hubmap-clt [-h | --help] [transfer manifest-file | login | logout | whoami]

HuBMAP Command Line Transfer

A utility to bulk download HuBMAP data by specifying the directories and/or
files in a manifest file. For detailed documentation see:
    https://software.docs.hubmapconsortium.org/using-hubmap-clt.html

Commands: One of the following commands is required:

   transfer manifest-file   Transfer files specified in manifest-file (see
                            below for example) using Globus Transfer.
			    The transfered files will be stored in the
			    directory "hubmap-download" under the user's
			    home directory.

   login                    Login to Globus

   logout 		    Logout of Globus

   whoami                   Displays the information of the user who is
                            currently logged in.  If no user is logged
                            a message will be displayed prompting the user
			    to log in.

-h or --help  Show this help message.

-v or --version Show current installed version of hubmap-clt.

-d or --destination	Manually select a download location within the user's
                        home direcotry. For example:
                          'hubmap-clt transfer manifest-file -d Desktop'
			will download to the user's Desktop directory. The 
			directory will be created under the user home directory
			if it doesn't already exist.

Manifest Files:
Manifest files contain two columns, the first with a HuBMAP identifer the
second with a file or directory specifier. Additional information to the
right of the second column, separated by a tab can be included. An
optional single header line starting with the column specifier "dataset_id"
will be ignored.

Example manifest files:

654418415bed5ecb9596b17a0320a2c6 /	#retrieves all files for given dataset uuid
HBM455.XGQZ.542 /rawMicroscopy/VAN0009-LK-102-7-AF_preIMS_unregistered.czi	#retrieves czi file for dataset HBM455.XGQZ.542


dataset_id	file_or_dir_specifier	#header line is ignored
60ed8e03152b51d5d9c8fc04e20fa5e3 /	#retrieve all files for given dataset uuid
HBM525.DLPN.575 /ometiffs/VAN0016-LK-202-89-IMS_PosMode_multilayer.ome.tiff #retrives image file for dataset HBM525.DLPN.575
HBM525.DLPN.575 /ometiffs/separate/	#retrievs directory of mages files for dataset HBM525.DLPN.575

