galaxy package¶
Galaxy root package – this is a namespace package.
Subpackages¶
- galaxy.actions package
- galaxy.auth package
- galaxy.authnz package
- galaxy.config package
- galaxy.containers package
- galaxy.datatypes package
- Subpackages
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.converters.bed_to_gff_converter module
- galaxy.datatypes.converters.bgzip module
- galaxy.datatypes.converters.cram_to_bam module
- galaxy.datatypes.converters.fasta_to_len module
- galaxy.datatypes.converters.fasta_to_tabular_converter module
- galaxy.datatypes.converters.fastq_to_fqtoc module
- galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module
- galaxy.datatypes.converters.fastqsolexa_to_qual_converter module
- galaxy.datatypes.converters.gff_to_bed_converter module
- galaxy.datatypes.converters.gff_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_bed_converter module
- galaxy.datatypes.converters.interval_to_bedstrict_converter module
- galaxy.datatypes.converters.interval_to_fli module
- galaxy.datatypes.converters.interval_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_tabix_converter module
- galaxy.datatypes.converters.lped_to_fped_converter module
- galaxy.datatypes.converters.lped_to_pbed_converter module
- galaxy.datatypes.converters.maf_to_fasta_converter module
- galaxy.datatypes.converters.maf_to_interval_converter module
- galaxy.datatypes.converters.pbed_ldreduced_converter module
- galaxy.datatypes.converters.pbed_to_lped_converter module
- galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module
- galaxy.datatypes.converters.pileup_to_interval_index_converter module
- galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module
- galaxy.datatypes.converters.tabular_csv module
- galaxy.datatypes.converters.tabular_to_dbnsfp module
- galaxy.datatypes.converters.vcf_to_interval_index_converter module
- galaxy.datatypes.converters.vcf_to_vcf_bgzip module
- galaxy.datatypes.converters.wiggle_to_simple_converter module
- galaxy.datatypes.dataproviders package
- Submodules
- galaxy.datatypes.dataproviders.base module
- galaxy.datatypes.dataproviders.chunk module
- galaxy.datatypes.dataproviders.column module
- galaxy.datatypes.dataproviders.dataset module
- galaxy.datatypes.dataproviders.decorators module
- galaxy.datatypes.dataproviders.exceptions module
- galaxy.datatypes.dataproviders.external module
- galaxy.datatypes.dataproviders.hierarchy module
- galaxy.datatypes.dataproviders.line module
- galaxy.datatypes.display_applications package
- galaxy.datatypes.util package
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.annotation module
- galaxy.datatypes.anvio module
- galaxy.datatypes.assembly module
- galaxy.datatypes.binary module
- galaxy.datatypes.blast module
- galaxy.datatypes.checkers module
- galaxy.datatypes.chrominfo module
- galaxy.datatypes.constructive_solid_geometry module
- galaxy.datatypes.coverage module
- galaxy.datatypes.data module
- galaxy.datatypes.genetics module
- galaxy.datatypes.gis module
- galaxy.datatypes.graph module
- galaxy.datatypes.images module
- galaxy.datatypes.interval module
- galaxy.datatypes.isa module
- galaxy.datatypes.metadata module
- galaxy.datatypes.microarrays module
- galaxy.datatypes.molecules module
- galaxy.datatypes.mothur module
- galaxy.datatypes.msa module
- galaxy.datatypes.neo4j module
- galaxy.datatypes.ngsindex module
- galaxy.datatypes.phylip module
- galaxy.datatypes.plant_tribes module
- galaxy.datatypes.proteomics module
- galaxy.datatypes.qualityscore module
- galaxy.datatypes.registry module
- galaxy.datatypes.sequence module
- galaxy.datatypes.sniff module
- galaxy.datatypes.spaln module
- galaxy.datatypes.tabular module
- galaxy.datatypes.text module
- galaxy.datatypes.tracks module
- galaxy.datatypes.triples module
- galaxy.datatypes.upload_util module
- galaxy.datatypes.xml module
- Subpackages
- galaxy.dependencies package
- galaxy.eggs package
- galaxy.exceptions package
- galaxy.forms package
- galaxy.job_execution package
- galaxy.job_metrics package
- Subpackages
- galaxy.job_metrics.collectl package
- galaxy.job_metrics.instrumenters package
- Submodules
- galaxy.job_metrics.instrumenters.cgroup module
- galaxy.job_metrics.instrumenters.collectl module
- galaxy.job_metrics.instrumenters.core module
- galaxy.job_metrics.instrumenters.cpuinfo module
- galaxy.job_metrics.instrumenters.env module
- galaxy.job_metrics.instrumenters.hostname module
- galaxy.job_metrics.instrumenters.meminfo module
- galaxy.job_metrics.instrumenters.uname module
- Submodules
- galaxy.job_metrics.formatting module
- Subpackages
- galaxy.jobs package
- Subpackages
- galaxy.jobs.actions package
- galaxy.jobs.rules package
- galaxy.jobs.runners package
