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.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to