I used changeset: 7148:17d57db9a7c0 for the clone. I don't recall
making any changes, but have removed it and am about to start fresh and
see if the issue still exists.
Iry
On 6/22/12 11:50 AM, "Nate Coraor" <n...@bx.psu.edu> wrote:
>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/parameter
>>s/basic.py", line 176, in build
>> return parameter_types[param_type]( tool, param )
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameter
>>s/basic.py", line 626, in __init__
>> self.options = dynamic_options.DynamicOptions( options, self )
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameter
>>s/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/parameter
>>s/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/parameter
>>s/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/parameter
>>s/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/parameter
>>s/basic.py", line 176, in build
>> return parameter_types[param_type]( tool, param )
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameter
>>s/basic.py", line 626, in __init__
>> self.options = dynamic_options.DynamicOptions( options, self )
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameter
>>s/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/parameter
>>s/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/parameter
>>s/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/parameter
>>s/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/parameter
>>s/basic.py", line 176, in build
>> return parameter_types[param_type]( tool, param )
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameter
>>s/basic.py", line 626, in __init__
>> self.options = dynamic_options.DynamicOptions( options, self )
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/tools/parameter
>>s/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/parameter
>>s/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/parameter
>>s/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/parameter
>>s/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__.p
>>y", 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/pb
>>s.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__.p
>>y", 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.
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>
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.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