- Subpackages
- galaxy.jobs.runners.state_handlers package
- galaxy.jobs.runners.util package
- Subpackages
- Submodules
- galaxy.jobs.runners.util.env module
- galaxy.jobs.runners.util.external module
- galaxy.jobs.runners.util.kill module
- galaxy.jobs.runners.util.process_groups module
- galaxy.jobs.runners.util.pykube_util module
- galaxy.jobs.runners.util.sudo module
- Submodules
- galaxy.jobs.runners.chronos module
- galaxy.jobs.runners.cli module
- galaxy.jobs.runners.condor module
- galaxy.jobs.runners.drmaa module
- galaxy.jobs.runners.godocker module
- galaxy.jobs.runners.kubernetes module
- galaxy.jobs.runners.local module
- galaxy.jobs.runners.pbs module
- galaxy.jobs.runners.pulsar module
- galaxy.jobs.runners.slurm module
- galaxy.jobs.runners.state_handler_factory module
- galaxy.jobs.runners.tasks module
- galaxy.jobs.runners.univa module
- Subpackages
- galaxy.jobs.splitters package
- Submodules
- galaxy.jobs.command_factory module
- galaxy.jobs.dynamic_tool_destination module
- galaxy.jobs.handler module
- galaxy.jobs.manager module
- galaxy.jobs.mapper module
- galaxy.jobs.rule_helper module
- galaxy.jobs.stock_rules module
- galaxy.jobs.transfer_manager module
- Subpackages
- galaxy.managers package
- Submodules
- galaxy.managers.annotatable module
- galaxy.managers.api_keys module
- galaxy.managers.base module
- galaxy.managers.citations module
- galaxy.managers.cloud module
- galaxy.managers.cloudauthzs module
- galaxy.managers.collections module
- galaxy.managers.collections_util module
- galaxy.managers.configuration module
- galaxy.managers.containers module
- galaxy.managers.context module
- galaxy.managers.datasets module
- galaxy.managers.deletable module
- galaxy.managers.executables module
- galaxy.managers.folders module
- galaxy.managers.hdas module
- galaxy.managers.hdcas module
- galaxy.managers.histories module
- galaxy.managers.history_contents module
- galaxy.managers.interactivetool module
- galaxy.managers.jobs module
- galaxy.managers.lddas module
- galaxy.managers.libraries module
- galaxy.managers.library_datasets module
- galaxy.managers.markdown_parse module
- galaxy.managers.markdown_util module
- galaxy.managers.pages module
- galaxy.managers.ratable module
- galaxy.managers.rbac_secured module
- galaxy.managers.roles module
- galaxy.managers.secured module
- galaxy.managers.sharable module
- galaxy.managers.taggable module
- galaxy.managers.tools module
- galaxy.managers.users module
- galaxy.managers.visualizations module
- galaxy.managers.workflows module
- galaxy.metadata package
- galaxy.model package
- Subpackages
- galaxy.model.dataset_collections package
- Subpackages
- Submodules
- galaxy.model.dataset_collections.builder module
- galaxy.model.dataset_collections.matching module
- galaxy.model.dataset_collections.registry module
- galaxy.model.dataset_collections.structure module
- galaxy.model.dataset_collections.subcollections module
- galaxy.model.dataset_collections.type_description module
- galaxy.model.migrate package
- Subpackages
- galaxy.model.migrate.versions package
- Submodules
- galaxy.model.migrate.versions.0001_initial_tables module
- galaxy.model.migrate.versions.0002_metadata_file_table module
- galaxy.model.migrate.versions.0003_security_and_libraries module
- galaxy.model.migrate.versions.0004_indexes_and_defaults module
- galaxy.model.migrate.versions.0005_cleanup_datasets_fix module
- galaxy.model.migrate.versions.0006_change_qual_datatype module
- galaxy.model.migrate.versions.0007_sharing_histories module
- galaxy.model.migrate.versions.0008_galaxy_forms module
- galaxy.model.migrate.versions.0009_request_table module
- galaxy.model.migrate.versions.0010_hda_display_at_authz_table module
- galaxy.model.migrate.versions.0011_v0010_mysql_index_fix module
- galaxy.model.migrate.versions.0012_user_address module
- galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms module
- galaxy.model.migrate.versions.0014_pages module
- galaxy.model.migrate.versions.0015_tagging module
- galaxy.model.migrate.versions.0016_v0015_mysql_index_fix module
- galaxy.model.migrate.versions.0017_library_item_indexes module
- galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags module
- galaxy.model.migrate.versions.0019_request_library_folder module
- galaxy.model.migrate.versions.0020_library_upload_job module
- galaxy.model.migrate.versions.0021_user_prefs module
- galaxy.model.migrate.versions.0022_visualization_tables module
- galaxy.model.migrate.versions.0023_page_published_and_deleted_columns module
- galaxy.model.migrate.versions.0024_page_slug_unique_constraint module
- galaxy.model.migrate.versions.0025_user_info module
- galaxy.model.migrate.versions.0026_cloud_tables module
