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 >> >> Thanks >> _______________________________________________ >> The Galaxy User list should be used for the discussion >> of Galaxy analysis and other features on the public >> server at usegalaxy.org. For discussion of local Galaxy >> instances and the Galaxy source code, please use the >> Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other >> Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > _______________________________________________ > To manage your subscriptions to this and other Galaxy lists, please use the > interface at: > > http://lists.bx.psu.edu/ _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
