I've gotten the database to load trying it a second time - it may be some kind of NFS issue. However, you can't run the tool because it seems to fail to read the input dataset. Here's what's logged when you 1. load the tool and 2. click Insert Plots:

galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,859 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,860 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,861 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,862 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.actions INFO 2018-06-04 14:38:15,864 [p:8313,w:5,m:0] [uWSGIWorker5Core1] Added output datasets to history (21.072 ms)
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,864 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,865 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,866 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,867 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,867 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,868 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,869 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,870 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,871 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,872 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,874 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,875 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,876 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,877 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,878 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,878 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,879 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,880 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,882 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,882 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,885 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,886 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,887 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,888 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,889 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,889 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,890 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,891 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,892 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,892 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,894 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,895 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,896 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,897 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,898 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,898 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,900 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,900 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,901 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,902 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,903 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,904 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,905 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,906 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined

Uh oh!

update cummerbund #110

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