- galaxy.model.migrate.versions.0027_request_events module
- galaxy.model.migrate.versions.0028_external_metadata_file_override module
- galaxy.model.migrate.versions.0029_user_actions module
- galaxy.model.migrate.versions.0030_history_slug_column module
- galaxy.model.migrate.versions.0031_community_and_workflow_tags module
- galaxy.model.migrate.versions.0032_stored_workflow_slug_column module
- galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows module
- galaxy.model.migrate.versions.0034_page_user_share_association module
- galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags module
- galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables module
- galaxy.model.migrate.versions.0037_samples_library module
- galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables module
- galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table module
- galaxy.model.migrate.versions.0040_page_annotations module
- galaxy.model.migrate.versions.0041_workflow_invocation module
- galaxy.model.migrate.versions.0042_workflow_invocation_fix module
- galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating module
- galaxy.model.migrate.versions.0044_add_notify_column_to_request_table module
- galaxy.model.migrate.versions.0045_request_type_permissions_table module
- galaxy.model.migrate.versions.0046_post_job_actions module
- galaxy.model.migrate.versions.0047_job_table_user_id_column module
- galaxy.model.migrate.versions.0048_dataset_instance_state_column module
- galaxy.model.migrate.versions.0049_api_keys_table module
- galaxy.model.migrate.versions.0050_drop_cloud_tables module
- galaxy.model.migrate.versions.0051_imported_col_for_jobs_table module
- galaxy.model.migrate.versions.0052_sample_dataset_table module
- galaxy.model.migrate.versions.0053_item_ratings module
- galaxy.model.migrate.versions.0054_visualization_dbkey module
- galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs module
- galaxy.model.migrate.versions.0056_workflow_outputs module
- galaxy.model.migrate.versions.0057_request_notify module
- galaxy.model.migrate.versions.0058_history_import_export module
- galaxy.model.migrate.versions.0059_sample_dataset_file_path module
- galaxy.model.migrate.versions.0060_history_archive_import module
- galaxy.model.migrate.versions.0061_tasks module
- galaxy.model.migrate.versions.0062_user_openid_table module
- galaxy.model.migrate.versions.0063_sequencer_table module
- galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables module
- galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values module
- galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables module
- galaxy.model.migrate.versions.0067_populate_sequencer_table module
- galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services module
- galaxy.model.migrate.versions.0069_rename_sequencer_form_type module
- galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table module
- galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample module
- galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table module
- galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table module
- galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table module
- galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table module
- galaxy.model.migrate.versions.0076_fix_form_values_data_corruption module
- galaxy.model.migrate.versions.0077_create_tool_tag_association_table module
- galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting module
- galaxy.model.migrate.versions.0079_input_library_to_job_table module
- galaxy.model.migrate.versions.0080_quota_tables module
- galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda module
- galaxy.model.migrate.versions.0082_add_tool_shed_repository_table module
- galaxy.model.migrate.versions.0083_add_prepare_files_to_task module
- galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table module
- galaxy.model.migrate.versions.0085_add_task_info module
- galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns module
- galaxy.model.migrate.versions.0087_tool_id_guid_map_table module
- galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column module
- galaxy.model.migrate.versions.0089_add_object_store_id_columns module
- galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns module
- galaxy.model.migrate.versions.0091_add_tool_version_tables module
- galaxy.model.migrate.versions.0092_add_migrate_tools_table module
- galaxy.model.migrate.versions.0093_add_job_params_col module
- galaxy.model.migrate.versions.0094_add_job_handler_col module
- galaxy.model.migrate.versions.0095_hda_subsets module
- galaxy.model.migrate.versions.0096_openid_provider module
