cummeRbund 1.0.1 error - plots fail against sqlite database content

I have no clue why the following errors occurred.
- When loading:

```
galaxy.tools.parameters.basic DEBUG 2016-02-24 04:04:17,191 Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.1':
Traceback (most recent call last):
File "/home/galaxy/dev/lib/galaxy/tools/parameters/basic.py", line 879, in get_options
return eval( self.dynamic_options, self.tool.code_namespace, call_other_values )
File "", line 1, in
NameError: name 'input_database' is not defined
```
- When executing:

```
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,270 Building dependency shell command for dependency 'CUMMERBUND_SCRIPT_PATH'
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,270 Find dependency CUMMERBUND_SCRIPT_PATH version None
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,299 Resolver tool_shed_packages returned (isnull? False)
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,300 Building dependency shell command for dependency 'R'
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,300 Find dependency R version 3.1.2
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,301 Resolver tool_shed_packages returned (isnull? False)
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,301 Building dependency shell command for dependency 'cummeRbund'
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,301 Find dependency cummeRbund version 2.8.2
galaxy.tools.deps DEBUG 2016-02-24 04:04:59,301 Resolver tool_shed_packages returned (isnull? False)
galaxy.jobs.runners ERROR 2016-02-24 04:04:59,515 (137) Failure preparing job
Traceback (most recent call last):
File "/home/galaxy/dev/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job
include_work_dir_outputs=include_work_dir_outputs,
File "/home/galaxy/dev/lib/galaxy/jobs/runners/__init__.py", line 200, in build_command_line
container=container
File "/home/galaxy/dev/lib/galaxy/jobs/command_factory.py", line 41, in build_command
raise Exception("Attempting to run a tool with empty command definition.")
Exception: Attempting to run a tool with empty command definition.
```

Thanks,
Justin.