[galaxy-dev] Re: galaxy not running after galaxy.yml changes

2019-05-10 Thread Jochen Bick 
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  > 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 
>     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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>
-- 
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
jochen.b...@usys.ethz.ch 
www.ap.ethz.ch

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[galaxy-dev] Re: galaxy not running after galaxy.yml changes

2019-05-10 Thread Nicola Soranzo 
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 > > 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 
>>     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/
>>
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[galaxy-dev] Re: galaxy not running after galaxy.yml changes

2019-05-09 Thread Nate Coraor 
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  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 
> 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/
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