On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric <epaniagu@cshl.edu> wrote:

Thanks for pointing that out! I missed it. I am now connecting to the remote database. I ran "sh manage_db.sh upgrade" and it upgraded from schema 114 to 118 without error messages. I then ran "sh ./scripts/migrate_tools/0010_tools.sh install_dependencies" and received the following error:

line 35, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'gatk_picard_indexes'

I fixed this by adding the appropriate entries to tool_data_table_conf.xml. I then reran the migrate_tools command successfully. However, now my "history_dataset_association" table in the database was blown away at some point. The table is now completely empty. Have you ever seen this before?

I have not seen the tool migration issue before, but it seems harmless. The fact that your history_dataset_association table is empty is concerning if there was ever anything in it. Can you verify that there are datasets in the same database that *should* be associated to a history? It sounds like this galaxy instance has been used with different databases, and my hope is that the wires are crossed up here and there actually should not be any.