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flake8_lint_include_list.txt
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flake8_lint_include_list.txt
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contrib/
cron/add_manual_builds.py
cron/cleanup_datasets.py
cron/parse_builds_3_sites.py
cron/parse_builds.py
lib/galaxy/actions/
lib/galaxy/auth/__init__.py
lib/galaxy/auth/providers/__init__.py
lib/galaxy/config.py
lib/galaxy/dataset_collections/builder.py
lib/galaxy/dataset_collections/__init__.py
lib/galaxy/dataset_collections/structure.py
lib/galaxy/dataset_collections/subcollections.py
lib/galaxy/dataset_collections/type_description.py
lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
lib/galaxy/datatypes/converters/bed_to_gff_converter.py
lib/galaxy/datatypes/converters/bgzip.py
lib/galaxy/datatypes/converters/fasta_to_len.py
lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
lib/galaxy/datatypes/converters/gff_to_bed_converter.py
lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
lib/galaxy/datatypes/converters/__init__.py
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
lib/galaxy/datatypes/converters/interval_to_coverage.py
lib/galaxy/datatypes/converters/interval_to_fli.py
lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
lib/galaxy/datatypes/converters/lped_to_fped_converter.py
lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
lib/galaxy/datatypes/coverage.py
lib/galaxy/datatypes/dataproviders/exceptions.py
lib/galaxy/datatypes/display_applications/__init__.py
lib/galaxy/datatypes/display_applications/util.py
lib/galaxy/datatypes/__init__.py
lib/galaxy/datatypes/msa.py
lib/galaxy/datatypes/proteomics.py
lib/galaxy/datatypes/tabular.py
lib/galaxy/datatypes/text.py
lib/galaxy/datatypes/tracks.py
lib/galaxy/datatypes/util/generic_util.py
lib/galaxy/datatypes/util/__init__.py
lib/galaxy/eggs/
lib/galaxy/exceptions/__init__.py
lib/galaxy/external_services/__init__.py
lib/galaxy/external_services/parameters.py
lib/galaxy/external_services/result_handlers/basic.py
lib/galaxy/external_services/result_handlers/__init__.py
lib/galaxy_ext/
lib/galaxy/forms/__init__.py
lib/galaxy/jobs/actions/
lib/galaxy/jobs/datasets.py
lib/galaxy/jobs/deferred/
lib/galaxy/jobs/error_level.py
lib/galaxy/jobs/manager.py
lib/galaxy/jobs/metrics/collectl/__init__.py
lib/galaxy/jobs/metrics/collectl/stats.py
lib/galaxy/jobs/metrics/collectl/subsystems.py
lib/galaxy/jobs/metrics/formatting.py
lib/galaxy/jobs/metrics/instrumenters/meminfo.py
lib/galaxy/jobs/metrics/instrumenters/uname.py
lib/galaxy/jobs/rules/
lib/galaxy/jobs/runners/state_handlers/
lib/galaxy/jobs/runners/util/cli/factory.py
lib/galaxy/jobs/runners/util/cli/job/__init__.py
lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
lib/galaxy/jobs/runners/util/cli/job/torque.py
lib/galaxy/jobs/runners/util/cli/shell/__init__.py
lib/galaxy/jobs/runners/util/drmaa/
lib/galaxy/jobs/runners/util/env.py
lib/galaxy/jobs/runners/util/external.py
lib/galaxy/jobs/runners/util/__init__.py
lib/galaxy/jobs/splitters/basic.py
lib/galaxy/jobs/splitters/__init__.py
lib/galaxy/jobs/stock_rules.py
lib/galaxy/jobs/transfer_manager.py
lib/galaxy/main.py
lib/galaxy/managers/annotatable.py
lib/galaxy/managers/api_keys.py
lib/galaxy/managers/base.py
lib/galaxy/managers/context.py
lib/galaxy/managers/deletable.py
lib/galaxy/managers/__init__.py
lib/galaxy/managers/lddas.py
lib/galaxy/managers/libraries.py
lib/galaxy/managers/secured.py
lib/galaxy/managers/taggable.py
lib/galaxy/model/__init__.py
lib/galaxy/model/migrate/__init__.py
lib/galaxy/model/migrate/versions/0001_initial_tables.py
lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
lib/galaxy/model/migrate/versions/0007_sharing_histories.py
lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
lib/galaxy/model/migrate/versions/0009_request_table.py
lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
lib/galaxy/model/migrate/versions/0012_user_address.py
lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
lib/galaxy/model/migrate/versions/0014_pages.py
lib/galaxy/model/migrate/versions/0015_tagging.py
lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
lib/galaxy/model/migrate/versions/0019_request_library_folder.py
lib/galaxy/model/migrate/versions/0020_library_upload_job.py
lib/galaxy/model/migrate/versions/0021_user_prefs.py
lib/galaxy/model/migrate/versions/0022_visualization_tables.py
lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
lib/galaxy/model/migrate/versions/0025_user_info.py
