Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known
Hello all, I'm trying to install Galaxy in a production server using CentOS 6.3, with python 2.6.6 (default CentOS) and PostgreSQL 9.2. I've followed instructions in http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay/WS5 After typing galaxy@myhost$ sh run.sh --reload the script produces the following output, resulting in a Python exception. Do you have any solution or hint for solving this issue? Maybe a service is missing? /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /home/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/boto-2.5.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Fabric-1.4.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/ssh-1.7.14-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /home/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /home/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /home/galaxy/galaxy-dist/lib, /home/galaxy/galaxy_env/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg, /home/galaxy/galaxy_env/lib/python2.6/site-packages/pip-1.2.1-py2.6.egg, /home/galaxy/galaxy_env/lib64/python26.zip, /home/galaxy/galaxy_env/lib64/python2.6, /home/galaxy/galaxy_env/lib64/python2.6/plat-linux2, /home/galaxy/galaxy_env/lib64/python2.6/lib-tk, /home/galaxy/galaxy_env/lib64/python2.6/lib-old, /home/galaxy/galaxy_env/lib64/python2.6/lib-dynload, /usr/lib/python2.6, /usr/lib64/python2.6, /home/galaxy/galaxy_env/lib/python2.6/site-packages galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-01 10:35:47,749 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-01 10:35:47,749 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-11-01 10:35:47,749 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-11-01 10:35:47,857 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-11-01 10:35:48,010 At database version 107 galaxy.tool_shed.migrate.check DEBUG 2012-11-01 10:35:48,025 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.migrate.check INFO 2012-11-01 10:35:48,054 At migrate_tools version 5 galaxy.model.custom_types DEBUG 2012-11-01 10:35:48,060 psycopg2 egg successfully loaded for postgres dialect galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,341 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,353 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,354 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,355 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,356 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,357 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,358 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,359 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,360 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,360 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:48,360 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2012-11-01 10:35:48,378 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2012-11-01 10:35:48,378 Loaded tool data table 'bfast_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,378 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'bowtie2_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,379 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data WARNING 2012-11-01 10:35:48,380 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'bwa_indexes' galaxy.tools.data WARNING 2012-11-01 10:35:48,380 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'bwa_indexes_color' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'indexed_maf_files' galaxy.tools.data DEBUG 2012-11-01 10:35:48,380 Loaded tool data table 'ngs_sim_fasta' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,381 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'gatk_picard_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'gatk_annotations' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,382 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'tophat_indexes_color' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'tophat2_indexes' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'ccat_configurations' galaxy.tools.data DEBUG 2012-11-01 10:35:48,383 Loaded tool data table 'mosaik_indexes' galaxy.tools INFO 2012-11-01 10:35:48,398 Parsing the tool configuration ./tool_conf.xml galaxy.tools WARNING 2012-11-01 10:35:51,637 A when tag has not been defined for 'master_variable_type (master_variable_type_selector) --> allPairs', assuming empty inputs. galaxy.tools WARNING 2012-11-01 10:35:53,858 A when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. galaxy.tools.test DEBUG 2012-11-01 10:35:55,561 Error in add_param for report_discordant_pairs: Unable to determine parameter type of test input 'report_discordant_pairs'. Ensure that the parameter exists and that any container groups are defined first. docutils WARNING 2012-11-01 10:35:55,606 <string>:50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2012-11-01 10:35:55,621 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 2012-11-01 10:35:55,622 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.test DEBUG 2012-11-01 10:35:57,402 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 2012-11-01 10:35:58,305 Parsing the tool configuration ./migrated_tools_conf.xml galaxy.tools DEBUG 2012-11-01 10:35:58,305 Loading section: Get Data galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: bx_browser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,306 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: biomart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: biomart_test, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: gramenemart, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: flymine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: flymine_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,307 Loaded tool id: modmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: ratmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: yeastmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: wormbase, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: eupathdb, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,308 Loaded tool id: encode_db1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: epigraph_import, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: epigraph_import_test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: hbvar, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: fix_errors, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loading section: Send Data galaxy.tools DEBUG 2012-11-01 10:35:58,309 Loaded tool id: epigraph_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: epigraph_test_export, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: genomespace_exporter, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loading section: ENCODE Tools galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: gencode_partition1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: random_intervals1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loading section: Lift-Over galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loaded tool id: liftOver1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,310 Loading section: Text Manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: addValue, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: Add_a_column1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: cat1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: Cut1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: createInterval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,311 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Paste1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: random_lines1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: Show tail1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: trimmer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,312 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: dna_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: tables_arithmetic_operations, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loading section: Filter and Sort galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: Filter1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: sort1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: Grep1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded label: GFF galaxy.tools DEBUG 2012-11-01 10:35:58,313 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loading section: Join, Subtract and Group galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: join1, version: 2.