I already had that entry to the tool_data_table_conf.xml but still getting
the same error.

After some debugging and print statement, I found that it initially finds
the correct path to the 'sam_fa_indexes' when reading
tool_data_table_conf.xml in Galaxy installation directory but re-reads
another file in the shed_tools dir.
It's the sample tool_data_table_conf.xml from the freebayes directory.
../shed_tools/
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/213a3d6b579a/freebayes/tool_data_table_conf.xml.sample
.

Maybe the  tool_data_table_conf.xml.sample is invalid?

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


On Mon, Aug 27, 2012 at 9:41 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> 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 <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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