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tool_shed.tool_shed_registry DEBUG 2013-07-16 15:27:28,322 Loading references to tool sheds from tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2013-07-16 15:27:28,322 Loaded reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2013-07-16 15:27:28,322 Loaded reference to tool shed: Galaxy test tool shed
galaxy.eggs WARNING 2013-07-16 15:27:28,585 Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched
migrate.versioning.repository DEBUG 2013-07-16 15:27:28,653 Loading repository lib/galaxy/model/migrate...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,654 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0014_pages.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,655 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,656 Script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0037_samples_library.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0037_samples_library.py loaded successfully
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migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0040_page_annotations.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0040_page_annotations.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Loading script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py...
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migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,657 Script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py loaded successfully
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migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py...
migrate.versioning.script.base DEBUG 2013-07-16 15:27:28,713 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully
migrate.versioning.repository DEBUG 2013-07-16 15:27:28,714 Repository lib/tool_shed/galaxy_install/migrate loaded successfully
migrate.versioning.repository DEBUG 2013-07-16 15:27:28,714 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))])
tool_shed.galaxy_install.migrate.check DEBUG 2013-07-16 15:27:28,716 pysqlite>=2 egg successfully loaded for sqlite dialect
tool_shed.galaxy_install.migrate.check INFO 2013-07-16 15:27:28,730 At migrate_tools version 7
galaxy.model.mapping DEBUG 2013-07-16 15:27:28,733 pysqlite>=2 egg successfully loaded for sqlite dialect
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,747 Loading datatypes from /home/fmareuil/Travail/Galaxy/galaxy-dist/database/tmp/tmpaUF47Z
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,748 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,752 Loading datatypes from datatypes_conf.xml
galaxy.datatypes.registry WARNING 2013-07-16 15:27:28,752 Overriding conflicting datatype with extension 'data', using datatype from datatypes_conf.xml.
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,756 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,756 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,756 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,756 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,756 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,756 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,756 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,757 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2013-07-16 15:27:28,758 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,766 Loaded tool data table 'all_fasta'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,766 Loaded tool data table 'bfast_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'blastdb'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'bowtie2_indexes'
galaxy.tools.data WARNING 2013-07-16 15:27:28,767 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'bwa_indexes'
galaxy.tools.data WARNING 2013-07-16 15:27:28,767 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'indexed_maf_files'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'ngs_sim_fasta'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'perm_base_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,767 Loaded tool data table 'perm_color_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'sam_fa_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'picard_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'gatk_picard_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'gatk_annotations'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'srma_indexes'
galaxy.tools.data WARNING 2013-07-16 15:27:28,768 Cannot find index file 'tool-data/bowtie_indices.loc' for tool data table 'tophat_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'tophat_indexes'
galaxy.tools.data WARNING 2013-07-16 15:27:28,768 Cannot find index file 'tool-data/bowtie_indices_color.loc' for tool data table 'tophat_indexes_color'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'tophat_indexes_color'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'tophat2_indexes'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'ccat_configurations'
galaxy.tools.data DEBUG 2013-07-16 15:27:28,768 Loaded tool data table 'mosaik_indexes'
galaxy.jobs WARNING 2013-07-16 15:27:28,769 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/home/fmareuil/Travail/Galaxy/galaxy-dist/universe_wsgi.ini" instead
galaxy.jobs DEBUG 2013-07-16 15:27:28,769 Loading job configuration from /home/fmareuil/Travail/Galaxy/galaxy-dist/universe_wsgi.ini
galaxy.jobs DEBUG 2013-07-16 15:27:28,769 Done loading job configuration
galaxy.tools INFO 2013-07-16 15:27:28,774 Parsing the tool configuration ./tool_conf.xml
galaxy.tools ERROR 2013-07-16 15:27:28,778 Error reading tool from path: ../../../repos/deseq_yufei/deseq/deseq.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/../../../repos/deseq_yufei/deseq/deseq.xml'
docutils WARNING 2013-07-16 15:27:28,883 <string>:37: (ERROR/3) Document may not end with a transition.
galaxy.tools WARNING 2013-07-16 15:27:28,949 Tool htseqCount: a when tag has not been defined for 'samout (flag) --> yes', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:28,949 Tool htseqCount: a when tag has not been defined for 'samout (flag) --> no', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:28,949 Tool htseqCount: a when tag has not been defined for 'samout (flag) --> yes', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:28,949 Tool htseqCount: a when tag has not been defined for 'samout (flag) --> no', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:28,949 Tool htseqCount: a when tag has not been defined for 'quiet (flag) --> yes', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:28,949 Tool htseqCount: a when tag has not been defined for 'quiet (flag) --> no', assuming empty inputs.
docutils WARNING 2013-07-16 15:27:28,953 <string>:17: (WARNING/2) Literal block expected; none found.
galaxy.tools WARNING 2013-07-16 15:27:29,402 Tool clc_unmapped_reads: a when tag has not been defined for 'paired_selector (flag_paired) --> yes', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:29,402 Tool clc_unmapped_reads: a when tag has not been defined for 'paired_selector (flag_paired) --> no', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:29,402 Tool clc_unmapped_reads: a when tag has not been defined for 'paired_selector (flag_paired) --> yes', assuming empty inputs.
