I just upgrade our galaxy to the latest release : 7487:be81990d148a and ran the migration tool script for freebayes.
No handlers could be found for logger "galaxy.tools"
/opt/galaxy/galaxy_dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
from csamtools import *
Repositories will be installed into configured tool_path location ../shed_tools
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 load_tool
return ToolClass( config_file, root, self.app, guid=guid )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 790, in __init__
self.parse( root, guid=guid )
File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 961, in parse
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'
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.
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 directory)