From chris@compbio.dundee.ac.uk Mon Dec  6 10:21:11 2010
From: Chris Cole <chris@compbio.dundee.ac.uk>
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Error setting-up and running bowtie tasks
Date: Mon, 06 Dec 2010 15:20:47 +0000
Message-ID: <4CFCFF4F.6050406@compbio.dundee.ac.uk>
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I have previously been able to run bowtie jobs successfully, but now I=20
get this error:
galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure running=20
job 2248
Traceback (most recent call last):
   File=20
"/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line=20
124, in queue_job
     job_wrapper.prepare()
   File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py",=20
line 368, in prepare
     self.command_line =3D self.tool.build_command_line( param_dict )
   File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py",=20
line 1524, in build_command_line
     command_line =3D fill_template( self.command, context=3Dparam_dict )
   File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py",=20
line 9, in fill_template
     return str( Template( source=3Dtemplate_text, searchList=3D[context] ) )
   File=20
"/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.eg=
g/Cheetah/Template.py",=20
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=20
it's associated entry in tool_data_table_conf.xml. I can see that the=20
format for the .loc file has changed (it now has four columns instead of=20
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=3D"bowtie_indexes">
         <columns>name, value</columns>
         <file path=3D"tool-data/bowtie_indices.loc" />
     </table>

What should there be in the 'columns' section?
Thanks,

Chris

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