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