galaxy.tools WARNING 2013-07-16 15:27:29,402 Tool clc_unmapped_reads: a when tag has not been defined for 'paired_selector (flag_paired) --> no', assuming empty inputs.
galaxy.tools ERROR 2013-07-16 15:27:33,871 Error reading tool from path: variant_detection/freebayes.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/variant_detection/freebayes.xml'
galaxy.tools WARNING 2013-07-16 15:27:34,406 Tool fastq_manipulation: a when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable.
galaxy.tools ERROR 2013-07-16 15:27:34,922 Error reading tool from path: sr_mapping/bowtie_wrapper.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/bowtie_wrapper.xml'
galaxy.tools ERROR 2013-07-16 15:27:34,922 Error reading tool from path: sr_mapping/bowtie2beta_wrapper.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/bowtie2beta_wrapper.xml'
galaxy.tools ERROR 2013-07-16 15:27:34,923 Error reading tool from path: sr_mapping/bwa_wrapper.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/bwa_wrapper.xml'
galaxy.tools ERROR 2013-07-16 15:27:34,923 Error reading tool from path: sr_mapping/pbwa_wrapper.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/pbwa_wrapper.xml'
galaxy.tools ERROR 2013-07-16 15:27:34,923 Error reading tool from path: sr_mapping/lastz_wrapper.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/lastz_wrapper.xml'
galaxy.tools ERROR 2013-07-16 15:27:34,974 Error reading tool from path: sr_mapping/bowtie_color_wrapper.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/bowtie_color_wrapper.xml'
galaxy.tools ERROR 2013-07-16 15:27:34,974 Error reading tool from path: sr_mapping/bwa_color_wrapper.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/sr_mapping/bwa_color_wrapper.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,011 Error reading tool from path: variant_detection/freebayes.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/variant_detection/freebayes.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,096 Error reading tool from path: variant_detection/freebayes.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/variant_detection/freebayes.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/picard_FastqToSam.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/picard_FastqToSam.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/picard_SamToFastq.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/picard_SamToFastq.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/picard_BamIndexStats.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/picard_BamIndexStats.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/rgPicardASMetrics.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/rgPicardASMetrics.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/rgPicardGCBiasMetrics.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/rgPicardGCBiasMetrics.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/rgPicardLibComplexity.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/rgPicardLibComplexity.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/rgPicardInsertSize.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/rgPicardInsertSize.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,409 Error reading tool from path: picard/rgPicardHsMetrics.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/rgPicardHsMetrics.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,410 Error reading tool from path: picard/picard_AddOrReplaceReadGroups.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/picard_AddOrReplaceReadGroups.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,410 Error reading tool from path: picard/picard_ReorderSam.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/picard_ReorderSam.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,410 Error reading tool from path: picard/picard_ReplaceSamHeader.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/picard_ReplaceSamHeader.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,410 Error reading tool from path: picard/rgPicardFixMate.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/rgPicardFixMate.xml'
galaxy.tools ERROR 2013-07-16 15:27:36,410 Error reading tool from path: picard/rgPicardMarkDups.xml
Traceback (most recent call last):
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 475, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 584, in load_tool
tree = load_tool( config_file )
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 132, in parse_xml
tree = ElementTree.parse(fname)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/fmareuil/Travail/Galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/picard/rgPicardMarkDups.xml'
galaxy.tools INFO 2013-07-16 15:27:36,923 Parsing the tool configuration ./shed_tool_conf.xml
galaxy.tools INFO 2013-07-16 15:27:37,518 Parsing the tool configuration ./migrated_tools_conf.xml
galaxy.tools DEBUG 2013-07-16 15:27:37,518 Loading section: MyTools
galaxy.tools DEBUG 2013-07-16 15:27:37,518 Loaded tool id: pe_filter, version: 0.01 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,518 Loaded tool id: ReadFastaFile, version: 0.38 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,518 Loaded tool id: GetDistance, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,518 Loaded tool id: htseqCount, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,518 Loaded tool id: export, version: 2.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,518 Loaded tool id: aria_convert, version: 2.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: aria_launchor, version: 2.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: fa_gc_content_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: rankoptimizer, version: 2.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: sleep, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: clc_novo_assemble, version: 3.22.55705 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: snpEff2, version: 0.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: ptaxoptimizer, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: findpromoter, version: 1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: setuppromoter, version: 1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: fqconvert, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: GemReads, version: 0.1 beta into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: clc_unmapped_reads, version: 4.010.83648 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: clean_ngs, version: 0.7 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loading section: Get Data
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: upload1, version: 1.1.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: bx_browser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: biomart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,519 Loaded tool id: flymine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: modmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: ratmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: wormbase, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: encode_db1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: epigraph_import, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loading section: Send Data
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: export, version: 2.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: epigraph_export, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loading section: ENCODE Tools
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: gencode_partition1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: random_intervals1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loading section: Lift-Over
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: liftOver1, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loading section: Text Manipulation
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: addValue, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: Add_a_column1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: cat1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,520 Loaded tool id: Condense characters1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: createInterval, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: Cut1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: Paste1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: trimmer, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loading section: Convert Formats
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,521 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loading section: FASTA manipulation
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: fasta_compute_length, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: fasta_filter_by_length, version: 1.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: fasta_concatenate0, version: 0.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: cshl_fasta_formatter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: cshl_fasta_nucleotides_changer, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loading section: Filter and Sort
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: Filter1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: sort1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: Grep1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: dna_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded label: GFF
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,522 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loading section: Join, Subtract and Group
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: join1, version: 2.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: comp1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: subtract_query1, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: Grouping1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: column_join, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loading section: Extract Features
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loading section: Fetch Sequences
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: Extract genomic DNA 1, version: 2.2.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loading section: Fetch Alignments
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,523 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loading section: Get Genomic Scores