lib/galaxy/model/migrate/versions/0026_cloud_tables.py
lib/galaxy/model/migrate/versions/0027_request_events.py
lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
lib/galaxy/model/migrate/versions/0029_user_actions.py
lib/galaxy/model/migrate/versions/0030_history_slug_column.py
lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
lib/galaxy/model/migrate/versions/0037_samples_library.py
lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
lib/galaxy/model/migrate/versions/0040_page_annotations.py
lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
lib/galaxy/model/migrate/versions/0046_post_job_actions.py
lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
lib/galaxy/model/migrate/versions/0049_api_keys_table.py
lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
lib/galaxy/model/migrate/versions/0053_item_ratings.py
lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
lib/galaxy/model/migrate/versions/0057_request_notify.py
lib/galaxy/model/migrate/versions/0058_history_import_export.py
lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
lib/galaxy/model/migrate/versions/0060_history_archive_import.py
lib/galaxy/model/migrate/versions/0061_tasks.py
lib/galaxy/model/migrate/versions/0062_user_openid_table.py
lib/galaxy/model/migrate/versions/0063_sequencer_table.py
lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
lib/galaxy/model/migrate/versions/0080_quota_tables.py
lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
lib/galaxy/model/migrate/versions/0085_add_task_info.py
lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
lib/galaxy/model/migrate/versions/0095_hda_subsets.py
lib/galaxy/model/migrate/versions/0096_openid_provider.py
lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
lib/galaxy/model/migrate/versions/0117_add_user_activation.py
lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
lib/galaxy/model/migrate/versions/0119_job_metrics.py
lib/galaxy/model/migrate/versions/0120_dataset_collections.py
lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
lib/galaxy/model/migrate/versions/0124_job_state_history.py
lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
lib/galaxy/model/migrate/versions/0126_password_reset.py
lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
lib/galaxy/model/migrate/versions/0128_session_timeout.py
lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
lib/galaxy/model/orm/
lib/galaxy/model/tool_shed_install/migrate/__init__.py
lib/galaxy/model/tool_shed_install/migrate/versions/
lib/galaxy/model/util.py
lib/galaxy/objectstore/pulsar.py
lib/galaxy/objectstore/s3_multipart_upload.py
lib/galaxy/openid/__init__.py
lib/galaxy/quota/
lib/galaxy/sample_tracking/data_transfer.py
lib/galaxy/sample_tracking/__init__.py
lib/galaxy/sample_tracking/sample.py
lib/galaxy/security/validate_user_input.py
lib/galaxy/tags/
lib/galaxy/tools/actions/metadata.py
lib/galaxy/tools/cwl/cwltool_deps.py
lib/galaxy/tools/cwl/parser.py
lib/galaxy/tools/cwl/runtime_actions.py
lib/galaxy/tools/data_manager/__init__.py
lib/galaxy/tools/deps/brew_util.py
lib/galaxy/tools/deps/commands.py
lib/galaxy/tools/deps/dependencies.py
lib/galaxy/tools/deps/docker_util.py
lib/galaxy/tools/deps/requirements.py
lib/galaxy/tools/deps/resolvers/homebrew.py
lib/galaxy/tools/filters/
lib/galaxy/tools/imp_exp/export_history.py
lib/galaxy/tools/imp_exp/__init__.py
lib/galaxy/tools/linters/
lib/galaxy/tools/lint.py
lib/galaxy/tools/lint_util.py
lib/galaxy/tools/loader_directory.py
lib/galaxy/tools/parameters/history_query.py
lib/galaxy/tools/parameters/input_translation.py
lib/galaxy/tools/parameters/sanitize.py
lib/galaxy/tools/parameters/validation.py
lib/galaxy/tools/parameters/wrapped_json.py
lib/galaxy/tools/parser/interface.py
lib/galaxy/tools/parser/output_collection_def.py
lib/galaxy/tools/parser/output_objects.py
lib/galaxy/tools/parser/util.py
lib/galaxy/tools/special_tools.py
lib/galaxy/tools/test.py
lib/galaxy/tools/toolbox/cache.py
lib/galaxy/tools/toolbox/integrated_panel.py
lib/galaxy/tools/toolbox/lineages/__init__.py
lib/galaxy/tools/toolbox/lineages/interface.py
lib/galaxy/tools/toolbox/lineages/stock.py
lib/galaxy/tools/toolbox/lineages/tool_shed.py
lib/galaxy/tools/toolbox/watcher.py
lib/galaxy/tools/util/galaxyops/
lib/galaxy/tools/util/__init__.py
lib/galaxy/tools/verify/asserts/__init__.py
lib/galaxy/tools/verify/asserts/tabular.py
lib/galaxy/tools/verify/asserts/text.py
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