> Hi all,
>
> I am upgrading to the most recent galaxy-dist
> 720455407d1c<https://bitbucket.org/galaxy/galaxy-dist/changeset/720455407d1c>
> .
> First time run.sh shows following errors as in attachment.
> It seems when I use 'manage_db.sh upgrade' it doesn't create necessary
> tables for these tools.
> Wonder if these are known issues?
>
> Thanks
>
>
>
[epigraph]
galaxy.tools ERROR 2011-07-05 10:34:12,556 error reading tool from path:
data_destination/epigraph.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 385, in
parse
self.interpreter = command.get("interpreter", None)
AttributeError: 'NoneType' object has no attribute 'get'
galaxy.tools ERROR 2011-07-05 10:34:12,559 error reading tool from path:
data_destination/epigraph_test.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 385, in
parse
self.interpreter = command.get("interpreter", None)
AttributeError: 'NoneType' object has no attribute 'get'
[manipulation]
galaxy.tools WARNING 2011-07-05 10:34:16,151 A when tag has been defined for
'manipulation (manipulation_selector) --> modify_each_score', but does not
appear to be selectable.
[picard]
galaxy.tools ERROR 2011-07-05 10:34:16,700 error reading tool from path:
picard/picard_ReorderSam.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in
parse
self.parse_inputs( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in
parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in
parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in
parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in
parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in
parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
161, in build
return parameter_types[param_type]( tool, param )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
607, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
line 411, in __init__
"Data table named '%s' is required by tool but not configured" %
tool_data_table_name
AssertionError: Data table named 'picard_indexes' is required by tool but not
configured
[mosaik]
galaxy.tools ERROR 2011-07-05 10:34:17,217 error reading tool from path:
sr_mapping/mosaik.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in
parse
self.parse_inputs( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in
parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in
parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in
parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in
parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in
parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
161, in build
return parameter_types[param_type]( tool, param )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
607, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
line 411, in __init__
"Data table named '%s' is required by tool but not configured" %
tool_data_table_name
AssertionError: Data table named 'mosaik_indexes' is required by tool but not
configured
[gatk]
galaxy.tools ERROR 2011-07-05 10:34:17,605 error reading tool from path:
gatk/realigner_target_creator.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in
parse
self.parse_inputs( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in
parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in
parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in
parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in
parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in
parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
161, in build
return parameter_types[param_type]( tool, param )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
607, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
line 411, in __init__
"Data table named '%s' is required by tool but not configured" %
tool_data_table_name
AssertionError: Data table named 'picard_indexes' is required by tool but not
configured
galaxy.tools ERROR 2011-07-05 10:34:17,612 error reading tool from path:
gatk/indel_realigner.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in
parse
self.parse_inputs( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in
parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in
parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in
parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in
parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in
parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
161, in build
return parameter_types[param_type]( tool, param )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
607, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
line 411, in __init__
"Data table named '%s' is required by tool but not configured" %
tool_data_table_name
AssertionError: Data table named 'picard_indexes' is required by tool but not
configured
galaxy.tools ERROR 2011-07-05 10:34:17,620 error reading tool from path:
gatk/count_covariates.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in
parse
self.parse_inputs( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in
parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in
parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in
parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in
parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in
parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
161, in build
return parameter_types[param_type]( tool, param )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
607, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
line 411, in __init__
"Data table named '%s' is required by tool but not configured" %
tool_data_table_name
AssertionError: Data table named 'picard_indexes' is required by tool but not
configured
galaxy.tools ERROR 2011-07-05 10:34:17,628 error reading tool from path:
gatk/table_recalibration.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in
parse
self.parse_inputs( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in
parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in
parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in
parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in
parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in
parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
161, in build
return parameter_types[param_type]( tool, param )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
607, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
line 411, in __init__
"Data table named '%s' is required by tool but not configured" %
tool_data_table_name
AssertionError: Data table named 'picard_indexes' is required by tool but not
configured
galaxy.tools DEBUG 2011-07-05 10:34:17,641 Loaded tool: gatk_analyze_covariates
0.0.1
galaxy.tools ERROR 2011-07-05 10:34:17,648 error reading tool from path:
gatk/unified_genotyper.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 441, in
parse
self.parse_inputs( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 523, in
parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 703, in
parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 770, in
parse_input_elem
case.inputs = self.parse_input_elem( case_elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 796, in
parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 808, in
parse_param_elem
param = ToolParameter.build( self, input_elem )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
161, in build
return parameter_types[param_type]( tool, param )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
607, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/home/galaxy2/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
line 411, in __init__
"Data table named '%s' is required by tool but not configured" %
tool_data_table_name
AssertionError: Data table named 'picard_indexes' is required by tool but not
configured
[data_sources]
galaxy.tools ERROR 2011-07-05 10:34:17,767 error reading tool from path:
data_source/access_libraries.xml
Traceback (most recent call last):
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 77, in
load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 169, in
load_tool
return ToolClass( config_file, root, self.app )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 340, in
__init__
self.parse( root )
File "/home/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 385, in
parse
self.interpreter = command.get("interpreter", None)
AttributeError: 'NoneType' object has no attribute 'get'
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