galaxy packageļ
Galaxy root package ā this is a namespace package.
Subpackagesļ
- galaxy.actions package
- galaxy.app_unittest_utils package
- Submodules
- galaxy.app_unittest_utils.galaxy_mock module
buildMockEnviron()MockAppMockApp.configMockApp.amqp_typeMockApp.job_searchMockApp.tool_cacheMockApp.watchersMockApp.dataset_collection_managerMockApp.hda_managerMockApp.workflow_managerMockApp.history_managerMockApp.job_metricsMockApp.stopMockApp.is_webappMockApp.__init__()MockApp.install_modelMockApp.toolboxMockApp.wait_for_toolbox_reload()MockApp.reindex_tool_search()MockApp.setup_test_vault()
MockLockMockAppConfigMockWebappmock_url_builder()MockTransMockTrans.__init__()MockTrans.tag_handlerMockTrans.check_csrf_token()MockTrans.handle_user_login()MockTrans.log_event()MockTrans.get_user()MockTrans.set_user()MockTrans.userMockTrans.get_history()MockTrans.set_history()MockTrans.fill_template()MockTrans.usernameMockTrans.emailMockTrans.init_user_in_database()MockTrans.user_vault
MockVisualizationsRegistryMockDirMockTemplateHelpers
- galaxy.app_unittest_utils.tools_support module
- galaxy.auth package
- galaxy.authnz package
IdentityProvider- Submodules
- galaxy.authnz.custos_authnz module
InvalidAuthnzConfigExceptionCustosAuthnzConfigurationCustosAuthnzConfiguration.providerCustosAuthnzConfiguration.verify_sslCustosAuthnzConfiguration.urlCustosAuthnzConfiguration.labelCustosAuthnzConfiguration.client_idCustosAuthnzConfiguration.client_secretCustosAuthnzConfiguration.require_create_confirmationCustosAuthnzConfiguration.redirect_uriCustosAuthnzConfiguration.ca_bundleCustosAuthnzConfiguration.pkce_supportCustosAuthnzConfiguration.accepted_audiencesCustosAuthnzConfiguration.extra_paramsCustosAuthnzConfiguration.extra_scopesCustosAuthnzConfiguration.authorization_endpointCustosAuthnzConfiguration.token_endpointCustosAuthnzConfiguration.end_session_endpointCustosAuthnzConfiguration.well_known_oidc_config_uriCustosAuthnzConfiguration.iam_client_secretCustosAuthnzConfiguration.userinfo_endpointCustosAuthnzConfiguration.credential_urlCustosAuthnzConfiguration.issuerCustosAuthnzConfiguration.jwks_uriCustosAuthnzConfiguration.__init__()
OIDCAuthnzBaseOIDCAuthnzBaseKeycloakOIDCAuthnzBaseCiLogonCustosAuthFactoryOIDCAuthnzBaseCustos
- galaxy.authnz.managers module
AuthnzManagerAuthnzManager.__init__()AuthnzManager.get_allowed_idps()AuthnzManager.can_user_assume_authn()AuthnzManager.try_get_authz_config()AuthnzManager.refresh_expiring_oidc_tokens_for_provider()AuthnzManager.refresh_expiring_oidc_tokens()AuthnzManager.authenticate()AuthnzManager.callback()AuthnzManager.create_user()AuthnzManager.match_access_token_to_user()AuthnzManager.logout()AuthnzManager.disconnect()AuthnzManager.get_cloud_access_credentials()AuthnzManager.get_cloud_access_credentials_in_file()
- galaxy.authnz.psa_authnz module
PSAAuthnzStrategyStrategy.__init__()Strategy.get_setting()Strategy.session_get()Strategy.session_set()Strategy.session_pop()Strategy.request_data()Strategy.request_host()Strategy.build_absolute_uri()Strategy.redirect()Strategy.html()Strategy.render_html()Strategy.start()Strategy.complete()Strategy.continue_pipeline()
