From chris@compbio.dundee.ac.uk Mon Dec  6 11:35:20 2010
From: Chris Cole <chris@compbio.dundee.ac.uk>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Error setting-up and running bowtie tasks
Date: Mon, 06 Dec 2010 16:34:58 +0000
Message-ID: <4CFD10B2.1000700@compbio.dundee.ac.uk>
In-Reply-To: <A4FFF49D-1A27-45D3-925C-54A0AA22DEE7@bx.psu.edu>
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Hi Kelly,

Thanks. That solved the error. However, the job never ends in the UI=20
despite there being a 'job finished normally' entry in the logs.
Cheers,

Chris

On 06/12/10 15:30, Kelly Vincent wrote:
> 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 =3D 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 =3D fill_template( self.command, context=3Dparam_dict )
>> File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py",
>> line 9, in fill_template
>> return str( Template( source=3Dtemplate_text, searchList=3D[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=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
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>


--=20
Dr Chris Cole
Senior Bioinformatics Research Officer
School of Life Sciences Research
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris(a)compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096

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