[galaxy-dev] bwa failure preparing job

[Kelly Vincent]

Branden,

Sorry for the delay in response. Have you gotten things working yet?  
If not, what changeset are you on now? The data tables issue is what's  
going on here. But it's odd that you're still seeing "from_file" in  
BWA and Bowtie, because they (plus all NGS tools except the samtools  
ones) have been using data tables for some time. Let us know if you  
are still having problems with this.

Thanks,
Kelly


On Tue Apr 26, at 5:11 PM, Branden Timm wrote:

> 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 at 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 at 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 at glbrc.wisc.edu
>>>
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