Storageon_the_fly_config()contains_required_data()verify()allowed_to_disconnect()disconnect()
- galaxy.celery package
- galaxy.config package
LOGGING_CONFIG_DEFAULTDEPENDENT_CONFIG_DEFAULTSconfigure_logging()find_root()expand_pretty_datetime_format()BaseAppConfigurationBaseAppConfiguration.renamed_optionsBaseAppConfiguration.deprecated_dirsBaseAppConfiguration.paths_to_check_against_rootBaseAppConfiguration.add_sample_file_to_defaultsBaseAppConfiguration.listify_optionsBaseAppConfiguration.object_store_store_byBaseAppConfiguration.shed_tools_dirBaseAppConfiguration.__init__()BaseAppConfiguration.is_set()BaseAppConfiguration.resolve_path()
CommonConfigurationMixinGalaxyAppConfigurationGalaxyAppConfiguration.renamed_optionsGalaxyAppConfiguration.deprecated_optionsGalaxyAppConfiguration.default_config_file_nameGalaxyAppConfiguration.deprecated_dirsGalaxyAppConfiguration.paths_to_check_against_rootGalaxyAppConfiguration.add_sample_file_to_defaultsGalaxyAppConfiguration.listify_optionsGalaxyAppConfiguration.allowed_origin_hostnamesGalaxyAppConfiguration.builds_file_pathGalaxyAppConfiguration.container_resolvers_config_fileGalaxyAppConfiguration.database_connectionGalaxyAppConfiguration.drmaa_external_runjob_scriptGalaxyAppConfiguration.email_fromGalaxyAppConfiguration.enable_tool_shed_checkGalaxyAppConfiguration.galaxy_data_manager_data_pathGalaxyAppConfiguration.galaxy_infrastructure_urlGalaxyAppConfiguration.hours_between_checkGalaxyAppConfiguration.integrated_tool_panel_configGalaxyAppConfiguration.involucro_pathGalaxyAppConfiguration.len_file_pathGalaxyAppConfiguration.manage_dependency_relationshipsGalaxyAppConfiguration.monitor_thread_join_timeoutGalaxyAppConfiguration.mulled_channelsGalaxyAppConfiguration.new_file_pathGalaxyAppConfiguration.nginx_upload_storeGalaxyAppConfiguration.password_expiration_periodGalaxyAppConfiguration.preserve_python_environmentGalaxyAppConfiguration.pretty_datetime_formatGalaxyAppConfiguration.sanitize_allowlist_fileGalaxyAppConfiguration.shed_tool_data_pathGalaxyAppConfiguration.themesGalaxyAppConfiguration.themes_by_hostGalaxyAppConfiguration.tool_data_pathGalaxyAppConfiguration.tool_dependency_dirGalaxyAppConfiguration.tool_filtersGalaxyAppConfiguration.tool_label_filtersGalaxyAppConfiguration.tool_pathGalaxyAppConfiguration.tool_section_filtersGalaxyAppConfiguration.toolbox_filter_base_modulesGalaxyAppConfiguration.track_jobs_in_databaseGalaxyAppConfiguration.trust_jupyter_notebook_conversionGalaxyAppConfiguration.tus_upload_storeGalaxyAppConfiguration.use_remote_userGalaxyAppConfiguration.user_library_import_dir_auto_creationGalaxyAppConfiguration.user_library_import_symlink_allowlistGalaxyAppConfiguration.user_tool_filtersGalaxyAppConfiguration.user_tool_label_filtersGalaxyAppConfiguration.user_tool_section_filtersGalaxyAppConfiguration.visualization_plugins_directoryGalaxyAppConfiguration.workflow_resource_params_mapperGalaxyAppConfiguration.__init__()GalaxyAppConfiguration.config_value_for_host()GalaxyAppConfiguration.reload_sanitize_allowlist()GalaxyAppConfiguration.ensure_tempdir()GalaxyAppConfiguration.check()GalaxyAppConfiguration.is_fetch_with_celery_enabled()
