From kpvincent@bx.psu.edu Mon Dec  6 10:30:41 2010
From: Kelly Vincent <kpvincent@bx.psu.edu>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Error setting-up and running bowtie tasks
Date: Mon, 06 Dec 2010 10:30:53 -0500
Message-ID: <A4FFF49D-1A27-45D3-925C-54A0AA22DEE7@bx.psu.edu>
In-Reply-To: <4CFCFF4F.6050406@compbio.dundee.ac.uk>
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Chris,

The tool_data_table_conf.xml.sample file has been updated to the  
correct column values, so just copy that or the relevant sections  
over. Let us know if you have any problems getting things working.

Regards,
Kelly


On Dec 6, 2010, at 10:20 AM, Chris Cole wrote:

> I have previously been able to run bowtie jobs successfully, but now  
> I get this error:
> galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure  
> running job 2248
> Traceback (most recent call last):
>  File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/ 
> drmaa.py", line 124, in queue_job
>    job_wrapper.prepare()
>  File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py",  
> line 368, in prepare
>    self.command_line = self.tool.build_command_line( param_dict )
>  File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py",  
> line 1524, in build_command_line
>    command_line = fill_template( self.command, context=param_dict )
>  File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py",  
> line 9, in fill_template
>    return str( Template( source=template_text,  
> searchList=[context] ) )
>  File "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux- 
> x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__
>    return getattr(self, mainMethName)()
>  File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond
> IndexError: list index out of range
>
> I've a feeling it has something to with the bowtie_indices.loc file  
> and it's associated entry in tool_data_table_conf.xml. I can see  
> that the format for the .loc file has changed (it now has four  
> columns instead of two):
> h_sapiens37     NCBI37  Homo sapiens ncbi37     /db/bowtie/ 
> h_sapiens_37_asm
>
> But the xml doesn't match (it only has two columns):
>
>    <!-- Locations of indexes in the Bowtie mapper format -->
>    <table name="bowtie_indexes">
>        <columns>name, value</columns>
>        <file path="tool-data/bowtie_indices.loc" />
>    </table>
>
> What should there be in the 'columns' section?
> Thanks,
>
> Chris
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> galaxy-dev(a)lists.bx.psu.edu
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