On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric <epani...@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.
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