- galaxy.model.migrate.versions.0097_add_ctx_rev_column module
- galaxy.model.migrate.versions.0098_genome_index_tool_data_table module
- galaxy.model.migrate.versions.0099_add_tool_dependency_table module
- galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column module
- galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column module
- galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns module
- galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns module
- galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters module
- galaxy.model.migrate.versions.0105_add_cleanup_event_table module
- galaxy.model.migrate.versions.0106_add_missing_indexes module
- galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task module
- galaxy.model.migrate.versions.0108_add_extended_metadata module
- galaxy.model.migrate.versions.0109_add_repository_dependency_tables module
- galaxy.model.migrate.versions.0110_add_dataset_uuid module
- galaxy.model.migrate.versions.0111_add_job_destinations module
- galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables module
- galaxy.model.migrate.versions.0113_update_migrate_tools_table module
- galaxy.model.migrate.versions.0114_update_migrate_tools_table_again module
- galaxy.model.migrate.versions.0115_longer_user_password_field module
- galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col module
- galaxy.model.migrate.versions.0117_add_user_activation module
- galaxy.model.migrate.versions.0118_add_hda_extended_metadata module
- galaxy.model.migrate.versions.0119_job_metrics module
- galaxy.model.migrate.versions.0120_dataset_collections module
- galaxy.model.migrate.versions.0121_workflow_uuids module
- galaxy.model.migrate.versions.0122_grow_mysql_blobs module
- galaxy.model.migrate.versions.0123_add_workflow_request_tables module
- galaxy.model.migrate.versions.0124_job_state_history module
- galaxy.model.migrate.versions.0125_workflow_step_tracking module
- galaxy.model.migrate.versions.0126_password_reset module
- galaxy.model.migrate.versions.0127_output_collection_adjustments module
- galaxy.model.migrate.versions.0128_session_timeout module
- galaxy.model.migrate.versions.0129_job_external_output_metadata_validity module
- galaxy.model.migrate.versions.0130_change_pref_datatype module
- galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules module
- galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user module
- galaxy.model.migrate.versions.0133_add_dependency_column_to_job module
- galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged module
- galaxy.model.migrate.versions.0135_add_library_tags module
- galaxy.model.migrate.versions.0136_collection_and_workflow_state module
- galaxy.model.migrate.versions.0137_add_copied_from_job_id_column module
- galaxy.model.migrate.versions.0138_add_hda_version module
- galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table module
- galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table module
- galaxy.model.migrate.versions.0141_add_oidc_tables module
- galaxy.model.migrate.versions.0142_change_numeric_metric_precision module
- galaxy.model.migrate.versions.0143_add_cloudauthz_tables module
- galaxy.model.migrate.versions.0144_add_cleanup_event_user_table module
- galaxy.model.migrate.versions.0145_add_workflow_step_input module
- galaxy.model.migrate.versions.0146_workflow_paths module
- galaxy.model.migrate.versions.0147_job_messages module
- galaxy.model.migrate.versions.0148_add_checksum_table module
- galaxy.model.migrate.versions.0149_dynamic_tools module
- galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz module
- galaxy.model.migrate.versions.0151_add_worker_process module
- galaxy.model.migrate.versions.0152_add_metadata_file_uuid module
- galaxy.model.migrate.versions.0153_add_custos_authnz_token_table module
- galaxy.model.migrate.versions.0154_created_from_basename module
- galaxy.model.migrate.versions.0155_job_galaxy_version module
- galaxy.model.migrate.versions.0156_add_interactivetools module
- galaxy.model.migrate.versions.0157_rework_dataset_validation module
- galaxy.model.migrate.versions.0158_workflow_reports module
- galaxy.model.migrate.versions.0159_add_job_external_id_index module
- galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again module
- galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table module
- galaxy.model.migrate.versions.0162_job_only_pjas module
- galaxy.model.migrate.versions.0163_worker_process_pid module
- galaxy.model.migrate.versions.0164_page_format module
- galaxy.model.migrate.versions.0165_add_content_update_time module
- galaxy.model.migrate.versions.util module
- galaxy.model.migrate.versions package
- Submodules
