trouble running the new galaxy instance

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trouble running the new galaxy instance

Jochen
Hi

since we updated some loc files our galaxy (19.01) does start but is
unavailable in the browser.

# systemctl status galaxy
? galaxy.service - SYSV: Galaxy http://galaxyproject.org/
   Loaded: loaded (/etc/rc.d/init.d/galaxy; bad; vendor preset: disabled)
   Active: active (exited) since Mon 2019-07-15 10:23:11 CEST; 1 weeks 0
days ago
     Docs: man:systemd-sysv-generator(8)
  Process: 5840 ExecStop=/etc/rc.d/init.d/galaxy stop (code=exited,
status=0/SUCCESS)
  Process: 5957 ExecStart=/etc/rc.d/init.d/galaxy start (code=exited,
status=0/SUCCESS)

Jul 15 10:23:11 green-galaxy galaxy[5957]: File
"/opt/galaxy/galaxy/.venv/li...n
Jul 15 10:23:11 green-galaxy galaxy[5957]: self.fetch_more_tokens()
Jul 15 10:23:11 green-galaxy galaxy[5957]: File
"/opt/galaxy/galaxy/.venv/li...s
Jul 15 10:23:11 green-galaxy galaxy[5957]: return self.fetch_value()
Jul 15 10:23:11 green-galaxy galaxy[5957]: File
"/opt/galaxy/galaxy/.venv/li...e
Jul 15 10:23:11 green-galaxy galaxy[5957]: self.get_mark())
Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError:
mappin...e
Jul 15 10:23:11 green-galaxy galaxy[5957]: in
"/opt/galaxy/galaxy/config/gal...0
Jul 15 10:23:11 green-galaxy galaxy[5957]: ...done.
Jul 15 10:23:11 green-galaxy systemd[1]: Started SYSV: Galaxy
http://galaxyp....
Hint: Some lines were ellipsized, use -l to show in full.


Has anyone a good hint?

Cheers Jochen

--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch

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Re: trouble running the new galaxy instance

Marius van den Beek
Hi Jochen,

can you post out the full logs ?

Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError:
mappin...e
Jul 15 10:23:11 green-galaxy galaxy[5957]: in
"/opt/galaxy/galaxy/config/gal...0

probably means that you have syntax error in galaxy.yml, but the full logs
will tell you more.

Best,
Marius

On Tue, 23 Jul 2019 at 09:26, Jochen Bick <[hidden email]> wrote:

> Hi
>
> since we updated some loc files our galaxy (19.01) does start but is
> unavailable in the browser.
>
> # systemctl status galaxy
> ? galaxy.service - SYSV: Galaxy http://galaxyproject.org/
>    Loaded: loaded (/etc/rc.d/init.d/galaxy; bad; vendor preset: disabled)
>    Active: active (exited) since Mon 2019-07-15 10:23:11 CEST; 1 weeks 0
> days ago
>      Docs: man:systemd-sysv-generator(8)
>   Process: 5840 ExecStop=/etc/rc.d/init.d/galaxy stop (code=exited,
> status=0/SUCCESS)
>   Process: 5957 ExecStart=/etc/rc.d/init.d/galaxy start (code=exited,
> status=0/SUCCESS)
>
> Jul 15 10:23:11 green-galaxy galaxy[5957]: File
> "/opt/galaxy/galaxy/.venv/li...n
> Jul 15 10:23:11 green-galaxy galaxy[5957]: self.fetch_more_tokens()
> Jul 15 10:23:11 green-galaxy galaxy[5957]: File
> "/opt/galaxy/galaxy/.venv/li...s
> Jul 15 10:23:11 green-galaxy galaxy[5957]: return self.fetch_value()
> Jul 15 10:23:11 green-galaxy galaxy[5957]: File
> "/opt/galaxy/galaxy/.venv/li...e
> Jul 15 10:23:11 green-galaxy galaxy[5957]: self.get_mark())
> Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError:
> mappin...e
> Jul 15 10:23:11 green-galaxy galaxy[5957]: in
> "/opt/galaxy/galaxy/config/gal...0
> Jul 15 10:23:11 green-galaxy galaxy[5957]: ...done.
> Jul 15 10:23:11 green-galaxy systemd[1]: Started SYSV: Galaxy
> http://galaxyp....
> Hint: Some lines were ellipsized, use -l to show in full.
>
>
> Has anyone a good hint?
>
> Cheers Jochen
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone +41 52 354 92 06
> [hidden email] <mailto:[hidden email]>
> www.ap.ethz.ch
>
> ___________________________________________________________
> 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:
>   %(web_page_url)s
>
> 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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
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Re: trouble running the new galaxy instance

Jochen
Thanks Marius for your quick reply,

I will check the yml and send you the full report once I have feedback
from my sysadmin.

Cheer Jochen

On 23.07.19 10:03, Marius van den Beek wrote:

> Hi Jochen,
>
> can you post out the full logs ?
>
> Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError:
> mappin...e
> Jul 15 10:23:11 green-galaxy galaxy[5957]: in
> "/opt/galaxy/galaxy/config/gal...0
>
> probably means that you have syntax error in galaxy.yml, but the full
> logs will tell you more.
>
> Best,
> Marius
>
> On Tue, 23 Jul 2019 at 09:26, Jochen Bick <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi
>
>     since we updated some loc files our galaxy (19.01) does start but is
>     unavailable in the browser.
>
>     # systemctl status galaxy
>     ? galaxy.service - SYSV: Galaxy http://galaxyproject.org/
>        Loaded: loaded (/etc/rc.d/init.d/galaxy; bad; vendor preset:
>     disabled)
>        Active: active (exited) since Mon 2019-07-15 10:23:11 CEST; 1
>     weeks 0
>     days ago
>          Docs: man:systemd-sysv-generator(8)
>       Process: 5840 ExecStop=/etc/rc.d/init.d/galaxy stop (code=exited,
>     status=0/SUCCESS)
>       Process: 5957 ExecStart=/etc/rc.d/init.d/galaxy start (code=exited,
>     status=0/SUCCESS)
>
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: File
>     "/opt/galaxy/galaxy/.venv/li...n
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: self.fetch_more_tokens()
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: File
>     "/opt/galaxy/galaxy/.venv/li...s
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: return self.fetch_value()
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: File
>     "/opt/galaxy/galaxy/.venv/li...e
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: self.get_mark())
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError:
>     mappin...e
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: in
>     "/opt/galaxy/galaxy/config/gal...0
>     Jul 15 10:23:11 green-galaxy galaxy[5957]: ...done.
>     Jul 15 10:23:11 green-galaxy systemd[1]: Started SYSV: Galaxy
>     http://galaxyp....
>     Hint: Some lines were ellipsized, use -l to show in full.
>
>
>     Has anyone a good hint?
>
>     Cheers Jochen
>
>     --
>     ETH Zurich
>     *Jochen Bick*
>     Animal Physiology
>     Institute of Agricultural Sciences
>     Postal address: Universitätstrasse 2 / LFW B 58.1
>     8092 Zurich, Switzerland
>     Office: Eschikon 27
>     8315 Lindau, Switzerland
>
>     Phone +41 52 354 92 06
>     [hidden email] <mailto:[hidden email]>
>     <mailto:[hidden email] <mailto:[hidden email]>>
>     www.ap.ethz.ch <http://www.ap.ethz.ch>
>
>     ___________________________________________________________
>     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:
>       %(web_page_url)s
>
>     To search Galaxy mailing lists use the unified search at:
>       http://galaxyproject.org/search/
>
--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch

___________________________________________________________
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:
  %(web_page_url)s

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