Galaxy Conda resolver install Issue

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Galaxy Conda resolver install Issue

evan clark
I just ran across an issue when attempting to load galaxy. I am not sure
how to fix this issue or what could be causing it. Conda is installed
properly.

   File
"/var/web_services/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
58, in paste_app_factory
     app = galaxy.app.UniverseApplication( global_conf=global_conf,
**kwargs )
   File "/var/web_services/galaxy/lib/galaxy/app.py", line 113, in __init__
     self._configure_toolbox()
   File "/var/web_services/galaxy/lib/galaxy/config.py", line 935, in
_configure_toolbox
     self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path,
self )
   File "/var/web_services/galaxy/lib/galaxy/tools/__init__.py", line
205, in __init__
     app=app,
   File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py",
line 1044, in __init__
     self._init_dependency_manager()
   File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py",
line 1057, in _init_dependency_manager
     self.dependency_manager = build_dependency_manager( self.app.config )
   File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py",
line 41, in build_dependency_manager
     dependency_manager = DependencyManager( **dependency_manager_kwds )
   File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py",
line 84, in __init__
     self.dependency_resolvers = self.__build_dependency_resolvers(
conf_file )
   File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py",
line 193, in __build_dependency_resolvers
     return self.__default_dependency_resolvers()
   File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py",
line 201, in __default_dependency_resolvers
     CondaDependencyResolver(self),
   File
"/var/web_services/galaxy/lib/galaxy/tools/deps/resolvers/conda.py",
line 134, in __init__
     self.disabled = not
galaxy.tools.deps.installable.ensure_installed(conda_context,
install_conda, self.auto_init)
   File "/var/web_services/galaxy/lib/galaxy/tools/deps/installable.py",
line 77, in ensure_installed
     return ensure_installed(installable_context, auto_init)
TypeError: ensure_installed() takes exactly 3 arguments (2 given)

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Re: Galaxy Conda resolver install Issue

Marius van den Beek
Hello Evan,

this looks suspiciously like a bug that Matthias Bernt has fixed on the development branch a while back.
I have backported this to Galaxy release 17.01 and release 17.05.

If you update your galaxy branch to the latest commit it should work (or you should receive a more instructive error message).

Hope that helps,
Marius

On 17 August 2017 at 18:32, evan clark <[hidden email]> wrote:
I just ran across an issue when attempting to load galaxy. I am not sure how to fix this issue or what could be causing it. Conda is installed properly.

  File "/var/web_services/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 58, in paste_app_factory
    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  File "/var/web_services/galaxy/lib/galaxy/app.py", line 113, in __init__
    self._configure_toolbox()
  File "/var/web_services/galaxy/lib/galaxy/config.py", line 935, in _configure_toolbox
    self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
  File "/var/web_services/galaxy/lib/galaxy/tools/__init__.py", line 205, in __init__
    app=app,
  File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line 1044, in __init__
    self._init_dependency_manager()
  File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line 1057, in _init_dependency_manager
    self.dependency_manager = build_dependency_manager( self.app.config )
  File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 41, in build_dependency_manager
    dependency_manager = DependencyManager( **dependency_manager_kwds )
  File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 84, in __init__
    self.dependency_resolvers = self.__build_dependency_resolvers( conf_file )
  File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 193, in __build_dependency_resolvers
    return self.__default_dependency_resolvers()
  File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 201, in __default_dependency_resolvers
    CondaDependencyResolver(self),
  File "/var/web_services/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 134, in __init__
    self.disabled = not galaxy.tools.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init)
  File "/var/web_services/galaxy/lib/galaxy/tools/deps/installable.py", line 77, in ensure_installed
    return ensure_installed(installable_context, auto_init)
TypeError: ensure_installed() takes exactly 3 arguments (2 given)

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Re: Galaxy Conda resolver install Issue

Matthias Bernt
In reply to this post by evan clark
Hi Evan,

just for completeness Marius is referring to these changes:

https://github.com/galaxyproject/galaxy/pull/4049

For testing you could also integrate these changes in your instance, but
upgrading to an up-to-date version is a good idea anyways.

Best,
Matthias

> Hello Evan,
>
> this looks suspiciously like a bug that Matthias Bernt has fixed on the
> development branch a while back.
> I have backported this to Galaxy release 17.01 and release 17.05.
>
> If you update your galaxy branch to the latest commit it should work (or
> you should receive a more instructive error message).
>
> Hope that helps,
> Marius
>
> On 17 August 2017 at 18:32, evan clark <[hidden email]> wrote:
>
>> I just ran across an issue when attempting to load galaxy. I am not sure
>> how to fix this issue or what could be causing it. Conda is installed
>> properly.
>>
>>    File "/var/web_services/galaxy/lib/galaxy/webapps/galaxy/buildapp.py",
>> line 58, in paste_app_factory
>>      app = galaxy.app.UniverseApplication( global_conf=global_conf,
>> **kwargs )
>>    File "/var/web_services/galaxy/lib/galaxy/app.py", line 113, in __init__
>>      self._configure_toolbox()
>>    File "/var/web_services/galaxy/lib/galaxy/config.py", line 935, in
>> _configure_toolbox
>>      self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path,
>> self )
>>    File "/var/web_services/galaxy/lib/galaxy/tools/__init__.py", line 205,
>> in __init__
>>      app=app,
>>    File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line
>> 1044, in __init__
>>      self._init_dependency_manager()
>>    File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line
>> 1057, in _init_dependency_manager
>>      self.dependency_manager = build_dependency_manager( self.app.config )
>>    File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line
>> 41, in build_dependency_manager
>>      dependency_manager = DependencyManager( **dependency_manager_kwds )
>>    File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line
>> 84, in __init__
>>      self.dependency_resolvers = self.__build_dependency_resolvers(
>> conf_file )
>>    File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line
>> 193, in __build_dependency_resolvers
>>      return self.__default_dependency_resolvers()
>>    File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line
>> 201, in __default_dependency_resolvers
>>      CondaDependencyResolver(self),
>>    File "/var/web_services/galaxy/lib/galaxy/tools/deps/resolvers/conda.py",
>> line 134, in __init__
>>      self.disabled = not galaxy.tools.deps.installable.
>> ensure_installed(conda_context, install_conda, self.auto_init)
>>    File "/var/web_services/galaxy/lib/galaxy/tools/deps/installable.py",
>> line 77, in ensure_installed
>>      return ensure_installed(installable_context, auto_init)
>> TypeError: ensure_installed() takes exactly 3 arguments (2 given)
>>
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