- galaxy.model.migrate.check module
- Subpackages
- galaxy.model.orm package
- galaxy.model.store package
- galaxy.model.tool_shed_install package
- galaxy.model.dataset_collections package
- Submodules
- galaxy.model.base module
- galaxy.model.custom_types module
- galaxy.model.database_heartbeat module
- galaxy.model.item_attrs module
- galaxy.model.mapping module
- galaxy.model.metadata module
- galaxy.model.none_like module
- galaxy.model.search module
- galaxy.model.security module
- galaxy.model.tags module
- galaxy.model.triggers module
- Subpackages
- galaxy.objectstore package
- galaxy.openid package
- galaxy.quota package
- galaxy.security package
- galaxy.selenium package
- galaxy.tool_shed package
- Subpackages
- galaxy.tool_shed.galaxy_install package
- Subpackages
- galaxy.tool_shed.galaxy_install.datatypes package
- galaxy.tool_shed.galaxy_install.metadata package
- galaxy.tool_shed.galaxy_install.migrate package
- Subpackages
- galaxy.tool_shed.galaxy_install.migrate.versions package
- Submodules
- galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools module
- galaxy.tool_shed.galaxy_install.migrate.versions package
- Submodules
- galaxy.tool_shed.galaxy_install.migrate.check module
- galaxy.tool_shed.galaxy_install.migrate.common module
- Subpackages
- galaxy.tool_shed.galaxy_install.repository_dependencies package
- galaxy.tool_shed.galaxy_install.tool_dependencies package
- Subpackages
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe package
- Submodules
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader module
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder module
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment module
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager module
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler module
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler module
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe package
- Submodules
- galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager module
- Subpackages
- galaxy.tool_shed.galaxy_install.tools package
- Submodules
- galaxy.tool_shed.galaxy_install.install_manager module
- galaxy.tool_shed.galaxy_install.installed_repository_manager module
- galaxy.tool_shed.galaxy_install.tool_migration_manager module
- galaxy.tool_shed.galaxy_install.update_repository_manager module
- Subpackages
- galaxy.tool_shed.metadata package
- galaxy.tool_shed.tools package
- galaxy.tool_shed.util package
- Submodules
- galaxy.tool_shed.util.basic_util module
- galaxy.tool_shed.util.container_util module
- galaxy.tool_shed.util.hg_util module
- galaxy.tool_shed.util.metadata_util module
- galaxy.tool_shed.util.repository_util module
- galaxy.tool_shed.util.shed_util_common module
- galaxy.tool_shed.util.tool_dependency_util module
- galaxy.tool_shed.util.tool_util module
- galaxy.tool_shed.galaxy_install package
- Submodules
- galaxy.tool_shed.repository_type module
- galaxy.tool_shed.tool_shed_registry module
- Subpackages
- galaxy.tool_util package
- Subpackages
- galaxy.tool_util.cwl package
- galaxy.tool_util.deps package
- Subpackages
- galaxy.tool_util.deps.container_resolvers package
- galaxy.tool_util.deps.mulled package
- Submodules
- galaxy.tool_util.deps.mulled.get_tests module
- galaxy.tool_util.deps.mulled.mulled_build module
- galaxy.tool_util.deps.mulled.mulled_build_channel module
- galaxy.tool_util.deps.mulled.mulled_build_files module
- galaxy.tool_util.deps.mulled.mulled_build_tool module
- galaxy.tool_util.deps.mulled.mulled_list module
- galaxy.tool_util.deps.mulled.mulled_search module
- galaxy.tool_util.deps.mulled.mulled_update_singularity_containers module
- galaxy.tool_util.deps.mulled.util module
- galaxy.tool_util.deps.resolvers package
- Submodules
- galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages module
- galaxy.tool_util.deps.resolvers.conda module
- galaxy.tool_util.deps.resolvers.galaxy_packages module
- galaxy.tool_util.deps.resolvers.homebrew module
- galaxy.tool_util.deps.resolvers.lmod module
- galaxy.tool_util.deps.resolvers.modules module
- galaxy.tool_util.deps.resolvers.resolver_mixins module
- galaxy.tool_util.deps.resolvers.tool_shed_packages module
- galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages module
- Submodules
- galaxy.tool_util.deps.brew_exts module
- galaxy.tool_util.deps.brew_util module
- galaxy.tool_util.deps.conda_compat module
- galaxy.tool_util.deps.conda_util module
- galaxy.tool_util.deps.container_classes module
- galaxy.tool_util.deps.containers module
- galaxy.tool_util.deps.dependencies module
- galaxy.tool_util.deps.docker_util module
- galaxy.tool_util.deps.dockerfiles module
- galaxy.tool_util.deps.installable module
