Question: Bug in Mpileup wrapper
gravatar for marc.chakiachvili
3.6 years ago by
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/", line 158, in prepare_job
  File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/", line 832, in prepare
    self.command_line, self.extra_filenames =
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/", line 408, in build
    self.__build_command_line( )
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/", line 424, in __build_command_line
    command_line = fill_template( command, context=param_dict )
  File "/home/galaxy/galaxy-dist/lib/galaxy/util/", 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/", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "", 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 • 836 views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by marc.chakiachvili10
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Thank you for reporting the issue so clearly. I created a Trello ticket to log the problem. Progress can be tracked here:

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 3.6 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour