Removing Deleted Datasets

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Question: Removing Deleted Datasets

7.6 years ago by

Simon Lank • 30

Simon Lank • 30 wrote:

Hi. Our current galaxy database is ~ 600 gb, most of which are user deleted datasets. I followed the instructions here: https://bitbucket.org/galaxy/galaxy- central/wiki/Config/PurgeHistoriesAndDatasets and ran the shell scripts in recommended order. One of them in particular (I think it was purge_histories.sh) took amost 24 hours to complete. However, it doesn't appear any / most of the files were actually deleted, since we still have ~ 600 gb of dataset files. Is there something obvious I can try to get the files purged correctly? Thanks. Simon Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389

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modified 7.6 years ago by Greg Von Kuster ♦ 810 • written 7.6 years ago by Simon Lank • 30

7.6 years ago by

Greg Von Kuster ♦ 810

Penn State University

Greg Von Kuster ♦ 810 wrote:

Simon, In order for a dataset file to be removed from disk, no active library associations (LibraryDatasetDatasetAssociations) or history associations (HistoryDatasetAssociations) can be pointing to it. When no active association objects are pointing to a dataset file, it will ultimate be removed from disk via option -3 (the purge_datasets option) in the cleanup_datasets.py script. However, another factor in removing the file from disk is that the configured number of days must have passed since everything pointing to the file was marked as deleted. The default number of days in the script is 60. To remove files from disk on the same day they were marked as deleted, override the default by setting the -d flag to 0. Greg Von Kuster Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

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