- galaxy.tool_util.deps.requirements module
- galaxy.tool_util.deps.singularity_util module
- galaxy.tool_util.deps.views module
- Subpackages
- galaxy.tool_util.linters package
- Submodules
- galaxy.tool_util.linters.citations module
- galaxy.tool_util.linters.command module
- galaxy.tool_util.linters.cwl module
- galaxy.tool_util.linters.general module
- galaxy.tool_util.linters.help module
- galaxy.tool_util.linters.inputs module
- galaxy.tool_util.linters.outputs module
- galaxy.tool_util.linters.stdio module
- galaxy.tool_util.linters.tests module
- galaxy.tool_util.linters.xml_order module
- galaxy.tool_util.locations package
- galaxy.tool_util.parser package
- Submodules
- galaxy.tool_util.parser.cwl module
- galaxy.tool_util.parser.factory module
- galaxy.tool_util.parser.interface module
- galaxy.tool_util.parser.output_actions module
- galaxy.tool_util.parser.output_collection_def module
- galaxy.tool_util.parser.output_objects module
- galaxy.tool_util.parser.stdio module
- galaxy.tool_util.parser.util module
- galaxy.tool_util.parser.xml module
- galaxy.tool_util.parser.yaml module
- galaxy.tool_util.verify package
- Submodules
- galaxy.tool_util.fetcher module
- galaxy.tool_util.lint module
- galaxy.tool_util.loader module
- galaxy.tool_util.loader_directory module
- galaxy.tool_util.output_checker module
- galaxy.tool_util.provided_metadata module
- Subpackages
- galaxy.tools package
- Subpackages
- galaxy.tools.actions package
- galaxy.tools.data package
- galaxy.tools.data_manager package
- galaxy.tools.error_reports package
- Subpackages
- galaxy.tools.error_reports.plugins package
- Submodules
- galaxy.tools.error_reports.plugins.base_git module
- galaxy.tools.error_reports.plugins.email module
- galaxy.tools.error_reports.plugins.github module
- galaxy.tools.error_reports.plugins.gitlab module
- galaxy.tools.error_reports.plugins.influxdb module
- galaxy.tools.error_reports.plugins.json module
- galaxy.tools.error_reports.plugins.sentry module
- galaxy.tools.error_reports.plugins package
- Subpackages
- galaxy.tools.expressions package
- galaxy.tools.filters package
- galaxy.tools.imp_exp package
- galaxy.tools.parameters package
- Submodules
- galaxy.tools.parameters.basic module
- galaxy.tools.parameters.dataset_matcher module
- galaxy.tools.parameters.dynamic_options module
- galaxy.tools.parameters.grouping module
- galaxy.tools.parameters.history_query module
- galaxy.tools.parameters.input_translation module
- galaxy.tools.parameters.meta module
- galaxy.tools.parameters.sanitize module
- galaxy.tools.parameters.validation module
- galaxy.tools.parameters.wrapped module
- galaxy.tools.parameters.wrapped_json module
- galaxy.tools.search package
- galaxy.tools.toolbox package
- galaxy.tools.util package
- Submodules
- galaxy.tools.cache module
- galaxy.tools.data_fetch module
- galaxy.tools.errors module
- galaxy.tools.evaluation module
- galaxy.tools.exception_handling module
- galaxy.tools.execute module
- galaxy.tools.recommendations module
- galaxy.tools.repositories module
- galaxy.tools.special_tools module
- galaxy.tools.test module
- galaxy.tools.wrappers module
- Subpackages
- galaxy.tours package
- galaxy.util package
- Subpackages
- Submodules
- galaxy.util.aliaspickler module
- galaxy.util.bunch module
- galaxy.util.bytesize module
- galaxy.util.checkers module
- galaxy.util.commands module
- galaxy.util.compression_utils module
- galaxy.util.dbkeys module
- galaxy.util.dictifiable module
- galaxy.util.expressions module
- galaxy.util.facts module
- galaxy.util.filelock module
- galaxy.util.form_builder module
- galaxy.util.getargspec module
- galaxy.util.hash_util module
- galaxy.util.heartbeat module
- galaxy.util.image_util module
- galaxy.util.inflection module
- galaxy.util.json module
- galaxy.util.jstree module
- galaxy.util.lazy_process module
- galaxy.util.monitors module
- galaxy.util.object_wrapper module
- galaxy.util.odict module
- galaxy.util.oset module
- galaxy.util.permutations module
- galaxy.util.plugin_config module
- galaxy.util.properties module
- galaxy.util.renamed_temporary_file module
- galaxy.util.rules_dsl module
- galaxy.util.sanitize_html module
- galaxy.util.script module
- galaxy.util.simplegraph module
- galaxy.util.sleeper module
- galaxy.util.sockets module
- galaxy.util.specs module
- galaxy.util.sqlite module
- galaxy.util.streamball module
- galaxy.util.submodules module
- galaxy.util.template module
- galaxy.util.tool_version module
- galaxy.util.topsort module
- galaxy.util.ucsc module
- galaxy.util.validation module
- galaxy.util.watcher module
- galaxy.util.web_compat module
- galaxy.util.xml_macros module
- galaxy.util.yaml_util module
- galaxy.visualization package