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: comp1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: subtract_query1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,314 Loaded tool id: Grouping1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: column_join, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loading section: Convert Formats galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,315 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,316 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loading section: Extract Features galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loading section: Fetch Sequences galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loaded tool id: Extract genomic DNA 1, version: 2.2.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,317 Loading section: Fetch Alignments galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,318 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loading section: Get Genomic Scores galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,319 Loaded tool id: phastOdds_for_intervals, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loading section: Operate on Genomic Intervals galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_intersect_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_subtract_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_merge_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_concat_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_basecoverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_coverage_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,320 Loaded tool id: gops_complement_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: gops_cluster_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: gops_join_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: get_flanks1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: flanking_features_1, version: 4.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: Annotation_Profiler_0, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loading section: Statistics galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,321 Loaded tool id: Count1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: cor2, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: generate_matrix_for_pca_and_lda1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: lda_analy1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: plot_for_lda_output1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: t_test_two_samples, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: compute_q_values, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded tool id: maximal_information_based_nonparametric_exploration, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,322 Loaded label: GFF galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: count_gff_features, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loading section: Wavelet Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: dwt_var1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loading section: Graph/Display Data galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: histogram_rpy, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: scatterplot_rpy, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,323 Loaded tool id: XY_Plot_1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: gmaj_1, version: 2.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: laj_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: build_ucsc_custom_track_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: mutation_visualize, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loading section: Regional Variation galaxy.tools DEBUG 2012-11-01 10:35:58,324 Loaded tool id: winSplitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: featureCoverage1, version: 2.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: wtavg, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: qualityFilter, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: cpgFilter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: getIndels_2way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: indels_3way, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: indelRates_3way, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,325 Loaded tool id: substitutions1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: subRate1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: microsats_align1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: microsats_mutability1, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: delete_overlapping_indels, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: compute_motifs_frequency, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: compute_motif_frequencies_for_all_motifs, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: categorize_elements_satisfying_criteria, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,326 Loaded tool id: draw_stacked_barplots, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loading section: Multiple regression galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: LinearRegression1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: LogisticRegression, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: BestSubsetsRegression1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: rcve1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: partialRsq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loading section: Multivariate Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,327 Loaded tool id: pca1, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: cca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: kpca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: kcca1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loading section: Evolution galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: hyphy_dnds_wrapper1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,328 Loaded tool id: mutate_snp_codon_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loading section: Motif Tools galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: meme_meme, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: meme_fimo, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: rgweblogo3, version: 0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loading section: Multiple Alignments galaxy.tools DEBUG 2012-11-01 10:35:58,329 Loaded tool id: clustalw, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loading section: Metagenomic analyses galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: Fetch Taxonomic Ranks, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: t2t_report, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: find_diag_hits, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: lca1, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loaded tool id: poisson2test, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,330 Loading section: FASTA manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta_compute_length, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta_filter_by_length, version: 1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta_concatenate0, version: 0.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: cshl_fasta_formatter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: cshl_fasta_nucleotides_changer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,331 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loading section: NGS: QC and manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded label: FastQC: fastq/sam/bam galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastqc, version: 0.51 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded label: Illumina fastq galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_groomer, version: 1.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_paired_end_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_paired_end_joiner, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,332 Loaded tool id: fastq_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded label: Roche-454 data galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: quality_score_distribution, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: trim_reads, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: fastq_combiner, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded label: AB-SOLiD data galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,333 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded label: Generic FASTQ manipulation galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_quality_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_masker_by_quality, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_paired_end_interlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_paired_end_deinterlacer, version: 1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,334 Loaded tool id: fastq_manipulation, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: fastq_to_tabular, version: 1.1.