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.
-----
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.
The runner0.log contains most the same errors as the web0.log with the following addition:
I am not quite sure where the issue lies, but your help will be appreciated.
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