All 1 test(s) executed passed. extract_graph_script[0]: passed christian@XPS-13-9343-CB:~/Dropbox/Manchester/galaxy_shed_tools/repr_tools$ planemo test --galaxy_root=/home/christian/galaxy_new columns.xml Testing using galaxy_root /home/christian/galaxy_new Testing tools with command [cd /home/christian/galaxy_new; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --skip-common-startup"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/christian/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then type virtualenv >/dev/null 2>&1 && virtualenv $GALAXY_VIRTUAL_ENV; else echo "Reusing existing virtualenv $GALAXY_VIRTUAL_ENV"; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/christian/Dropbox/Manchester/galaxy_shed_tools/repr_tools/tool_test_output.html --xunit_report_file /tmp/tmpuTVTx3/xunit.xml --structured_data_report_file /home/christian/Dropbox/Manchester/galaxy_shed_tools/repr_tools/tool_test_output.json functional.test_toolbox] Set COMMON_STARTUP_ARGS to --skip-venv --skip-common-startup Reusing existing virtualenv .venv [('app:main', 'new_file_path', '/tmp/tmpsI1vCk/tmpfflUPi/new_files_path_sivd4F'), ('app:main', 'database_connection', 'sqlite:////tmp/tmpsI1vCk/tmpfflUPi/database/universe.sqlite'), ('app:main', 'data_manager_config_file', 'config/data_manager_conf.xml.sample,test/functional/tools/sample_data_manager_conf.xml'), ('app:main', 'job_queue_workers', 5), ('app:main', 'log_destination', 'stdout'), ('app:main', 'allow_user_deletion', True), ('app:main', 'master_api_key', 'test_key'), ('app:main', 'tool_config_file', '/tmp/tmpuTVTx3/tool_conf.xml,/tmp/tmpuTVTx3/shed_tool_conf.xml'), ('app:main', 'template_cache_path', '/tmp/tmpsI1vCk/tmpfflUPi/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/tmpsI1vCk/tmpfflUPi/job_working_directory_uL1jGT'), ('app:main', 'tool_dependency_dir', '/tmp/tmpuTVTx3/deps'), ('app:main', 'tool_data_table_config_path', 'config/tool_data_table_conf.xml.sample,test/functional/tool-data/sample_tool_data_tables.xml'), ('app:main', 'tool_path', 'tools'), ('app:main', 'enable_beta_tool_formats', True), ('app:main', 'user_library_import_dir', None), ('app:main', 'galaxy_data_manager_data_path', '/tmp/tmpsI1vCk/data_manager_test_tmpmX73dC/data_manager_tool-datab2rC_J'), ('app:main', 'file_path', '/tmp/tmpsI1vCk/tmpfflUPi/database/files'), ('app:main', 'datatype_converters_config_file', 'datatype_converters_conf.xml.sample'), ('app:main', 'database_auto_migrate', True), ('app:main', 'use_tasked_jobs', True), ('app:main', 'auto_configure_logging', True), ('app:main', 'tool_parse_help', False), ('app:main', 'shed_tool_data_table_config', 'config/shed_tool_data_table_conf.xml'), ('app:main', 'update_integrated_tool_panel', False), ('app:main', 'admin_users', 'test@bx.psu.edu'), ('app:main', 'template_path', 'templates'), ('app:main', 'allow_user_creation', True), ('app:main', 'use_heartbeat', False), ('app:main', 'allow_library_path_paste', True), ('app:main', 'api_allow_run_as', 'test@bx.psu.edu'), ('app:main', 'test_conf', 'test.conf'), ('app:main', 'id_secret', 'changethisinproductiontoo'), ('app:main', 'library_import_dir', '/home/christian/Dropbox/Manchester/galaxy_shed_tools/repr_tools/test-data'), ('app:main', 'cleanup_job', 'onsuccess'), ('app:main', 'running_functional_tests', True)] No handlers could be found for logger "galaxy.config" galaxy.queue_worker INFO 2015-11-23 08:43:39,508 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// tool_shed.tool_shed_registry DEBUG 2015-11-23 08:43:39,528 Loading references to tool sheds from /tmp/tmpuTVTx3/tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2015-11-23 08:43:39,529 Loaded reference to tool shed: Target Shed galaxy.app DEBUG 2015-11-23 08:43:39,529 Using "galaxy.ini" config file: /tmp/tmpsI1vCk/functional_tests_wsgi.ini migrate.versioning.repository DEBUG 2015-11-23 08:43:39,566 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2015-11-23 08:43:39,567 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2015-11-23 08:43:39,567 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2015-11-23 08:43:39,567 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2015-11-23 08:43:39,567 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2015-11-23 08:43:39,567 Loading script 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INFO 2015-11-23 08:43:40,080 galaxy.model.migrate.check INFO 2015-11-23 08:43:40,080 Migration script to add session update time (used for timeouts) galaxy.model.migrate.check INFO 2015-11-23 08:43:40,080 galaxy.model.migrate.check INFO 2015-11-23 08:43:40,080 galaxy.model.migrate.check INFO 2015-11-23 08:43:40,080 Migrating 128 -> 129... galaxy.model.migrate.check INFO 2015-11-23 08:43:40,625 galaxy.model.migrate.check INFO 2015-11-23 08:43:40,626 Migration script to allow invalidation of job external output metadata temp files galaxy.model.migrate.check INFO 2015-11-23 08:43:40,626 galaxy.model.migrate.check INFO 2015-11-23 08:43:40,626 galaxy.model.migrate.check INFO 2015-11-23 08:43:40,626 Migrating 129 -> 130... galaxy.model.migrate.check INFO 2015-11-23 08:43:41,168 galaxy.model.migrate.check INFO 2015-11-23 08:43:41,168 Migration script to change the value column of user_preference from varchar to text. galaxy.model.migrate.check INFO 2015-11-23 08:43:41,168 galaxy.model.migrate.check INFO 2015-11-23 08:43:41,168 galaxy.config INFO 2015-11-23 08:43:41,183 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,226 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,226 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,226 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,227 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,227 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,227 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,227 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,227 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,227 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,228 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,229 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,230 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,232 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,233 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,233 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,233 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,233 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,233 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,233 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,234 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,234 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,234 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,234 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,234 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,235 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,236 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.proteomics:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,237 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,238 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,239 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,240 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,241 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,241 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,241 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,241 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,241 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,242 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,242 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,242 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,245 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,245 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,245 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,245 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,246 