I just updated my local Galaxy install to the latest galaxy-dist. The lastz tool seems to have been changed so it needs a lastz_seqs data table.
I added (as a guess)
<table name="lastz_seqs">
<columns>name, value</columns>
<file path="tool-data/lastz_seqs.loc" />
</table>
to tool_data_table_conf.xml.
the lastz tool will now load, and it shows my reference sequences in the drop down list. However, now when I run lastz I get an error while it is trying to setup the job:
Traceback (most recent call last):
File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 186, in queue_job
job_wrapper.prepare()
File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py", line 368, in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", line 1524, in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File "/galaxydata/galaxy-setup/galaxy-dist/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 119, in respond
IndexError: list index out of range
--
Glen L. Beane
Software Engineer
The Jackson Laboratory
Phone (207) 288-6153