I just upgrade our galaxy to the latest release :  7487:be81990d148a and
ran the migration tool script for freebayes.

I received the following error:

No handlers could be found for logger "galaxy.tools"
RuntimeWarning: __builtin__.file size changed, may indicate binary
  from csamtools import *
Repositories will be installed into configured tool_path location
Adding new row (or updating an existing row) for repository 'freebayes' in
the tool_shed_repository table.
Traceback (most recent call last):
  File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
    app = MigrateToolsApplication( sys.argv[ 1 ] )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/migrate/common.py",
line 150, in __init__
    install_dependencies=install_dependencies )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py",
line 37, in __init__
    self.install_repository( repository_elem, install_dependencies )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py",
line 262, in install_repository
    install_dependencies=install_dependencies )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py",
line 150, in handle_repository_contents
    repository_tools_tups = get_repository_tools_tups( self.app,
metadata_dict )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/util/shed_util.py", line 1077,
in get_repository_tools_tups
    tool = app.toolbox.load_tool( os.path.abspath( relative_path ),
guid=guid )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 452, in
    return ToolClass( config_file, root, self.app, guid=guid )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 790, in
    self.parse( root, guid=guid )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 961, in
    self.parse_inputs( root )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1045,
in parse_inputs
    display, inputs = self.parse_input_page( page, enctypes )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1447,
in parse_input_page
    inputs = self.parse_input_elem( input_elem, enctypes )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1514,
in parse_input_elem
    case.inputs = self.parse_input_elem( case_elem, enctypes, context )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1470,
in parse_input_elem
    group.inputs = self.parse_input_elem( elem, enctypes, context )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1540,
in parse_input_elem
    param = self.parse_param_elem( elem, enctypes, context )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1552,
in parse_param_elem
    param = ToolParameter.build( self, input_elem )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line
176, in build
    return parameter_types[param_type]( tool, param )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line
1361, in __init__
    ToolParameter.__init__( self, tool, elem )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py", line
43, in __init__
    self.validators.append( validation.Validator.from_element( self, elem )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/validation.py",
line 23, in from_element
    return validator_types[type].from_element( param, elem )
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/validation.py",
line 279, in from_element
    tool_data_table = param.tool.app.tool_data_tables[ table_name ]
  File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/data/__init__.py", line
25, in __getitem__
    return self.data_tables.__getitem__( key )
KeyError: 'sam_fa_indexes'

What happen is that the freebayes itself installs correctly into
the shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/* but the dependency on
samtools 1.1.8 fails.

The value 'sam_fa_indexes' is present in the tool_data_table_conf.xml  and
I know it works since all my samtools are functional.

The status column for the freebayes entry in the database is 'Cloning'.

I get the same error if I try to install freebayes thru the web front end.
( Had to delete the row in the db and remove the freebayes install

Any ideas Greg?


Philip Mabon (Takadonet)
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada
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