Globus CLI

Globus CLI is a command line wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.

Installation

Instructions for installing Globus CLI on your local compute can be found through the official Globus documentation. Globus CLI can be installed either with pip or pipx. Globus CLI is also available on Afton/Rivanna as an Lmod module and can be loaded with

module load gcc globus-cli

Ensure that Globus Connect Personal is installed on your local computer and a personal collection is created. This is reqired to serve as the source endpoint.

Authentication

Run globus login to log into Globus for Globus CLI credentials. Following this, run globus session update --all to update your active Globus CLI session.

Endpoint Configuration

Source Endpoint

Run globus endpoint local-id on the command line to obtain your local endpoint ID.

Destination Endpoint

The Destination endpoint for UVA Standard Security Storage is af187d15-768f-4449-8670-d00e1eb1ce6a

Note: Destination folders are user-specific and should not be hardcoded. Each researcher will have a unique destination path.

Sync Strategies

Below is a key command to perform recursive folder transfers:

globus transfer --recursive --sync-level checksum SOURCE DEST

Recursive Transfer The --recursive flag ensures:

Nested folders transfer correctly
Folder structure is preserved
All files inside subdirectories are included

Sync-Level Options

Option	Purpose
`exists`	Skip files that already exist at destination
`size`	Compare files by file size
`mtime`	Compare files by modification time
`checksum`	Compare actual file content (strongest guarantee)

Recommended Default: checksum

Checksum is recommended because:

It provides the strongest correctness guarantee
It avoids timestamp mismatch issues common across systems
It is best suited for research data integrity requirements

Alternative — mtime: Useful when speed matters more than strict verification and timestamps are reliable across systems.

Matlab Example

MATLAB’s system() function can be used to call Globus CLI commands.

Download matlab-globus.m for a simple template on how to configure a matlab script to transfer files automatically with Globus CLI.

The Matlab script sets source and destination endpoints and paths along with a filename and the full file path to the globus executible. The script then generates and saves a png plot. Finally, the globus transfer command is setup prior to calling the system() function to execute the transfer.

Note: Destination directories should not begin with a forward slash (/). The destination path needs to be relative since it's a Globus Connect Server v5 Mapped Collection endpoint.

Considerations and Error Handling

Authentication Expiry

rerun:

globus login

Missing Session Consent

rerun:

globus session update --all

Permission Denied

Usually indicates a destination write access issue. Verify endpoint permissions.

File Not Found

Usually caused by an incorrect source path. Verify the local path before running.

Duplicate Transfer Conflict (409 Conflict)

Occurs when an identical transfer is already running.
Resolution:

globus task list
globus task cancel <TASK_ID>

Important Constraint

Full reauthentication cannot be safely automated. Globus intentionally requires user-mediated consent for protected resources.

You may periodically need to:

Approve browser login
Complete session consent
Reauthenticate when tokens expire

Last updated on Feb 2, 2023