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,
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