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