I should have held onto that email a second longer. Also see the bowtie .loc files referenced in your tool_data_table_conf.xml, likely in tool-data/bowtie_indices.loc (and the corresponding .sample) to see that they match the new format. -Dannon On Feb 23, 2011, at 2:38 PM, Dannon Baker wrote:
Moving this to the galaxy-dev mailing list since it's about a local Galaxy installation.
The error here is likely a misconfigured tool_data_table_conf.xml. The format of this file has changed, see the tool_data_table_conf.xml.sample for an example of the new structure. Let me know if your file looks correct with the new format and you're still having issues.
-Dannon
On Feb 23, 2011, at 2:24 PM, Sonali Thakur wrote:
Hello,
We are getting below error with the Map with Bowtie for Illumina tool. Please suggest.
Traceback (most recent call last): File "/var/www/galaxy/lib/galaxy/jobs/runners/local.py", line 55, in run_job job_wrapper.prepare() File "/var/www/galaxy/lib/galaxy/jobs/__init__.py", line 347, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/var/www/galaxy/lib/galaxy/tools/__init__.py", line 1515, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/var/www/galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/var/www/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 222, in respond IndexError: list index out of range
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