galaxy not running after galaxy.yml changes

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galaxy not running after galaxy.yml changes

Jochen
Hi all,

we are testing a newly cloned galaxy. Which was running as expected a
few hours ago. After some modification to galaxy.yml file we got this
error message but after using the original galaxy.yml version it still
does not run.

Regenerating static plugin directories.
Activating virtualenv at .venv
Traceback (most recent call last):
  File "./scripts/manage_tool_dependencies.py", line 60, in <module>
    main()
  File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in main
    action_func(args, kwargs)
  File "./scripts/manage_tool_dependencies.py", line 20, in _init_if_needed
    _build_dependency_manager_no_config(kwargs)
  File "./scripts/manage_tool_dependencies.py", line 48, in
_build_dependency_manager_no_config
    dependency_manager = DependencyManager(**dependency_manager_kwds)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line 77,
in __init__
    self.dependency_resolvers = self.__build_dependency_resolvers(conf_file)
  File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line
241, in __build_dependency_resolvers
    plugin_source = plugin_config.plugin_source_from_path(conf_file)
  File "/opt/galaxy/galaxy/lib/galaxy/util/plugin_config.py ", line 78,
in plugin_source_from_path
    return ('xml', ElementTree.parse(path).getroot())
  File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse
    tree.parse(source, parser)
  File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse
    parser.feed(data)
  File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed
    self._raiseerror(v)
  File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in
_raiseerror
    raise err
xml.etree.ElementTree.ParseError: junk after document element: line 54,
column 0

Cheers Jochen


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Re: galaxy not running after galaxy.yml changes

Nate Coraor (nate@bx.psu.edu)
Hi Jochen,

Could you check the value of the 'dependency_resolvers_config_file' option
and verify that the file it points at (by
default, config/dependency_resolvers_conf.xml) is properly formatted?

--nate

On Thu, May 9, 2019 at 1:25 PM Jochen Bick <[hidden email]> wrote:

> Hi all,
>
> we are testing a newly cloned galaxy. Which was running as expected a
> few hours ago. After some modification to galaxy.yml file we got this
> error message but after using the original galaxy.yml version it still
> does not run.
>
> Regenerating static plugin directories.
> Activating virtualenv at .venv
> Traceback (most recent call last):
>   File "./scripts/manage_tool_dependencies.py", line 60, in <module>
>     main()
>   File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in main
>     action_func(args, kwargs)
>   File "./scripts/manage_tool_dependencies.py", line 20, in _init_if_needed
>     _build_dependency_manager_no_config(kwargs)
>   File "./scripts/manage_tool_dependencies.py", line 48, in
> _build_dependency_manager_no_config
>     dependency_manager = DependencyManager(**dependency_manager_kwds)
>   File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line 77,
> in __init__
>     self.dependency_resolvers =
> self.__build_dependency_resolvers(conf_file)
>   File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line
> 241, in __build_dependency_resolvers
>     plugin_source = plugin_config.plugin_source_from_path(conf_file)
>   File "/opt/galaxy/galaxy/lib/galaxy/util/plugin_config.py ", line 78,
> in plugin_source_from_path
>     return ('xml', ElementTree.parse(path).getroot())
>   File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse
>     tree.parse(source, parser)
>   File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse
>     parser.feed(data)
>   File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed
>     self._raiseerror(v)
>   File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in
> _raiseerror
>     raise err
> xml.etree.ElementTree.ParseError: junk after document element: line 54,
> column 0
>
> Cheers Jochen
>
>
> ___________________________________________________________
> 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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>
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>   http://galaxyproject.org/search/
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Re: galaxy not running after galaxy.yml changes

Jochen
Hej Nate,

thx for your email. We did not touch that file. Maybe we just have a
corrupted yml file? Is there a good way to check (lint) that file?