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: tabular_to_fastq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded label: FASTX-Toolkit for FASTQ data galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastq_quality_converter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastx_quality_statistics, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastq_quality_boxplot, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastx_nucleotides_distribution, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,335 Loaded tool id: cshl_fastq_to_fasta, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastq_quality_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_artifacts_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_barcode_splitter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_clipper, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_renamer, version: 0.0.11 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_reverse_complement, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,336 Loaded tool id: cshl_fastx_trimmer, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loading section: NGS: Picard (beta) galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded label: Conversion galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: picard_FastqToSam, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: picard_SamToFastq, version: 1.56.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded label: QC/Metrics for sam/bam galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: picard_BamIndexStats, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: PicardASMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,337 Loaded tool id: PicardGCBiasMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: rgEstLibComp, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: PicardInsertSize, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: PicardHsMetrics, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded label: bam/sam Cleaning galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: picard_ARRG, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: picard_ReorderSam, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: picard_ReplaceSamHeader, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,338 Loaded tool id: rgPicFixMate, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: rgPicardMarkDups, version: 1.56.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loading section: NGS: Mapping galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: lastz_wrapper_2, version: 1.2.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: lastz_paired_reads_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bowtie_wrapper, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bowtie2, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bowtie_color_wrapper, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,339 Loaded tool id: bfast_wrapper, version: 0.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: PerM, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: srma_wrapper, version: 0.2.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: mosaik_wrapper, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loading section: NGS: Indel Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: sam_indel_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,340 Loaded tool id: indel_sam2interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: indel_table, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: indel_analysis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loading section: NGS: RNA Analysis galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded label: RNA-seq galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: tophat, version: 1.5.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: tophat2, version: 0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: tophat_color, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,341 Loaded tool id: cufflinks, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: cuffcompare, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: express, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: cuffmerge, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: cuffdiff, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded label: Filtering galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: filter_combined_via_tracking, version: 0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loading section: NGS: SAM Tools galaxy.tools DEBUG 2012-11-01 10:35:58,342 Loaded tool id: sam_bw_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam2interval, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam_to_bam, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: bam_to_sam, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam_merge2, version: 1.1.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: samtools_mpileup, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: sam_pileup, version: 1.1.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: pileup_parser, version: 1.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,343 Loaded tool id: pileup_interval, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: samtools_flagstat, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: samtools_rmdup, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: samtools_slice_bam, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loading section: NGS: GATK Tools (beta) galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded label: Alignment Utilities galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: gatk_depth_of_coverage, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded tool id: gatk_print_reads, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,344 Loaded label: Realignment galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_realigner_target_creator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_indel_realigner, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded label: Base Recalibration galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_count_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_table_recalibration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_analyze_covariates, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded label: Genotyping galaxy.tools DEBUG 2012-11-01 10:35:58,345 Loaded tool id: gatk_unified_genotyper, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Annotation galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_annotator, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Filtration galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Variant Quality Score Recalibration galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,346 Loaded label: Variant Utilities galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: gatk_validate_variants, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: gatk_variant_eval, version: 0.0.8 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: gatk_variant_combine, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,347 Loaded tool id: bed2genetrack, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: predict2genetrack, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loading section: NGS: Simulation galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded label: Data: Import and upload galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded tool id: library_access1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,348 Loaded label: Data: Filter and Clean galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgClean1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgPedSub1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgLDIndep1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded label: Simulate galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: fakePhe1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded tool id: rgfakePed1, version: 0.02 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2012-11-01 10:35:58,349 Loaded label: QC; Eigenstrat galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgQC1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgEigPCA1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded