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
bt...@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
    bt...@wisc.edu <mailto:bt...@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
    bt...@glbrc.wisc.edu <mailto:bt...@glbrc.wisc.edu>


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