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,246 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,246 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,246 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,246 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,247 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,248 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,248 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,248 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,250 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,250 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,250 Retrieved datatype module galaxy.datatypes.graph:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,250 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,251 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,251 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,251 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,252 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,252 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,252 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,253 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,253 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,253 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,254 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,254 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,254 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,254 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,255 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,255 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,255 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,255 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,256 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,257 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,258 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,258 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,258 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,258 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,259 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,259 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,259 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,259 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,260 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,261 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,262 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,263 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,264 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,265 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,265 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,265 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,265 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,265 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,265 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,265 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,266 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,266 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,266 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,266 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,266 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,266 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,267 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzSQlite' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,268 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,269 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,270 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,271 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,273 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,273 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,273 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,273 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,273 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,274 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,274 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,274 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,274 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,275 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt galaxy.jobs WARNING 2015-11-23 08:43:41,308 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/tmpsI1vCk/functional_tests_wsgi.ini" instead galaxy.jobs DEBUG 2015-11-23 08:43:41,308 Loading job configuration from /tmp/tmpsI1vCk/functional_tests_wsgi.ini galaxy.jobs DEBUG 2015-11-23 08:43:41,308 Done loading job configuration beaker.container DEBUG 2015-11-23 08:43:41,322 data file /tmp/tmpuTVTx3/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.watcher INFO 2015-11-23 08:43:41,323 Failed to load ToolWatcher (watchdog is likely unavailable) - proceeding without tool monitoring. galaxy.tools.toolbox.base INFO 2015-11-23 08:43:41,323 Parsing the tool configuration /tmp/tmpuTVTx3/tool_conf.xml galaxy.tools.toolbox.base DEBUG 2015-11-23 08:43:41,331 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2015-11-23 08:43:41,333 Loaded tool id: extract_graph_script, version: 0.1 into tool panel.. galaxy.tools.toolbox.base INFO 2015-11-23 08:43:41,333 Parsing the tool configuration /tmp/tmpuTVTx3/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2015-11-23 08:43:41,333 Parsing the tool configuration /tmp/tmpuTVTx3/empty_tool_conf.xml galaxy.tools.deps WARNING 2015-11-23 08:43:41,334 Path '/tmp/tmpuTVTx3/deps' does not exist, ignoring galaxy.tools.deps WARNING 2015-11-23 08:43:41,334 Path '/tmp/tmpuTVTx3/deps' is not directory, ignoring galaxy.tools.deps DEBUG 2015-11-23 08:43:41,337 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2015-11-23 08:43:41,376 Starting to build toolbox index. galaxy.tools.search DEBUG 2015-11-23 08:43:41,485 Toolbox index finished. galaxy.tools.data_manager.manager DEBUG 2015-11-23 08:43:41,487 Loaded Data Manager: test_data_manager galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,489 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,490 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.display_applications.application ERROR 2015-11-23 08:43:41,491 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,492 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,492 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,492 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,493 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,494 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,495 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,496 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,497 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,502 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.display_applications.application ERROR 2015-11-23 08:43:41,503 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,503 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,504 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,508 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,515 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,516 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.display_applications.application ERROR 2015-11-23 08:43:41,518 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,518 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,521 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,523 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.display_applications.application ERROR 2015-11-23 08:43:41,526 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,527 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,529 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,530 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.display_applications.application ERROR 2015-11-23 08:43:41,534 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,534 