This is a FAQ that's best answered in the Wiki page
the most intuitive is to use the web GUI to upload but this creates unnecessary overhead and slowdown when you can point to the files
Options for Uploading Files from the Admin Perspective
There are currently four options available to a Galaxy admin user for uploading files to a data library. Some of these same options are available to all regular users that have been granted permission to add items to a Data Library or folder, but this section describes the features from the Galaxy admin perspective which is accessed by clicking on the "Admin" link in the top Galaxy menu bar.