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: phastOdds_for_intervals, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loading section: Operate on Genomic Intervals
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_intersect_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_subtract_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_merge_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_concat_1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_basecoverage_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_coverage_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_complement_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_cluster_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: gops_join_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: get_flanks1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: flanking_features_1, version: 4.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,524 Loaded tool id: Annotation_Profiler_0, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loading section: Statistics
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: Count1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: cor2, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: generate_matrix_for_pca_and_lda1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: lda_analy1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: plot_for_lda_output1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loading section: Graph/Display Data
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: histogram_rpy, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: scatterplot_rpy, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: XY_Plot_1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: gmaj_1, version: 2.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: build_ucsc_custom_track_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: mutation_visualize, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loading section: Regional Variation
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: winSplitter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: featureCoverage1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,525 Loaded tool id: wtavg, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: qualityFilter, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: cpgFilter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: getIndels_2way, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: indels_3way, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: indelRates_3way, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: substitutions1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: subRate1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: microsats_align1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: microsats_mutability1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loading section: Multiple regression
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: LinearRegression1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: LogisticRegression, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: BestSubsetsRegression1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: rcve1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: partialRsq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loading section: Multivariate Analysis
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: pca1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: cca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: kpca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loaded tool id: kcca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,526 Loading section: Evolution
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: mutate_snp_codon_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loading section: Motif Tools
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: rgweblogo3, version: 0.4 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loading section: Multiple Alignments
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: clustalw, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loading section: Metagenomic analyses
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: Fetch Taxonomic Ranks, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: t2t_report, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: find_diag_hits, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: lca1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: poisson2test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loading section: Phenotype Association
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: hgv_david, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,527 Loaded tool id: ctdBatch_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_funDo, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_snpFreq, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: hgv_hilbertvis, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: dividePgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loading section: NGS: QC and manipulation
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded label: Illumina data
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: fastq_groomer, version: 1.0.4 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: fastq_paired_end_splitter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: fastq_paired_end_joiner, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: fastq_stats, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded label: Roche-454 data
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: quality_score_distribution, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,528 Loaded tool id: trim_reads, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_combiner, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded label: AB-SOLiD data
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded label: Generic FASTQ manipulation
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_trimmer, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_quality_trimmer, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_masker_by_quality, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_manipulation, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: fastq_to_tabular, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: tabular_to_fastq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded label: FASTX-Toolkit for FASTQ data
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: cshl_fastq_quality_converter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: cshl_fastx_quality_statistics, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: cshl_fastq_quality_boxplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: cshl_fastx_nucleotides_distribution, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: cshl_fastq_to_fasta, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: cshl_fastq_quality_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,529 Loaded tool id: cshl_fastx_artifacts_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: cshl_fastx_barcode_splitter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: cshl_fastx_clipper, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: cshl_fastx_collapser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: cshl_fastx_renamer, version: 0.0.11 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: cshl_fastx_reverse_complement, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: cshl_fastx_trimmer, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded label: FASTQ QC
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: fastqc, version: 0.51 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loading section: NGS: Mapping
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded label: Illumina
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded label: Roche-454
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded label: AB-SOLiD
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loading section: NGS: SAM Tools
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: sam_bw_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: sam2interval, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: sam_to_bam, version: 1.1.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: bam_to_sam, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: sam_merge2, version: 1.1.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: samtools_mpileup, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: sam_pileup, version: 1.1.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,530 Loaded tool id: pileup_parser, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: pileup_interval, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: samtools_flagstat, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: samtools_rmdup, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loading section: NGS: GATK Tools (beta)
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded label: Alignment Utilities
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_depth_of_coverage, version: 0.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_print_reads, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded label: Realignment
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_realigner_target_creator, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_indel_realigner, version: 0.0.6 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded label: Base Recalibration
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_count_covariates, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_table_recalibration, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_analyze_covariates, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded label: Genotyping
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_unified_genotyper, version: 0.0.6 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded label: Annotation
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_variant_annotator, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded label: Filtration
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded label: Variant Quality Score Recalibration
galaxy.tools DEBUG 2013-07-16 15:27:37,531 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,532 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-07-16 15:27:37,532 Loaded label: Variant Utilities