Hi Matthias,

if your previous config had a separate database for tools you need to
use that. This is controlled by the install_database_connection setting.


On Wed, 19 Dec 2018 at 13:53, Matthias Bernt <m.bernt@ufz.de> wrote:
Dear list,

just tried to switch to galaxy.yml, which worked in general, but now
tools that have been installed from the TS disappeared. In the logs I
get for each tool:

galaxy.tools.toolbox.base ERROR 2018-12-19 13:28:15,815
[p:22877,w:0,m:0] [MainThread] Error reading tool from path:
Traceback (most recent call last):
   File "lib/galaxy/tools/toolbox/base.py", line 563, in _load_tool_tag_set
     tool_shed_repository = self.get_tool_repository_from_xml_item(item,
   File "lib/galaxy/tools/toolbox/base.py", line 629, in
     raise Exception(msg)
Exception: Attempted to load tool shed tool, but the repository with
name 'text_processing' from owner 'bgruening' was not found in database

Any idea what could be wrong here? The connection to the DB seems to be
functional, since I can see the users in the admin Panel.



Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt@ufz.de, www.ufz.de

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