Hi Nate, I removed to previous instillation just to be safe and performed a new clone. This time it appears to be less problematic. I am no longer getting all of the errors. However, I am getting an error due to my database version. The error is: galaxy.model.migrate.check DEBUG 2012-06-27 12:39:11,843 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 35, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/che ck.py", line 103, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '101' but this code expects version '97'. Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'. I have attempted to run sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade and that fails with the following error: galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in <module> main( repository=repo, url=db_url ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5. 4-py2.6.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5. 4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5. 4-py2.6.egg/migrate/versioning/api.py", line 327, in _migrate changeset = schema.changeset(version) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5. 4-py2.6.egg/migrate/versioning/schema.py", line 173, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5. 4-py2.6.egg/migrate/versioning/repository.py", line 170, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5. 4-py2.6.egg/migrate/versioning/repository.py", line 145, in version return self.versions.version(*p, **k) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5. 4-py2.6.egg/migrate/versioning/version.py", line 125, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(101)> It is getting closer, but I am not quite there yet. Thanks, Iry On 6/22/12 11:50 AM, "Nate Coraor" <nate@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.witham@jax.org

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