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