Vipin, thanks for the tip.  I was not aware of data tables at all.

I checked bwa_wrapper.xml and it is still using the from_file attribute for the reference genome parameter, not from_data_table.  It would appear then that BWA is not using data tables?  Additionally, I have now noticed that our bowtie runs are failing as well with the error:

AssertionError: Requested 'path' column missing from column def

I looked at bowtie_wrapper.xml, and it too seems to still be using from_file instead of from_data_table for the reference genome drop-down.  There is a line there using data tables, but it is commented out:

<!--<options from_data_table="bowtie_indexes"/>-->

I'm really confused as to what is going on here, but it seems like when I updated recently (first time since January probably) it broke all of my location files and I'm not sure how to fix them.  I'm also confused because it seems that even using data tables, the format of my .loc files shouldn't need to change because they both use four columns separated by tabs.

As always, any help is greatly appreciated.

--
Branden Timm
btimm@glbrc.wisc.edu

    

    

    On 4/26/2011 12:29 PM, Vipin TS wrote:
    
Hi Branden, 

      

      I find a wiki documentation here, 

       

      https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables

      

      Hope this will help you to experiment a bit around. 

      


        regards, Vipin

        

        

          
 Does anybody have any
            idea why I would be getting this error before the tool runs?

            

            --

            Branden Timm

            Great Lakes Bioenergy Research Center

            btimm@wisc.edu
            

              


                

                On 4/19/2011 10:45 AM, Branden Timm wrote: 

            

            

              

                

                  
 Hi All,

                      I'm having issues running BWA for Illumina with
                    the latest version of Galaxy (5433:c1aeb2f33b4a).

                    

                    It seems that the error is a python list error while
                    preparing the job:

                    

                      
                        
Traceback (most recent call last):
  File "/home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py", line 58, in run_job
    job_wrapper.prepare()
  File "/home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 371, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 1575, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/home/galaxy/galaxy-central/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "DynamicallyCompiledCheetahTemplate.py", line 106, in respond
IndexError: list index out of range

                      I checked the bwa_index.loc file for
                    errors, it seems that the line for the reference
                    genome I'm trying to map against is correct (all
                    whitespace is tab characters):

                    synpcc7002      synpcc7002      Synechococcus  
                    /home/galaxy/galaxy-central/bwa_

                    indices/SYNPCC7002

                    

                    I'm not sure what the next troubleshooting step is,
                    any ideas?

                    

                    --

                    Branden Timm

                    btimm@glbrc.wisc.edu

                  

                

              

              

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