EOF error with tool

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EOF error with tool

Francis, Warren
Hello,
I'm getting a strange error when trying to debug a tool.

Traceback (most recent call last):
   File "/var/project/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 157, in prepare_job
     job_wrapper.prepare()
   File "/var/project/galaxy-dist/lib/galaxy/jobs/__init__.py", line 811,
in prepare
     self.command_line, self.extra_filenames = tool_evaluator.build()
   File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line
348, in build
     self.__build_command_line( )
   File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line
364, in __build_command_line
     command_line = fill_template( command, context=param_dict )
   File "/var/project/galaxy-dist/lib/galaxy/util/template.py", line 9,
in fill_template
     return str( Template( source=template_text, searchList=[context] ) )
   File
"/var/project/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
line 1004, in __str__
     return getattr(self, mainMethName)()
   File
"cheetah_DynamicallyCompiledCheetahTemplate_1421072368_91_78155.py",
line 139, in respond
EOFError: EOF when reading a line

The tool is the assembler Trinity. The toolshed version is quite old and
the one from the Trinity website does not work, so I tried to fix it
(several problems to fix).

What is the EOFError? There were a bunch of posts reporting this but no
answer as to why this happens.

Is there a way to debug a tool without having to restart galaxy each
time? Something offline that can check for runtime errors, or at least
see if it generates the command correctly.

Best,
-Warren
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Re: EOF error with tool

John Chilton-4
There are a couple groups working on improved trinity wrappers - I
don't think they have reach the tool sheds though :(.

As for the details of your specific tool - I think I would really need
to see the tool to guess at the issue. Would it be possible to send us
the problematic tool XML file or paste it to a service like
gist.github.com?

As for reloading the tool - if you add yourself as an admin user in
galaxy's config/galaxy.ini file you should see a "Reload Tool
Configuration" option in the admin menu that will allow you to
manually reload the tool without restarting Galaxy (I generally
recommend keeping this open in its own tab).

Newer versions of Galaxy have some more experimental features designed
to help as well - for instance if you create a virtualenv for Galaxy
and install watchdog ("pip install watchdog") into it and then enable
"watch_tools = True " in config/galaxy.ini Galaxy should automatically
reload tools each time the tool config is updated. I am not sure
anyone is really using this feature so it might still have some bugs
(in particular I have noticed if the tool panel is really full there
are problems so trimming that down might be required to use it).

For the rare person like me who really hates using GUIs at all during
development - you might also want to write some tests for the tool and
run them using planemo (http://planemo.readthedocs.org/). It allows
linting and testing tools without a Galaxy interface so you can be
pretty confident the tool is working by the time you actually load it
into a web browser and view it.

-John


On Mon, Jan 12, 2015 at 9:36 AM, Francis, Warren
<[hidden email]> wrote:

> Hello,
> I'm getting a strange error when trying to debug a tool.
>
> Traceback (most recent call last):
>   File "/var/project/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line
> 157, in prepare_job
>     job_wrapper.prepare()
>   File "/var/project/galaxy-dist/lib/galaxy/jobs/__init__.py", line 811, in
> prepare
>     self.command_line, self.extra_filenames = tool_evaluator.build()
>   File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line 348,
> in build
>     self.__build_command_line( )
>   File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line 364,
> in __build_command_line
>     command_line = fill_template( command, context=param_dict )
>   File "/var/project/galaxy-dist/lib/galaxy/util/template.py", line 9, in
> fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/var/project/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
>     return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1421072368_91_78155.py",
> line 139, in respond
> EOFError: EOF when reading a line
>
> The tool is the assembler Trinity. The toolshed version is quite old and the
> one from the Trinity website does not work, so I tried to fix it (several
> problems to fix).
>
> What is the EOFError? There were a bunch of posts reporting this but no
> answer as to why this happens.
>
> Is there a way to debug a tool without having to restart galaxy each time?
> Something offline that can check for runtime errors, or at least see if it
> generates the command correctly.
>
> Best,
> -Warren
> ___________________________________________________________
> 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/mailinglists/
___________________________________________________________
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/mailinglists/