- Subpackages
- galaxy.visualization.data_providers package
- galaxy.visualization.genome package
- galaxy.visualization.plugins package
- Submodules
- galaxy.visualization.plugins.config_parser module
- galaxy.visualization.plugins.interactive_environments module
- galaxy.visualization.plugins.plugin module
- galaxy.visualization.plugins.registry module
- galaxy.visualization.plugins.resource_parser module
- galaxy.visualization.plugins.utils module
- galaxy.visualization.tracks package
- Submodules
- galaxy.visualization.genomes module
- Subpackages
- galaxy.web package
- Subpackages
- galaxy.web.framework package
- Subpackages
- galaxy.web.framework.helpers package
- galaxy.web.framework.middleware package
- Submodules
- galaxy.web.framework.middleware.batch module
- galaxy.web.framework.middleware.error module
- galaxy.web.framework.middleware.profile module
- galaxy.web.framework.middleware.remoteuser module
- galaxy.web.framework.middleware.request_id module
- galaxy.web.framework.middleware.sentry module
- galaxy.web.framework.middleware.sqldebug module
- galaxy.web.framework.middleware.static module
- galaxy.web.framework.middleware.statsd module
- galaxy.web.framework.middleware.translogger module
- galaxy.web.framework.middleware.xforwardedhost module
- Submodules
- galaxy.web.framework.base module
- galaxy.web.framework.decorators module
- galaxy.web.framework.webapp module
- Subpackages
- galaxy.web.proxy package
- galaxy.web.framework package
- Submodules
- galaxy.web.buildapp module
- galaxy.web.form_builder module
- galaxy.web.formatting module
- galaxy.web.params module
- galaxy.web.statsd_client module
- Subpackages
- galaxy.web_stack package
- galaxy.webapps package
- Subpackages
- galaxy.webapps.base package
- galaxy.webapps.galaxy package
- Subpackages
- galaxy.webapps.galaxy.api package
- Submodules
- galaxy.webapps.galaxy.api.annotations module
- galaxy.webapps.galaxy.api.authenticate module
- galaxy.webapps.galaxy.api.cloud module
- galaxy.webapps.galaxy.api.cloudauthz module
- galaxy.webapps.galaxy.api.configuration module
- galaxy.webapps.galaxy.api.container_resolution module
- galaxy.webapps.galaxy.api.dataset_collections module
- galaxy.webapps.galaxy.api.datasets module
- galaxy.webapps.galaxy.api.datatypes module
- galaxy.webapps.galaxy.api.display_applications module
- galaxy.webapps.galaxy.api.dynamic_tools module
- galaxy.webapps.galaxy.api.extended_metadata module
- galaxy.webapps.galaxy.api.folder_contents module
- galaxy.webapps.galaxy.api.folders module
- galaxy.webapps.galaxy.api.forms module
- galaxy.webapps.galaxy.api.genomes module
- galaxy.webapps.galaxy.api.group_roles module
- galaxy.webapps.galaxy.api.group_users module
- galaxy.webapps.galaxy.api.groups module
- galaxy.webapps.galaxy.api.histories module
- galaxy.webapps.galaxy.api.history_contents module
- galaxy.webapps.galaxy.api.item_tags module
- galaxy.webapps.galaxy.api.job_files module
- galaxy.webapps.galaxy.api.job_ports module
- galaxy.webapps.galaxy.api.jobs module
- galaxy.webapps.galaxy.api.libraries module
- galaxy.webapps.galaxy.api.library_contents module
- galaxy.webapps.galaxy.api.library_datasets module
- galaxy.webapps.galaxy.api.metrics module
- galaxy.webapps.galaxy.api.page_revisions module
- galaxy.webapps.galaxy.api.pages module
- galaxy.webapps.galaxy.api.plugins module
- galaxy.webapps.galaxy.api.provenance module
- galaxy.webapps.galaxy.api.quotas module
- galaxy.webapps.galaxy.api.remote_files module
- galaxy.webapps.galaxy.api.roles module
- galaxy.webapps.galaxy.api.search module
- galaxy.webapps.galaxy.api.tags module
- galaxy.webapps.galaxy.api.tool_data module
- galaxy.webapps.galaxy.api.tool_dependencies module
- galaxy.webapps.galaxy.api.tool_entry_points module
- galaxy.webapps.galaxy.api.tool_shed_repositories module
- galaxy.webapps.galaxy.api.tools module
- galaxy.webapps.galaxy.api.toolshed module
- galaxy.webapps.galaxy.api.tours module
- galaxy.webapps.galaxy.api.uploads module
- galaxy.webapps.galaxy.api.users module
- galaxy.webapps.galaxy.api.visualizations module
- galaxy.webapps.galaxy.api.webhooks module
- galaxy.webapps.galaxy.api.workflows module
- galaxy.webapps.galaxy.controllers package
- Submodules
- galaxy.webapps.galaxy.controllers.admin module
- galaxy.webapps.galaxy.controllers.admin_toolshed module
- galaxy.webapps.galaxy.controllers.async module
- galaxy.webapps.galaxy.controllers.authnz module
- galaxy.webapps.galaxy.controllers.data_manager module
- galaxy.webapps.galaxy.controllers.dataset module
- galaxy.webapps.galaxy.controllers.error module
- galaxy.webapps.galaxy.controllers.forms module
- galaxy.webapps.galaxy.controllers.history module
