Question: Bug in Mpileup wrapper
1
gravatar for marc.chakiachvili
3.5 years ago by
France
marc.chakiachvili10 wrote:

There is an error in samtools mpileup tool_shed wrapper (version : devteam/samtools_mpileup/c6fdfe3331d6/samtools_mpileup/samtools_mpileup.xml) : 

        #if str( $advanced_options.region_string ):
            -r "${advanced_options.region_string}"
        #end if

this line cause crash when preparing job in Galaxy :

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 158, in prepare_job
    job_wrapper.prepare()
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in prepare
    self.command_line, self.extra_filenames = tool_evaluator.build()
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 408, in build
    self.__build_command_line( )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 424, in __build_command_line
    command_line = fill_template( command, context=param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/home/galaxy/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_1430925903_57_40786.py", line 179, in respond
NotFound: cannot find 'region_string' while searching for 'advanced_options.region_string'

i removed the corresponding line, and tool seems to work now. 

I don't know if it's the rigth place to submit this error report. If it has to be placed elsewhere, tell me :-).

 

 

mpileup samtools • 810 views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson25k • written 3.5 years ago by marc.chakiachvili10
0
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Thank you for reporting the issue so clearly. I created a Trello ticket to log the problem. Progress can be tracked here: https://trello.com/c/ykmEqNYQ

Issues are best vetted through this forum or the galaxy-dev A.T galaxyproject D.O.T org mailing list, so this is all good.

Thanks again, Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson25k
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