On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:

> I have recently performed a fresh installation of Galaxy utilizing the latest 
> distribution and am getting a sizable number of errors when attempting to 
> start the server.  The issue started when I performed a merge so I decided to 
> do the clean install as a test.  The server appears to start just fine, but 
> with errors reported in the logs.  The web0.log gives the following errors 
> and warnings (I am truncating the file for space):
> 
> galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg 
> successfully loaded for postgres dialect
> galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database version 97
> galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2 egg 
> successfully loaded for postgres dialect
> galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At migrate_tools 
> version 2
> galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg 
> successfully loaded for postgres dialect
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loading 
> references to tool sheds from tool_sheds_conf.xml
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded 
> reference to tool shed: Galaxy main tool shed
> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded 
> reference to tool shed: Galaxy test tool shed
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading datatypes 
> from datatypes_conf.xml
> galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding 
> conflicting datatype with extension 'coverage', using datatype from 
> datatypes_conf.xml.
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for 
> datatype 'galaxy.datatypes.binary:Bam'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for 
> datatype 'galaxy.datatypes.binary:Sff'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for 
> datatype 'galaxy.datatypes.xml:BlastXml'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Maf'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Lav'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:csFasta'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.qualityscore:QualityScore454'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Fasta'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Fastq'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Wiggle'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.images:Html'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.images:Pdf'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for 
> datatype 'galaxy.datatypes.sequence:Axt'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Bed'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:CustomTrack'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Gtf'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Gff'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Gff3'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.tabular:Pileup'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.interval:Interval'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.tabular:Sam'
> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for 
> datatype 'galaxy.datatypes.tabular:Vcf'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table 
> 'all_fasta'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table 
> 'bfast_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table 
> 'blastdb'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,062 Loaded tool data table 
> 'blastdb_p'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,065 Loaded tool data table 
> 'bowtie_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,066 Loaded tool data table 
> 'bowtie_indexes_color'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,068 Loaded tool data table 
> 'rsem_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,075 Loaded tool data table 
> 'bwa_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,079 Loaded tool data table 
> 'bwa_indexes_color'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,081 Loaded tool data table 
> 'indexed_maf_files'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,084 Loaded tool data table 
> 'ngs_sim_fasta'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,087 Loaded tool data table 
> 'lastz_seqs'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,089 Loaded tool data table 
> 'perm_base_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,091 Loaded tool data table 
> 'perm_color_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,094 Loaded tool data table 
> 'picard_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,095 Loaded tool data table 
> 'gatk_picard_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,096 Loaded tool data table 
> 'srma_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,097 Loaded tool data table 
> 'tophat_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,098 Loaded tool data table 
> 'tophat_indexes_color'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,100 Loaded tool data table 
> 'ccat_configurations'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,101 Loaded tool data table 
> 'mosaik_indexes'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,104 Loaded tool data table 
> 'mousedivgeno_anno'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,106 Loaded tool data table 
> 'mousedivgeno_background_cel_dirs'
> galaxy.tools.data DEBUG 2012-06-20 18:29:21,108 Loaded tool data table 
> 'cnv_seq_refs'
> galaxy.tools INFO 2012-06-20 18:29:21,125 Parsing the tool configuration 
> ./tool_conf.xml
> galaxy.tools.test DEBUG 2012-06-20 18:29:21,579 Error in add_param for input: 
> Unable to determine parameter type of test input 'input'. Ensure that the 
> parameter exists and that any container groups are defined first.
> galaxy.tools.test DEBUG 2012-06-20 18:29:21,579 Error in add_param for input: 
> Unable to determine parameter type of test input 'input'. Ensure that the 
> parameter exists and that any container groups are defined first.
> galaxy.tools.test DEBUG 2012-06-20 18:29:21,706 Error in add_param for input: 
> Unable to determine parameter type of test input 'input'. Ensure that the 
> parameter exists and that any container groups are defined first.
> galaxy.tools.test DEBUG 2012-06-20 18:29:21,706 Error in add_param for input: 
> Unable to determine parameter type of test input 'input'. Ensure that the 
> parameter exists and that any container groups are defined first.
> docutils WARNING 2012-06-20 18:29:25,232 <string>:8: (WARNING/2) Title 
> underline too short.
> 
> This tool uses raw orthologous microsatellite clusters (identified by the 
> tool "Extract orthologous microsatellites") to identify microsatellite births 
> and deaths along individual lineages of a phylogenetic tree.