- galaxy.webapps.galaxy.controllers.interactive_environments module
- galaxy.webapps.galaxy.controllers.interactivetool module
- galaxy.webapps.galaxy.controllers.library module
- galaxy.webapps.galaxy.controllers.openid module
- galaxy.webapps.galaxy.controllers.page module
- galaxy.webapps.galaxy.controllers.root module
- galaxy.webapps.galaxy.controllers.shed_tool_static module
- galaxy.webapps.galaxy.controllers.tag module
- galaxy.webapps.galaxy.controllers.tool_runner module
- galaxy.webapps.galaxy.controllers.user module
- galaxy.webapps.galaxy.controllers.userskeys module
- galaxy.webapps.galaxy.controllers.visualization module
- galaxy.webapps.galaxy.controllers.workflow module
- galaxy.webapps.galaxy.api package
- Submodules
- galaxy.webapps.galaxy.buildapp module
- Subpackages
- galaxy.webapps.reports package
- Subpackages
- galaxy.webapps.reports.controllers package
- Submodules
- galaxy.webapps.reports.controllers.history module
- galaxy.webapps.reports.controllers.home module
- galaxy.webapps.reports.controllers.jobs module
- galaxy.webapps.reports.controllers.query module
- galaxy.webapps.reports.controllers.root module
- galaxy.webapps.reports.controllers.system module
- galaxy.webapps.reports.controllers.tools module
- galaxy.webapps.reports.controllers.users module
- galaxy.webapps.reports.controllers.workflows module
- galaxy.webapps.reports.framework package
- galaxy.webapps.reports.controllers package
- Submodules
- galaxy.webapps.reports.app module
- galaxy.webapps.reports.buildapp module
- galaxy.webapps.reports.config module
- Subpackages
- Submodules
- galaxy.webapps.util module
- Subpackages
- galaxy.webhooks package
- galaxy.work package
- galaxy.workflow package
Submodules¶
galaxy.app module¶
-
class
galaxy.app.
UniverseApplication
(**kwargs)[source]¶ Bases:
galaxy.config.ConfiguresGalaxyMixin
Encapsulates the state of a Universe application
-
is_job_handler
¶
-
galaxy.config_watchers module¶
galaxy.main module¶
Entry point for starting Galaxy without starting as part of a web server.
Example Usage: Start a job/workflow handler without a web server and with a given name using.
galaxy-main –server-name handler0
Start as a daemon with (requires daemonized - install with ‘pip install daemonize’):
galaxy-main -d –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –server-name handler0
In daemon mode logging of Galaxy (as opposed to this script) is configured via a loggers section in Galaxy’s ini file - this can be overridden with sensible defaults logging to a single file with the following:
galaxy-main -d –server-name handler0 –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –log-file handler0.log
This can also be used to start Galaxy as a uWSGI mule, e.g. for job handling:
uwsgi … –py-call-osafterfork –mule=lib/galaxy/main.py –mule=lib/galaxy/main.py –farm=job-handlers:1,2
The –py-call-osafterfork allows for proper shutdown on SIGTERM/SIGINT.
-
galaxy.main.
load_galaxy_app
(config_builder, config_env=False, log=None, attach_to_pools=None, **kwds)[source]¶
galaxy.queue_worker module¶
Galaxy control queue and worker. This is used to handle ‘app’ control like reloading the toolbox, etc., across multiple processes.
-
galaxy.queue_worker.
send_local_control_task
(app, task, get_response=False, kwargs=None)[source]¶ This sends a message to the process-local control worker, which is useful for one-time asynchronous tasks like recalculating user disk usage.
-
galaxy.queue_worker.
send_control_task
(app, task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None)[source]¶ This sends a control task out to all processes, useful for things like reloading a data table, which needs to happen individually in all processes. Set noop_self to True to not run task for current process. Set get_response to True to wait for and return the task results as a list.
-
class
galaxy.queue_worker.
ControlTask
(queue_worker)[source]¶ Bases:
object
-
connection
¶
-
control_queues
¶
-
exchange
¶
-
declare_queues
¶
-
-
galaxy.queue_worker.
create_panel_section
(app, **kwargs)[source]¶ Updates in memory toolbox dictionary.
-
class
galaxy.queue_worker.
GalaxyQueueWorker
(app, task_mapping=None)[source]¶ Bases:
kombu.mixins.ConsumerProducerMixin
,threading.Thread
This is a flexible worker for galaxy’s queues. Each process, web or handler, will have one of these used for dispatching so called ‘control’ tasks.
-
send_control_task
(task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None)[source]¶
-
declare_queues
¶
-
galaxy.queues module¶
All message queues used by Galaxy
-
galaxy.queues.
all_control_queues_for_declare
(application_stack)[source]¶ For in-memory routing (used by sqlalchemy-based transports), we need to be able to build the entire routing table in producers.