Question: Bug in Mpileup wrapper
1
marc.chakiachvili • 10 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 :-).
ADD COMMENT
• link
•
modified 3.6 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
3.6 years ago by
marc.chakiachvili • 10