Cheers Jochen

On 09.05.19 19:56, Nate Coraor wrote:

> Hi Jochen,
>
> Could you check the value of the 'dependency_resolvers_config_file'
> option and verify that the file it points at (by
> default, config/dependency_resolvers_conf.xml) is properly formatted?
>
> --nate
>
> On Thu, May 9, 2019 at 1:25 PM Jochen Bick <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi all,
>
>     we are testing a newly cloned galaxy. Which was running as expected a
>     few hours ago. After some modification to galaxy.yml file we got this
>     error message but after using the original galaxy.yml version it still
>     does not run.
>
>     Regenerating static plugin directories.
>     Activating virtualenv at .venv
>     Traceback (most recent call last):
>       File "./scripts/manage_tool_dependencies.py", line 60, in <module>
>         main()
>       File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in
>     main
>         action_func(args, kwargs)
>       File "./scripts/manage_tool_dependencies.py", line 20, in
>     _init_if_needed
>         _build_dependency_manager_no_config(kwargs)
>       File "./scripts/manage_tool_dependencies.py", line 48, in
>     _build_dependency_manager_no_config
>         dependency_manager = DependencyManager(**dependency_manager_kwds)
>       File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ",
>     line 77,
>     in __init__
>         self.dependency_resolvers =
>     self.__build_dependency_resolvers(conf_file)
>       File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line
>     241, in __build_dependency_resolvers
>         plugin_source = plugin_config.plugin_source_from_path(conf_file)
>       File "/opt/galaxy/galaxy/lib/galaxy/util/plugin_config.py ",
>     line 78,
>     in plugin_source_from_path
>         return ('xml', ElementTree.parse(path).getroot())
>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182,
>     in parse
>         tree.parse(source, parser)
>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656,
>     in parse
>         parser.feed(data)
>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642,
>     in feed
>         self._raiseerror(v)
>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in
>     _raiseerror
>         raise err
>     xml.etree.ElementTree.ParseError: junk after document element:
>     line 54,
>     column 0
>
>     Cheers Jochen
>
>
>     ___________________________________________________________
>     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

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Re: galaxy not running after galaxy.yml changes

Nicola Soranzo-3
Hi Jochen,
try with:

make config-validate

Cheers,
Nicola

On 10/05/2019 09:13, Jochen Bick wrote:

> Hej Nate,
>
> thx for your email. We did not touch that file. Maybe we just have a
> corrupted yml file? Is there a good way to check (lint) that file?
>
> Cheers Jochen
>
> On 09.05.19 19:56, Nate Coraor wrote:
>> Hi Jochen,
>>
>> Could you check the value of the 'dependency_resolvers_config_file'
>> option and verify that the file it points at (by
>> default, config/dependency_resolvers_conf.xml) is properly formatted?
>>
>> --nate
>>
>> On Thu, May 9, 2019 at 1:25 PM Jochen Bick <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Hi all,
>>
>>     we are testing a newly cloned galaxy. Which was running as expected a
>>     few hours ago. After some modification to galaxy.yml file we got this
>>     error message but after using the original galaxy.yml version it still
>>     does not run.
>>
>>     Regenerating static plugin directories.
>>     Activating virtualenv at .venv
>>     Traceback (most recent call last):
>>       File "./scripts/manage_tool_dependencies.py", line 60, in <module>
>>         main()
>>       File "/opt/galaxy/galaxy/lib/galaxy/util/script.py", line 45, in
>>     main
>>         action_func(args, kwargs)
>>       File "./scripts/manage_tool_dependencies.py", line 20, in
>>     _init_if_needed
>>         _build_dependency_manager_no_config(kwargs)
>>       File "./scripts/manage_tool_dependencies.py", line 48, in
>>     _build_dependency_manager_no_config
>>         dependency_manager = DependencyManager(**dependency_manager_kwds)
>>       File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ",
>>     line 77,
>>     in __init__
>>         self.dependency_resolvers =
>>     self.__build_dependency_resolvers(conf_file)
>>       File "/opt/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py ", line
>>     241, in __build_dependency_resolvers
>>         plugin_source = plugin_config.plugin_source_from_path(conf_file)
>>       File "/opt/galaxy/galaxy/lib/galaxy/util/plugin_config.py ",
>>     line 78,
>>     in plugin_source_from_path
>>         return ('xml', ElementTree.parse(path).getroot())
>>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182,
>>     in parse
>>         tree.parse(source, parser)
>>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656,
>>     in parse
>>         parser.feed(data)
>>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642,
>>     in feed
>>         self._raiseerror(v)
>>       File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in
>>     _raiseerror
>>         raise err
>>     xml.etree.ElementTree.ParseError: junk after document element:
>>     line 54,
>>     column 0
>>
>>     Cheers Jochen
>>
>>
>>     ___________________________________________________________
>>     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:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/