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,534 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,534 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,534 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,534 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,535 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,536 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,537 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,537 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,537 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,537 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,537 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,537 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,538 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,539 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,539 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,540 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,541 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,541 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,542 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,543 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,543 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,544 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,545 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,545 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,546 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,547 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,547 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,548 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,549 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,549 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,550 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,551 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,551 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,552 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,553 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,555 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,556 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,557 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,557 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,560 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,561 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,562 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,564 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,565 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,567 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,570 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,571 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,573 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,574 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,574 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,575 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,576 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,577 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,577 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,578 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,579 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,579 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,580 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,581 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,581 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,583 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,584 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,585 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,586 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,587 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,588 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,593 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,595 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,598 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2015-11-23 08:43:41,601 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.imp_exp DEBUG 2015-11-23 08:43:41,603 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2015-11-23 08:43:41,604 Loaded history import tool: __IMPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2015-11-23 08:43:41,605 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2015-11-23 08:43:41,605 Visualizations plugin disabled: Circster. Skipping... galaxy.web.base.pluginframework INFO 2015-11-23 08:43:41,606 VisualizationsRegistry, loaded plugin: graphview galaxy.visualization.plugins.config_parser INFO 2015-11-23 08:43:41,606 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2015-11-23 08:43:41,606 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2015-11-23 08:43:41,607 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2015-11-23 08:43:41,608 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2015-11-23 08:43:41,608 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2015-11-23 08:43:41,609 VisualizationsRegistry, loaded plugin: trackster galaxy.jobs.manager DEBUG 2015-11-23 08:43:41,611 Starting job handler galaxy.jobs INFO 2015-11-23 08:43:41,611 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2015-11-23 08:43:41,612 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2015-11-23 08:43:41,612 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2015-11-23 08:43:41,613 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners.state_handler_factory DEBUG 2015-11-23 08:43:41,613 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2015-11-23 08:43:41,613 Starting 2 TaskRunner workers galaxy.jobs DEBUG 2015-11-23 08:43:41,613 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' galaxy.jobs DEBUG 2015-11-23 08:43:41,613 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2015-11-23 08:43:41,614 Loaded job runners plugins: tasks:local galaxy.jobs.handler INFO 2015-11-23 08:43:41,615 job handler stop queue started galaxy.jobs.handler INFO 2015-11-23 08:43:41,636 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2015-11-23 08:43:41,641 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2015-11-23 08:43:41,643 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2015-11-23 08:43:41,646 Starting workflow schedulers functional_tests.py INFO 2015-11-23 08:43:41,647 Embedded Universe application started galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,671 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,676 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,689 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,800 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,802 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,802 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,838 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,838 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,840 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,841 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,841 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,842 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,843 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,844 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,844 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,845 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,845 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,845 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,846 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,849 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,849 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,850 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,850 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,850 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,850 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,851 