Hello Erick, On Mar 22, 2010, at 12:32 PM, Erick Antezana wrote: Just to confirm, this option is available only for uploading datasets to a data library ( but not a history ). I assume when you "delete a specific dataset (as admin) that was imported as non-admin" , you are marking the dataset as deleted in the data library. Doing this will not alter (delete) the history item that points to the deleted library dataset. This is why any user that imported the library dataset into their history before it was marked deleted in the library will still see the item in their history that points to the deleted library dataset. When you first upload a file to a data library, an association object (a LibraryDatasetDatasetAssociation object) is created that associates the library dataset with the file on disk (stored in ~/database/files/000/*). At this point, there is only 1 reference to the disk file. However, when you import the library dataset into a history, another association object (a HistoryDatasetAssociation object) is created that associates the history item with the same file on disk. This, of course, creates another reference to the same disk file. In order for the ~/scripts/cleanup_datasets/cleanup_datasets.py script to remove the file from disk, every reference to the disk file must be marked as deleted. In other words, not only the library dataset must be marked as deleted, but every history item that was created by importing the library dataset into a history must be marked as deleted as well. If any of these association objects remain undeleted, the disk file will not be removed. Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu