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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