Hi Iry,

These warnings can be ignored.

> -----
> 
> galaxy.tools WARNING 2012-06-20 18:29:26,871 A when tag has been defined for 
> 'manipulation (manipulation_selector) --> modify_each_score', but does not 
> appear to be selectable.
> galaxy.tools WARNING 2012-06-20 18:29:28,304 A when tag has been defined for 
> 'input (format) --> None', but does not appear to be selectable.
> galaxy.tools WARNING 2012-06-20 18:29:28,304 A when tag has not been defined 
> for 'useci (ci) --> no', assuming empty inputs.
> docutils WARNING 2012-06-20 18:29:28,360 <string>:285: (ERROR/3) Unexpected 
> indentation.
> 
> docutils WARNING 2012-06-20 18:29:28,362 <string>:301: (ERROR/3) Unexpected 
> indentation.
> 
> docutils WARNING 2012-06-20 18:29:28,484 <string>:50: (WARNING/2) Literal 
> block expected; none found.
> 
> galaxy.tools.test DEBUG 2012-06-20 18:29:28,495 Error in add_param for 
> min_coverage_intron: Unable to determine parameter type of test input 
> 'min_coverage_intron'. Ensure that the parameter exists and that any 
> container groups are defined first.
> galaxy.tools.test DEBUG 2012-06-20 18:29:28,495 Error in add_param for 
> max_coverage_intron: Unable to determine parameter type of test input 
> 'max_coverage_intron'. Ensure that the parameter exists and that any 
> container groups are defined first.
> galaxy.tools WARNING 2012-06-20 18:29:28,760 A when tag has not been defined 
> for 'indel (call_indels) --> false', assuming empty inputs.
> galaxy.tools ERROR 2012-06-20 18:29:29,082 Error reading tool from path: None
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 315, in load_tool_tag_set
>     tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
>   File "/usr/lib64/python2.6/posixpath.py", line 65, in join
>     if b.startswith('/'):
> AttributeError: 'NoneType' object has no attribute 'startswith'

