Matthias Dodt wrote: Hi Matthias, There are two options: user_library_import_dir and library_import_dir. Can you confirm that user_library_import_dir is the one you want? library_import_dir should point to a directory which contains other directories which can be selected (by administrators only) to upload the contents of. user_library_import_dir should point to a directory which contains other directories whose names match Galaxy user's email addresses. These directories, in turn, contain directories which can be selected (by the matching user) to upload the contents of. This feature was not designed with home directories in mind - it was added so administrators could have a "drop box" type system: A per-user FTP space or somewhere on disk, where each user could create their own upload directories. Note that symlinks are valid, so this is often an easy way to avoid having to move too much data around. There's metadata processing that also happens at this time. If you select the file type manually (instead of leaving it as "automatic") this should speed things up. There's not a simple way for Galaxy to know what files it has already imported from a specific directory (or to know that you intentionally did not want to upload duplicates). This would probably be a good use for allow_library_path_paste, if you're doing this as an administrator. allow_library_path_paste adds a new upload page ("Upload files from filesystem paths") to the admin-side library upload pages. This form contains a textarea that allows Galaxy admins to paste any number of filesystem paths (files or directories) from which Galaxy will import library datasets, saving the directory structure (if desired). Since such ability allows admins access to any file on the Galaxy server which is readable by Galaxy's system user, this option is disabled by default, and system administrators should take care in assigning Galaxy administrators when this feature is enabled. As with many of the security and library features, we have a certain way of using them here at PSU, but are aware that other people use them differently or need different features: if you have suggestions on how we can make feature improvements, this helps us determine what direction to go in the future. Thanks, --nate