label: LD; Manhattan/QQ; GRR galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgHaploView1, version: 0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgGRR1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2012-11-01 10:35:58,350 Loaded tool id: rgCaCo1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: rgTDT1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: rgGLM1, version: 0.2 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loading section: Phenotype Association galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,351 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_david, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: ctdBatch_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_funDo, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_snpFreq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,352 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: hgv_hilbertvis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: hgv_master2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: dividePgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loading section: VCF Tools galaxy.tools DEBUG 2012-11-01 10:35:58,353 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,354 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,354 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-11-01 10:35:58,354 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,498 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,501 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,503 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,504 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,505 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,506 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,509 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,510 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,514 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,515 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,521 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,522 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,531 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,540 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,541 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,544 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,548 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,550 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,551 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,553 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,555 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,555 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,555 Adding inherited display application 'genetrack_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'genetrack_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,556 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'genetrack_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,557 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,558 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'genetrack_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'genetrack_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,559 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,560 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,560 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,567 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,574 Loaded converter: CONVERTER_bam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,581 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,588 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,595 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,602 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,609 Loaded converter: CONVERTER_bed_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,616 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,623 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,632 Loaded converter: CONVERTER_bed_to_genetrack_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,639 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,646 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,653 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,660 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,667 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,674 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,681 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,688 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,695 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,702 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,712 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,718 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,725 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,732 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,739 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,746 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,753 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,760 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,767 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,774 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,781 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,788 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,798 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,805 Loaded converter: CONVERTER_interval_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,812 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,819 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,826 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,833 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,840 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,847 Loaded converter: CONVERTER_encodepeak_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,854 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,861 Loaded converter: CONVERTER_sam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,868 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,875 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,885 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,892 Loaded converter: CONVERTER_vcf_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,899 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,900 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,907 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,914 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,921 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,928 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,935 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2012-11-01 10:35:58,936 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.imp_exp DEBUG 2012-11-01 10:35:58,938 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2012-11-01 10:35:58,939 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2012-11-01 10:35:58,940 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.runners.local INFO 2012-11-01 10:35:58,942 starting workers galaxy.jobs.runners.local DEBUG 2012-11-01 10:35:58,943 5 workers ready galaxy.jobs.handler DEBUG 2012-11-01 10:35:58,943 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.lwr INFO 2012-11-01 10:35:58,944 starting workers galaxy.jobs.runners.lwr DEBUG 2012-11-01 10:35:58,949 5 workers ready galaxy.jobs.handler DEBUG 2012-11-01 10:35:58,950 Loaded job runner: galaxy.jobs.runners.lwr:LwrJobRunner galaxy.jobs.handler DEBUG 2012-11-01 10:35:58,950 Job runners: local:lwr galaxy.jobs.handler INFO 2012-11-01 10:35:58,950 job handler stop queue started galaxy.jobs.manager INFO 2012-11-01 10:35:58,957 job manager queue started galaxy.jobs.manager INFO 2012-11-01 10:35:58,958 job manager stop queue started galaxy.jobs.handler INFO 2012-11-01 10:35:58,963 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2012-11-01 10:35:58,966 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2012-11-01 10:35:58,970 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers ['/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers'] galaxy.webapps.galaxy.controllers root galaxy.webapps.galaxy.controllers.root galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,978 Enabling 'root' controller, class: RootController galaxy.webapps.galaxy.controllers mobile galaxy.webapps.galaxy.controllers.mobile galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,979 Enabling 'mobile' controller, class: Mobile galaxy.webapps.galaxy.controllers user