tools gone after switching to galaxy.yml
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 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.bernt@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 -------------------------------------------
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.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:
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.bernt@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/
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.bernt@ufz.de <mailto: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: 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.bernt@ufz.de <mailto:m.bernt@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 ------------------------------------------- ___________________________________________________________ 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/
-- ------------------------------------------- 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 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 -------------------------------------------
participants (2)
-
Marius van den Beek -
Matthias Bernt