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" /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'
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 directory)
Any ideas Greg?
Thanks!
Philip Mabon (Takadonet) Senior Bioinformatician National Microbiology Laboratory Public Health Agency of Canada