Installing and Getting Started with the HuBMAP Command Line Transfer

The HuBMAP Command Line Transfer utility provides the functionality to download HuBMAP data of individual files and directories across multiple datasets/uploads at one time by specifying all downloaded data files and directories in a single manifest file.

This document covers installation of the HuBMAP CLT along with the Globus Connect Personal endpoint which is required to download data from HuBMAP.

Globus Prerequisites

In order to download any content from Globus, users must install Globus Connect Personal on their device. This creates a globus “Endpoint” locally. Downloads take the form of transfers from the desired Collection to the endpoint created on the local machine. Instructions on installing Globus Connect Personal can be found Here

During setup, users will have the opportunity to name their Endpoint and login with their Globus Credentials


While GCP on linux chooses your home directory as the download location by default, if you are using windows, it is likely that the default download location will not be your home directory. This must be changed or you will experience some difficulty finding your downloaded files. To change the download directory on windows 10/11, find the GCP icon in the system tray. If the “g” logo is neither on the right side of the task bar, nor in the hidden icons menu, GCP may not be running; in this case you must launch GCP before chaning any settings.

GCP System Tray Icon

Right-click on the GCP icon to see the context menu. This menu will contain an options button

GCP Options Button

Inside the options menu, navigate to the General Tab

GCP General Tab

Next, inside the text box labeled “Home Folder”, change this to be your home directory as shown below. Replace “Your-User-Name” to be the name associated with your home directory

GCP Home Location

Now we must navigate to the Access tab next to the General tab and give ourselves permission to use this new directory

Globus Access Tab

Once here, press the plus sign in the bottom right corner to add a new authorized directory

Add Access

You will be prompted to select a directory. Choose the same directory you chose to be your default directory. After adding the new authorized directory, we can remove the old one. Select the previous directory and press the minus button in the bottom right corner to remove it. Be sure to save after you’re done

Remove Access

Once this is all complete, all Globus files will be downloaded relative to this directory.

Installing the HuBMAP CLT

The HuBMAP CLT is available as a Python package.

  • Python 3 is required to run the HuBMAP CLT, an installer for it can be downloaded here.
  • It is recommended that you create a new Python virtual environment first with python3 -m venv /path/to/new/virtual/environment, more information on Python virtual environments is available here.
  • To install the HuBMAP CLT run the pip command shown below after installing Python and creating and activating a new Python virtual environment.
pip install hubmap-clt

This will also install other requirements needed by the the HuBMAP CLT including the Globus Command Line Tool

The globus command line tool is a separate tool from Globus Connect Personal. It is likely that users may have to log in separately through Globus CLI. To see if a user is currently logged in, use the command:

hubmap-clt whoami

If a user is logged in, their username will be displayed. If not logged in, users will be prompted to login with the following command:

hubmap-clt login

The Globus login screen will open in the default web browser. Follow login instructions.

Using the HuBMAP CLT

At this point, user should be setup and ready to use the Hubmap Command Line Transfer tool. Detailed instructions of its usage can be found here.