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