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:
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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:
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-dev@lists.galaxyproject.org
-
Dannon Baker