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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/