> galaxy.tools.parameters.dynamic_options WARNING 2012-06-20 18:29:29,382 Data 
> table named 'gatk_annotations' is required by tool but not configured
> galaxy.tools ERROR 2012-06-20 18:29:29,382 Error reading tool from path: 
> gatk/unified_genotyper.xml
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 315, in load_tool_tag_set
>     tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 433, in load_tool
>     return ToolClass( config_file, root, self.app, guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 769, in __init__
>     self.parse( root, guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 933, in parse
>     self.parse_inputs( root )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1015, in parse_inputs
>     display, inputs = self.parse_input_page( page, enctypes )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1214, in parse_input_page
>     inputs = self.parse_input_elem( input_elem, enctypes )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1281, in parse_input_elem
>     case.inputs = self.parse_input_elem( case_elem, enctypes, context )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1307, in parse_input_elem
>     param = self.parse_param_elem( elem, enctypes, context )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1319, in parse_param_elem
>     param = ToolParameter.build( self, input_elem )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
>  line 176, in build
>     return parameter_types[param_type]( tool, param )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
>  line 626, in __init__
>     self.options = dynamic_options.DynamicOptions( options, self )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 449, in __init__
>     self.filters.append( Filter.from_element( self, filter_elem ) )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 22, in from_element
>     return filter_types[type.strip()]( d_option, elem )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 213, in __init__
>     self.columns = [ d_option.column_spec_to_index( column ) for column in 
> columns.split( "," ) ]
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 571, in column_spec_to_index
>     return int( column_spec )
> ValueError: invalid literal for int() with base 10: 'tools_valid_for'
> galaxy.tools.parameters.dynamic_options WARNING 2012-06-20 18:29:29,398 Data 
> table named 'gatk_annotations' is required by tool but not configured
> galaxy.tools ERROR 2012-06-20 18:29:29,398 Error reading tool from path: 
> gatk/variant_annotator.xml
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 315, in load_tool_tag_set
>     tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 433, in load_tool
>     return ToolClass( config_file, root, self.app, guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 769, in __init__
>     self.parse( root, guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 933, in parse
>     self.parse_inputs( root )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1015, in parse_inputs
>     display, inputs = self.parse_input_page( page, enctypes )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1214, in parse_input_page
>     inputs = self.parse_input_elem( input_elem, enctypes )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1281, in parse_input_elem
>     case.inputs = self.parse_input_elem( case_elem, enctypes, context )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1307, in parse_input_elem
>     param = self.parse_param_elem( elem, enctypes, context )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1319, in parse_param_elem
>     param = ToolParameter.build( self, input_elem )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
>  line 176, in build
>     return parameter_types[param_type]( tool, param )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
>  line 626, in __init__
>     self.options = dynamic_options.DynamicOptions( options, self )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 449, in __init__
>     self.filters.append( Filter.from_element( self, filter_elem ) )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 22, in from_element
>     return filter_types[type.strip()]( d_option, elem )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 213, in __init__
>     self.columns = [ d_option.column_spec_to_index( column ) for column in 
> columns.split( "," ) ]
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 571, in column_spec_to_index
>     return int( column_spec )
> ValueError: invalid literal for int() with base 10: 'tools_valid_for'
> galaxy.tools.parameters.dynamic_options WARNING 2012-06-20 18:29:29,445 Data 
> table named 'gatk_annotations' is required by tool but not configured
> galaxy.tools ERROR 2012-06-20 18:29:29,445 Error reading tool from path: 
> gatk/variant_recalibrator.xml
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 315, in load_tool_tag_set
>     tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 433, in load_tool
>     return ToolClass( config_file, root, self.app, guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 769, in __init__
>     self.parse( root, guid=guid )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 933, in parse
>     self.parse_inputs( root )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1015, in parse_inputs
>     display, inputs = self.parse_input_page( page, enctypes )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1214, in parse_input_page
>     inputs = self.parse_input_elem( input_elem, enctypes )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1307, in parse_input_elem
>     param = self.parse_param_elem( elem, enctypes, context )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", 
> line 1319, in parse_param_elem
>     param = ToolParameter.build( self, input_elem )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
>  line 176, in build
>     return parameter_types[param_type]( tool, param )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
>  line 626, in __init__
>     self.options = dynamic_options.DynamicOptions( options, self )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 449, in __init__
>     self.filters.append( Filter.from_element( self, filter_elem ) )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 22, in from_element
>     return filter_types[type.strip()]( d_option, elem )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 213, in __init__
>     self.columns = [ d_option.column_spec_to_index( column ) for column in 
> columns.split( "," ) ]
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py",
>  line 571, in column_spec_to_index
>     return int( column_spec )
> ValueError: invalid literal for int() with base 10: 'tools_valid_for'
> galaxy.tools.test DEBUG 2012-06-20 18:29:29,993 Error in add_param for force: 
> Unable to determine parameter type of test input 'force'. Ensure that the 
> parameter exists and that any container groups are defined first.
> galaxy.tools INFO 2012-06-20 18:29:30,785 Parsing the tool configuration 
> ./migrated_tools_conf.xml
> galaxy.tools DEBUG 2012-06-20 18:29:30,787 Loading section: JAX Custom Tools
> galaxy.tools DEBUG 2012-06-20 18:29:30,787 Loaded tool id: export_to_igv, 
> version: 1.0.0.
> --
> --
> galaxy.tools.imp_exp DEBUG 2012-06-20 18:29:33,190 Loaded history export 
> tool: __EXPORT_HISTORY__
> galaxy.tools.imp_exp DEBUG 2012-06-20 18:29:33,191 Loaded history import 
> tool: __IMPORT_HISTORY__
> galaxy.jobs.runners.local INFO 2012-06-20 18:29:33,204 starting workers
> galaxy.jobs.runners.local DEBUG 2012-06-20 18:29:33,205 5 workers ready
> galaxy.jobs.handler DEBUG 2012-06-20 18:29:33,205 Loaded job runner: 
> galaxy.jobs.runners.local:LocalJobRunner
> galaxy.jobs.handler INFO 2012-06-20 18:29:33,206 job handler stop queue 
> started
> galaxy.jobs.manager INFO 2012-06-20 18:29:33,211 job manager queue started
> galaxy.jobs.manager INFO 2012-06-20 18:29:33,211 job manager stop queue 
> started
> galaxy.jobs.handler INFO 2012-06-20 18:29:33,214 job handler queue started
> galaxy.sample_tracking.external_service_types ERROR 2012-06-20 18:29:33,214 
> ExternalServiceTypesCollection error reading ./external_service_types_conf.xml
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py",
>  line 21, in __init__
>     self.load_all( config_filename )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py",
>  line 26, in load_all
>     tree = util.parse_xml( config_filename )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/util/__init__.py", 
> line 105, in parse_xml
>     tree = ElementTree.parse(fname)
>   File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 
> 859, in parse
>     tree.parse(source, parser)
>   File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 
> 576, in parse
>     source = open(source, "rb")
> IOError: [Errno 2] No such file or directory: 
> './external_service_types_conf.xml'
> galaxy.web.framework.base DEBUG 2012-06-20 18:29:33,224 Enabling 'async' 
> controller, class: ASync
> galaxy.web.framework.base DEBUG 2012-06-20 18:29:33,251 Enabling 'workflow' 
> controller, class: WorkflowController
> galaxy.web.framework.base DEBUG 2012-06-20 18:29:33,267 Enabling 
> 'admin_toolshed' controller, class: AdminGalaxy
> --
> --
> galaxy.web.buildapp DEBUG 2012-06-20 18:29:33,654 Enabling 'config' middleware
> galaxy.web.buildapp DEBUG 2012-06-20 18:29:33,655 Enabling 'x-forwarded-host' 
> middleware
> Starting server in PID 956.
> serving on 0.0.0.0:8080 view at http://127.0.0.1:8080
> 10.20.22.8 - - [20/Jun/2012:18:29:57 -0400] "GET / HTTP/1.0" 500 - "-" 
> "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.19) 
> Gecko/20110707 Firefox/3.6.19"
> Error - <type 'exceptions.AttributeError'>: 'Configuration' object has no 
> attribute 'cloud_controller_instance'

