Hi Marius,
heureka. That solved it. Thanks a lot.
Cheers,
Matthias
On 19.12.18 13:57, Marius van den Beek wrote:
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.
Best,
Marius
On Wed, 19 Dec 2018 at 13:53, Matthias Bernt <m.be...@ufz.de
<mailto:m.be...@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:
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/74a8bef53a00/text_processing/cat.xml
<http://toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/74a8bef53a00/text_processing/cat.xml>
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,
path)
File "lib/galaxy/tools/toolbox/base.py", line 629, in
get_tool_repository_from_xml_item
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.
Cheers,
Matthias
--
-------------------------------------------
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.be...@ufz.de <mailto:m.be...@ufz.de>, www.ufz.de <http://www.ufz.de>
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
-------------------------------------------
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--
-------------------------------------------
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.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
-------------------------------------------
___________________________________________________________
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:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
