Any ideas anyone?

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


On Tue, Aug 21, 2012 at 10:34 AM, Philip Mabon <philipma...@gmail.com>wrote:

> 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
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