Although there are some tool configuration errors above, they aren't critical.  
However, this one is a bit confusing.  There should be no references to 
cloud_controller_instance in the current galaxy-dist.  Are you sure that this 
clone is a completely unaltered version of galaxy-dist?  Can you provide the 
changeset id?

> 
> --------------------------------------------
> 
> 
> The runner0.log contains most the same errors as the web0.log with the 
> following addition:
> 
> 
> galaxy.jobs.runners.local INFO 2012-06-20 16:18:25,622 starting workers
> galaxy.jobs.runners.local DEBUG 2012-06-20 16:18:25,622 3 workers ready
> galaxy.jobs.handler DEBUG 2012-06-20 16:18:25,623 Loaded job runner: 
> galaxy.jobs.runners.local:LocalJobRunner
> galaxy.jobs.handler ERROR 2012-06-20 16:18:25,758 Job runner is not loadable: 
> galaxy.jobs.runners.pbs
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/handler.py", 
> line 375, in _load_plugin
>     module = __import__( module_name )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",
>  line 30, in <module>
>     raise Exception( egg_message % str( e ) )
> Exception: 
> 
> The 'pbs' runner depends on 'pbs_python' which is not installed or not
> configured properly.  Galaxy's "scramble" system should make this installation
> simple, please follow the instructions found at:
> 
>     http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
> 
> Additional errors may follow:
> ['pbs_python']

To fix this, please scramble the pbs_python egg as explained in the 
documentation at the above URL.

