[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 * 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

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/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