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