> 
> galaxy.jobs.handler INFO 2012-06-20 16:18:25,761 job handler stop queue 
> started
> galaxy.jobs.manager INFO 2012-06-20 16:18:25,766 job manager queue started
> galaxy.jobs.manager INFO 2012-06-20 16:18:25,767 job manager stop queue 
> started
> galaxy.jobs.handler INFO 2012-06-20 16:18:25,770 job handler queue started
> galaxy.sample_tracking.external_service_types ERROR 2012-06-20 16:18:25,771 
> ExternalServiceTypesCollection error reading ./external_service_types_conf.xml
> Traceback (most recent call last):
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py",
>  line 21, in __init__
>     self.load_all( config_filename )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py",
>  line 26, in load_all
>     tree = util.parse_xml( config_filename )
>   File 
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/util/__init__.py", 
> line 105, in parse_xml
>     tree = ElementTree.parse(fname)
>   File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 
> 859, in parse
>     tree.parse(source, parser)
>   File "build/bdist.linux-x86_64-ucs4/egg/elementtree/ElementTree.py", line 
> 576, in parse
>     source = open(source, "rb")
> IOError: [Errno 2] No such file or directory: 
> './external_service_types_conf.xml'

Not a critical error, but you can get rid of it by copying the 
external_service_types_conf.xml.sample file to the non-.sample name.

> galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,782 Enabling 'async' 
> controller, class: ASync
> galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,816 Enabling 'workflow' 
> controller, class: WorkflowController
> galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,835 Enabling 
> 'admin_toolshed' controller, class: AdminGalaxy
> galaxy.web.framework.base DEBUG 2012-06-20 16:18:25,836 Enabling 
> 'admin_toolshed' controller, class: AdminToolshed
> 
> 
> This is the server error from the browser:
> 
> URL: http://galaxy2/
> Module paste.exceptions.errormiddleware:143 in __call__
> >>  app_iter = self.application(environ, start_response)
> Module paste.debug.prints:98 in __call__
> >>  environ, self.app)
> Module paste.wsgilib:539 in intercept_output
> >>  app_iter = application(environ, replacement_start_response)
> Module paste.recursive:80 in __call__
> >>  return self.application(environ, start_response)
> Module paste.httpexceptions:632 in __call__
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:160 in __call__
> >>  body = method( trans, **kwargs )
> Module galaxy.web.controllers.root:25 in index
> >>  m_c=m_c, m_a=m_a )
> Module galaxy.web.framework:733 in fill_template
> >>  return self.fill_template_mako( filename, **kwargs )
> Module galaxy.web.framework:744 in fill_template_mako
> >>  return template.render( **data )
> Module mako.template:296 in render
> >>  return runtime._render(self, self.callable_, args, data)
> Module mako.runtime:660 in _render
> >>  **_kwargs_for_callable(callable_, data))
> Module mako.runtime:692 in _render_context
> >>  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> Module mako.runtime:718 in _exec_template
> >>  callable_(context, *args, **kwargs)
> Module _base_panels_mako:53 in render_body
> >>  __M_writer(unicode(self.init()))
> Module root_index_mako:58 in render_init
> >>  if trans.app.config.cloud_controller_instance:
> AttributeError: 'Configuration' object has no attribute 
> 'cloud_controller_instance'
> 
> 
> I am not quite sure where the issue lies, but your help will be appreciated.
> 
> Thanks,
> Iry Witham
> Scientific Applications Administrator
> Scientific Computing Group
> Computational Sciences Dept.
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
> Phone: 207-288-6744
> email: iry.wit...@jax.org
> 
> 
> The information in this email, including attachments, may be confidential and 
> is intended solely for the addressee(s). If you believe you received this 
> email by mistake, please notify the sender by return email as soon as 
> possible.
> ___________________________________________________________
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> and other Galaxy lists, please use the interface at:
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