galaxy.webapps.galaxy.controllers.user galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,981 Enabling 'user' controller, class: User galaxy.webapps.galaxy.controllers requests galaxy.webapps.galaxy.controllers.requests galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,984 Enabling 'requests' controller, class: Requests galaxy.webapps.galaxy.controllers admin_toolshed galaxy.webapps.galaxy.controllers.admin_toolshed galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,996 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,996 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.webapps.galaxy.controllers external_services galaxy.webapps.galaxy.controllers.external_services galaxy.web.framework.base DEBUG 2012-11-01 10:35:58,998 Enabling 'external_services' controller, class: ExternalServiceController galaxy.webapps.galaxy.controllers library_admin galaxy.webapps.galaxy.controllers.library_admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,009 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.webapps.galaxy.controllers data_admin galaxy.webapps.galaxy.controllers.data_admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,016 Enabling 'data_admin' controller, class: DataAdmin galaxy.webapps.galaxy.controllers workflow galaxy.webapps.galaxy.controllers.workflow galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,067 Enabling 'workflow' controller, class: WorkflowController galaxy.webapps.galaxy.controllers forms galaxy.webapps.galaxy.controllers.forms galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,069 Enabling 'forms' controller, class: Forms galaxy.webapps.galaxy.controllers cloudlaunch galaxy.webapps.galaxy.controllers.cloudlaunch galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,083 Enabling 'cloudlaunch' controller, class: CloudController galaxy.webapps.galaxy.controllers tag galaxy.webapps.galaxy.controllers.tag galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,084 Enabling 'tag' controller, class: TagsController galaxy.webapps.galaxy.controllers history galaxy.webapps.galaxy.controllers.history galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,086 Enabling 'history' controller, class: HistoryController galaxy.webapps.galaxy.controllers requests_common galaxy.webapps.galaxy.controllers.requests_common galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,087 Enabling 'requests_common' controller, class: RequestsCommon galaxy.webapps.galaxy.controllers async galaxy.webapps.galaxy.controllers.async galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,088 Enabling 'async' controller, class: ASync galaxy.webapps.galaxy.controllers dataset galaxy.webapps.galaxy.controllers.dataset galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,096 Enabling 'dataset' controller, class: DatasetInterface galaxy.webapps.galaxy.controllers request_type galaxy.webapps.galaxy.controllers.request_type galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,098 Enabling 'request_type' controller, class: RequestType galaxy.webapps.galaxy.controllers tool_runner galaxy.webapps.galaxy.controllers.tool_runner galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,100 Enabling 'tool_runner' controller, class: ToolRunner galaxy.webapps.galaxy.controllers requests_admin galaxy.webapps.galaxy.controllers.requests_admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,119 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.webapps.galaxy.controllers page galaxy.webapps.galaxy.controllers.page galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,121 Enabling 'page' controller, class: PageController galaxy.webapps.galaxy.controllers visualization galaxy.webapps.galaxy.controllers.visualization galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,124 Enabling 'visualization' controller, class: VisualizationController galaxy.webapps.galaxy.controllers ucsc_proxy galaxy.webapps.galaxy.controllers.ucsc_proxy galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,125 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.webapps.galaxy.controllers external_service galaxy.webapps.galaxy.controllers.external_service galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,126 Enabling 'external_service' controller, class: ExternalService galaxy.webapps.galaxy.controllers library_common galaxy.webapps.galaxy.controllers.library_common galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,127 Enabling 'library_common' controller, class: LibraryCommon galaxy.webapps.galaxy.controllers admin galaxy.webapps.galaxy.controllers.admin galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,128 Enabling 'admin' controller, class: AdminGalaxy galaxy.webapps.galaxy.controllers library galaxy.webapps.galaxy.controllers.library galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,129 Enabling 'library' controller, class: Library galaxy.webapps.galaxy.controllers error galaxy.webapps.galaxy.controllers.error galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,130 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,132 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,133 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,134 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,135 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,136 Enabling 'permissions' API controller, class: PermissionsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,137 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,137 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,144 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,144 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,145 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,147 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,148 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,148 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,149 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,149 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,151 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,152 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,152 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,153 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,154 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,155 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2012-11-01 10:35:59,156 Enabling 'genomes' API controller, class: GenomesController galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,156 app.config.api_folders: False galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,498 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,499 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,500 Enabling 'print debug' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,506 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,507 Enabling 'trans logger' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,507 Enabling 'config' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-11-01 10:35:59,507 Enabling 'x-forwarded-host' middleware Starting server in PID 20622. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 303, in command serve() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 287, in serve server(app) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/home/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 402, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.gaierror: [Errno -2] Name or service not known
Nobody? Anyone knows if using nginx would avoid the internal HTTP Python server? Sorry guys but I have to tell you this is why Python is considered a crap for big projects. When things like this fail, only the original developer knows how to fix it. Cheers From: yjmrs@hotmail.com To: galaxy-dev@bx.psu.edu Date: Thu, 1 Nov 2012 23:47:54 +0000 Subject: [galaxy-dev] Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known Hello all, I'm trying to install Galaxy in a production server using CentOS 6.3, with python 2.6.6 (default CentOS) and PostgreSQL 9.2. I've followed instructions in http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay/WS5 After typing galaxy@myhost$ sh run.sh --reload the script produces the following output, resulting in a Python exception. Do you have any solution or hint for solving this issue? Maybe a service is missing? /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * ... File "/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 402, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.gaierror: [Errno -2] Name or service not known ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
On 04/11/12 16:39, Marcelo Timmerman wrote:
Nobody?
