tools gone after switching to galaxy.yml

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tools gone after switching to galaxy.yml

Matthias Bernt
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,
[hidden email], 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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Re: tools gone after switching to galaxy.yml

Marius van den Beek
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 <[hidden email]> 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,
[hidden email], 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/

___________________________________________________________
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:
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Re: tools gone after switching to galaxy.yml

Matthias Bernt
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 <[hidden email]
> <mailto:[hidden email]>> 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,
>     [hidden email] <mailto:[hidden email]>, 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,
[hidden email], 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/