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,852 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,852 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,852 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,854 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,854 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,855 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,855 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,855 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,856 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,856 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,856 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,856 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,856 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,856 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,856 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,857 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,857 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,857 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,858 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,858 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,858 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,865 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,866 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,866 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,866 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,867 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,867 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,867 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,868 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,868 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,869 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,870 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,871 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,871 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,872 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,872 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,873 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,874 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,874 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,874 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,876 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,876 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,877 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,878 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,881 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,881 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,883 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2015-11-23 08:43:41,883 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,081 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,081 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,083 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,083 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,084 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,086 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,086 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,086 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2015-11-23 08:43:42,086 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2015-11-23 08:43:42,087 Binding and starting galaxy control worker for main functional_tests.py DEBUG 2015-11-23 08:43:42,091 Attempting to serve app on randomly chosen port: 8751 /home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) functional_tests.py INFO 2015-11-23 08:43:42,225 Embedded web server started functional_tests.py INFO 2015-11-23 08:43:42,225 Functional tests will be run against localhost:8751 functional_tests.py ERROR 2015-11-23 08:43:42,227 Failure running tests Traceback (most recent call last): File "./scripts/functional_tests.py", line 494, in main success = _run_functional_test( ) File "./scripts/functional_tests.py", line 443, in _run_functional_test import functional.test_toolbox File "/home/christian/galaxy_new/test/functional/test_toolbox.py", line 3, in from base.twilltestcase import TwillTestCase File "/home/christian/galaxy_new/test/base/twilltestcase.py", line 21, in import twill ImportError: No module named twill functional_tests.py INFO 2015-11-23 08:43:42,227 Shutting down functional_tests.py INFO 2015-11-23 08:43:42,227 Shutting down embedded web server functional_tests.py INFO 2015-11-23 08:43:42,229 Embedded web server stopped functional_tests.py INFO 2015-11-23 08:43:42,229 Shutting down app galaxy.jobs.handler INFO 2015-11-23 08:43:42,229 sending stop signal to worker thread galaxy.jobs.handler INFO 2015-11-23 08:43:42,229 job handler queue stopped galaxy.jobs.runners INFO 2015-11-23 08:43:42,229 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2015-11-23 08:43:42,230 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2015-11-23 08:43:42,230 sending stop signal to worker thread galaxy.jobs.handler INFO 2015-11-23 08:43:42,230 job handler stop queue stopped functional_tests.py INFO 2015-11-23 08:43:42,230 Embedded Universe application stopped functional_tests.py INFO 2015-11-23 08:43:42,230 Cleaning up temporary files in /tmp/tmpsI1vCk/tmpfflUPi galaxy.jobs.handler INFO 2015-11-23 08:43:43,121 sending stop signal to worker thread galaxy.jobs.handler INFO 2015-11-23 08:43:43,121 job handler queue stopped galaxy.jobs.runners INFO 2015-11-23 08:43:43,122 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2015-11-23 08:43:43,122 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2015-11-23 08:43:43,122 sending stop signal to worker thread galaxy.jobs.handler INFO 2015-11-23 08:43:43,122 job handler stop queue stopped Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown. Traceback (most recent call last): File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/bin/planemo", line 9, in load_entry_point('planemo==0.20.0', 'console_scripts', 'planemo')() File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/vendor/lib/python2.7/site-packages/click/core.py", line 664, in __call__ return self.main(*args, **kwargs) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/vendor/lib/python2.7/site-packages/click/core.py", line 644, in main rv = self.invoke(ctx) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/vendor/lib/python2.7/site-packages/click/core.py", line 991, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/vendor/lib/python2.7/site-packages/click/core.py", line 837, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/vendor/lib/python2.7/site-packages/click/core.py", line 464, in invoke return callback(*args, **kwargs) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/vendor/lib/python2.7/site-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args[1:], **kwargs) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/vendor/lib/python2.7/site-packages/click/core.py", line 464, in invoke return callback(*args, **kwargs) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/lib/python2.7/site-packages/planemo/commands/cmd_test.py", line 59, in cli return_value = run_in_config(ctx, config, **kwds) File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/lib/python2.7/site-packages/planemo/galaxy_test/actions.py", line 109, in run_in_config **kwds File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/lib/python2.7/site-packages/planemo/galaxy_test/actions.py", line 126, in __handle_summary **kwds File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/lib/python2.7/site-packages/planemo/galaxy_test/actions.py", line 139, in __summarize_tests_full num_tests = test_results.num_tests File "/home/christian/.linuxbrew/Cellar/planemo/0.20.0/libexec/lib/python2.7/site-packages/planemo/galaxy_test/structures.py", line 170, in num_tests return self.sd.num_tests AttributeError: 'StructuredData' object has no attribute 'num_tests'