Hi, when I used freebayes to call SNPs with input filter parameters, there is a error in my local galaxy. when I closed the input filter parameters everything is OK. I just want to know how can I solve the problem.
the following is the error details
Traceback (most recent call last):
File “lib/galaxy/jobs/runners/init.py”, line 243, in prepare_job
job_wrapper.prepare()
File “lib/galaxy/jobs/init.py”, line 1161, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
File “lib/galaxy/tools/evaluation.py”, line 462, in build
raise e
File “lib/galaxy/tools/evaluation.py”, line 458, in build
self.__build_command_line()
File “lib/galaxy/tools/evaluation.py”, line 483, in __build_command_line
command_line = fill_template(command, context=param_dict, python_template_version=self.tool.python_template_version)
File “lib/galaxy/util/template.py”, line 107, in fill_template
raise first_exception or e
File “lib/galaxy/util/template.py”, line 80, in fill_template
return unicodify(t, log_exception=False)
File “lib/galaxy/util/init.py”, line 1060, in unicodify
value = str(value)
File “/home/ychen1/galaxy/galaxy-test/galaxy/.venv/lib/python3.7/site-packages/Cheetah/Template.py”, line 1053, in unicode
return getattr(self, mainMethName)()
File “cheetah_DynamicallyCompiledCheetahTemplate_1638720981_7731435_86611.py”, line 438, in respond
File “/home/ychen1/galaxy/galaxy-test/galaxy/.venv/lib/python3.7/site-packages/Cheetah/NameMapper.py”, line 293, in valueFromSearchList
_raiseNotFoundException(key, searchList)
File “/home/ychen1/galaxy/galaxy-test/galaxy/.venv/lib/python3.7/site-packages/Cheetah/NameMapper.py”, line 178, in _raiseNotFoundException
raise NotFound(excString)
Cheetah.NameMapper.NotFound: cannot find ‘standard_filters’
I will be very pleasure hearing from you,thx
Hi @yangchen,
I’m trying to reproduce the error; which tool version are you using? It would be great if you could do the analysis in usegalaxy.eu; in that way would be easier for us to identify the problem.
Regards
Hi gallardoalba,
Thanks for your reply, I use freebayes (1.3.5+galaxy0 1.3.5). I have tried most of versions in galaxy but all of them produced this error. I can analysis in usegalaxy.eu with the same version of freebayes (1.3.5+galaxy0 1.3.5) but it only produce this error in local galaxy. I have installed freebayes in my server and run it by command line without this error.I think my server might be absent of dependence environment but I do not know what I need to install.
My operating system is Ubuntu 20.04.3 LTS (GNU/Linux 5.11.0-40-generic x86_64)
Regards
Yangchen
It could be that you need to re-install the freebayes tool, see:
I see you posted your question 16 days ago, but maybe you already had it installed for a few days.
thanks for your help, I re-install freebayes and I can use the input-filter parameters successfully. It works well now!
Yangchen