Hi Phillip,

I'm not able to reproduce this behavior, so it's difficult to determine what may be the cause.  I have not seen others in the community encounter this problem, but that may simply be due to the fact that no one is yet installing the freebayes tool from the tool shed.

A possible work-aound is to add the following entry into your local tool_data_table_conf.xml file located in your Galaxy installation directory.

    <table name="sam_fa_indexes" comment_char="#">
        <columns>line_type, value, path</columns>
        <file path="tool-data/sam_fa_indices.loc" />
    </table>

Let us know if this still does not correct the problem.

Greg Von Kuster

On Aug 27, 2012, at 10:07 AM, Philip Mabon wrote:

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 <philipmabon@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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