Anyone knows if using nginx would avoid the internal HTTP Python server?
It appears that nginx is used as a proxy in front of the Python/Paste server, not as a replacement. You could use something like mod_wsgi with Apache instead of that server, but nobody seems to be doing that at the moment, as far as I can tell. Many Python Web projects seem to favour mod_wsgi as a deployment option for WSGI, so it's a safe choice.
Sorry guys but I have to tell you this is why Python is considered a crap for big projects. When things like this fail, only the original developer knows how to fix it.
There are a lot more factors affecting reliability and ease of maintenance in "big projects" than the matter of which programming language was used. What do you have for your host and port in your configuration file? Paul P.S. And you might want to look into this...
/home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
If you mix libraries from different Python versions or using different Unicode representations or which are compiled for different architectures, you may end up with some problems that really are difficult to diagnose. That's simply a matter of configuration management.
On Nov 5, 2012, at 5:39 AM, Paul Boddie wrote:
On 04/11/12 16:39, Marcelo Timmerman wrote:
Nobody?
Anyone knows if using nginx would avoid the internal HTTP Python server?
It appears that nginx is used as a proxy in front of the Python/Paste server, not as a replacement. You could use something like mod_wsgi with Apache instead of that server, but nobody seems to be doing that at the moment, as far as I can tell. Many Python Web projects seem to favour mod_wsgi as a deployment option for WSGI, so it's a safe choice.
Sorry guys but I have to tell you this is why Python is considered a crap for big projects. When things like this fail, only the original developer knows how to fix it.
There are a lot more factors affecting reliability and ease of maintenance in "big projects" than the matter of which programming language was used.
What do you have for your host and port in your configuration file?
This would appear to be the problem, the values of these options are not parsing to something the server can understand. --nate
Paul
P.S. And you might want to look into this...
/home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
If you mix libraries from different Python versions or using different Unicode representations or which are compiled for different architectures, you may end up with some problems that really are difficult to diagnose. That's simply a matter of configuration management. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Subject: Re: [galaxy-dev] Cannot run Galaxy : socket.gaierror: [Errno -2] Name or service not known From: nate@bx.psu.edu Date: Mon, 5 Nov 2012 12:07:59 -0500 CC: yjmrs@hotmail.com; galaxy-dev@bx.psu.edu To: paul.boddie@biotek.uio.no
On Nov 5, 2012, at 5:39 AM, Paul Boddie wrote:
On 04/11/12 16:39, Marcelo Timmerman wrote:
Nobody?
Anyone knows if using nginx would avoid the internal HTTP Python server?
It appears that nginx is used as a proxy in front of the Python/Paste server, not as a replacement. You could use something like mod_wsgi with Apache instead of that server, but nobody seems to be doing that at the moment, as far as I can tell. Many Python Web projects seem to favour mod_wsgi as a deployment option for WSGI, so it's a safe choice.
Sorry guys but I have to tell you this is why Python is considered a crap for big projects. When things like this fail, only the original developer knows how to fix it.
There are a lot more factors affecting reliability and ease of maintenance in "big projects" than the matter of which programming language was used.
Agree. But the fact that you cannot easily rapidly debug the failing expression is dissapointing.
What do you have for your host and port in your configuration file?
This would appear to be the problem, the values of these options are not parsing to something the server can understand.
Finally I've found the problem, yes it was a typo in the host setting in the universe file. Thanks for your tip. Cheers, Macelo
On 06/11/12 23:37, Marcelo Timmerman wrote:
Agree. But the fact that you cannot easily rapidly debug the failing expression is dissapointing.
A backtrace is a lot better than "Segmentation fault". Maybe there should be an exception handler that displays a nice message, but then there's the challenge of preserving whatever information there is about the nature of the failure and expressing it in a helpful way. Doing that properly isn't exactly a challenge unique to Python.
Finally I've found the problem, yes it was a typo in the host setting in the universe file. Thanks for your tip.
No problem! Paul
participants (3)
-
Marcelo Timmerman -
Nate Coraor -
Paul Boddie