

MacOS

If you’re using a MacOS system, open the Terminal app and use the command below to download:

curl -f -o txg-macos-v1.0.1.tar.gz https://cf.10xgenomics.com/cloud-cli/1.0.1/txg-macos-v1.0.1.tar.gz

and then to unpack:

tar -zxvf txg-macos-v1.0.1.tar.gz

Windows

If you’re using a Windows system, download the latest version here:
10x Genomics Cloud CLI for Windows v1.0.1 (beta)

Alternatively, open cmd.exe and use the command below to download:

curl -f -o txg-windows-beta-v1.0.1.zip https://cf.10xgenomics.com/cloud-cli/1.0.1/txg-windows-beta-v1.0.1.zip

Available commands

txg [command] [flags]

Command Description
auth Manage authentication
fastqs Upload and manage FASTQs
help Help about any command
projects Manage projects


Global flags

The 10x Genomics Cloud CLI supports a number of flags for every command.

Flags Description
--access-token string Specify an access token to use. Default: the saved token from txg auth setup.
-H, --header header Extra header to include in the request when sending HTTP requests to a server. May be given multiple times to add multiple headers. Each header must be of the form 'Header: value'. Default: no extra headers.
-h, --help Display help and exit.
-q, --quiet Don't show progress or messages. Default: off.
-v, --verbose Display extra debugging information. Default: off.
--version Display version and exit.

Authentication

txg auth [command]

Command Description
txg auth reset Delete the saved access token (if it exists)
txg auth setup Set up authentication. Interactively walk through the process of setting up authentication. Running this command will prompt you to visit the 10x Genomics Cloud Analysis site, copy your access token, and paste it here. The access token will then be saved locally and reused for subsequent requests.
txg auth verify Verify the stored access token is valid and that the 10x Genomics Cloud Analysis service can be successfully reached. Returns a zero exit code if successful, nonzero otherwise.

FASTQ file upload and management

txg fastqs upload --project-id PROJECT-ID [insert path to fastqs]

Upload FASTQ files to a project in your account. For detailed instructions on uploading FASTQ files to a project, view our tutorial here.

Flags Description
-n, --new-project string Create a new project with the specified name and immediately upload the FASTQs to it.
-p, --project-id id Upload the FASTQs to the project with the specified ID. The project ID is unique ID automatically created for each project. The project ID is provided in the upload command available in your project.

txg fastqs list PROJECT-ID

List FASTQ files for the specified project ID. You can find the ID of a project by running txg projects list.


Projects

txg projects create --name NAME [--description DESC]

Create a new project with the specified name and optional description. The project name must be unique across all your projects.

Flags Description
--description string Project description (optional).
--name string Project name (required).

txg projects list [flags]

Display a list of your projects, optionally sorted by a specific field.

Flags Description
--sort-by string Sort the list by the specified field, which must be one of: id, name, created. Default: unsorted.

txg projects update PROJECT-ID [flags]

Update the name and/or description of the specified project. A project's ID can be displayed by running txg projects list.

Flags Description
--description string Set the project description.
--name string Set the project name.