Configurationreload_config_options()get_database_engine_options()- Submodules
- galaxy.config.config_manage module
- galaxy.config.schema module
- galaxy.config.script module
- 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.parquet_to_csv_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
BinaryAb1IdatCelMashSketchCompressedArchiveMeryldbVisiumBref3DynamicCompressedArchiveGzDynamicCompressedArchiveBz2DynamicCompressedArchiveCompressedZipArchiveGenericAsn1BinaryBamNativeBamNative.edam_formatBamNative.edam_dataBamNative.file_extBamNative.sort_flagBamNative.set_meta()BamNative.merge()BamNative.init_meta()BamNative.sniff()BamNative.is_bam()BamNative.set_peek()BamNative.display_peek()BamNative.to_archive()BamNative.groom_dataset_content()BamNative.get_chunk()BamNative.display_data()BamNative.validate()BamNative.metadata_spec
BamBam.edam_formatBam.edam_dataBam.file_extBam.track_typeBam.data_sourcesBam.get_index_flag()Bam.dataset_content_needs_grooming()Bam.set_meta()Bam.sniff()Bam.line_dataprovider()Bam.regex_line_dataprovider()Bam.column_dataprovider()Bam.dict_dataprovider()Bam.header_dataprovider()Bam.id_seq_qual_dataprovider()Bam.genomic_region_dataprovider()Bam.genomic_region_dict_dataprovider()Bam.samtools_dataprovider()Bam.dataprovidersBam.metadata_spec
ProBamBamInputSortedBamQuerynameSortedCRAMBaseBcfBcfBcfUncompressedH5LoomAnndataGribGmxBinaryTrrCptXtcEdrBiom2CoolMCoolH5MLMH5MLM.file_extH5MLM.TARGET_URLH5MLM.max_peek_sizeH5MLM.max_preview_sizeH5MLM.CONFIGH5MLM.HTTP_REPRH5MLM.HYPERPARAMETERH5MLM.REPRH5MLM.URLH5MLM.set_meta()H5MLM.sniff()H5MLM.get_attribute()H5MLM.get_repr()H5MLM.get_html_repr()H5MLM.get_config_string()H5MLM.set_peek()H5MLM.display_peek()H5MLM.display_data()H5MLM.metadata_spec
LudwigModelHexrdMaterialsScfSffBigWigBigBedTwoBitSQliteGeminiSQLiteChiraSQLiteCuffDiffSQliteMzSQlitePQPOSWSQmassBlibSQliteDlibSQliteElibSQliteIdpDBGAFASQLiteNcbiTaxonomySQliteXlsxExcelXlsSraRDataRDSOxliBinaryOxliCountGraphOxliNodeGraphOxliTagSetOxliStopTagsOxliSubsetOxliGraphLabelsPostgresqlArchiveMongoDBArchiveGeneNoteBookFast5ArchiveFast5ArchiveGzFast5ArchiveXzFast5ArchiveBz2Pod5SearchGuiArchiveNetCDFDcdVelDAARMA6DMNDICMParquetBafTarYepTarTdfTarMassHunterTarMassLynxTarWiffTarWiff2TarPretextJP2NpzHexrdImagesNpzHexrdEtaOmeNpzFITSNumpy
- 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
DatatypeConverterNotFoundExceptionDatatypeValidationvalidate()get_params_and_input_name()DataMetaDataData.edam_dataData.edam_formatData.file_extData.CHUNKABLEData.metadata_specData.is_binaryData.composite_typeData.primary_file_nameData.allow_datatype_changeData.track_typeData.data_sourcesData.dataprovidersData.__init__()Data.supported_display_appsData.composite_filesData.is_datatype_change_allowed()Data.dataset_content_needs_grooming()Data.groom_dataset_content()Data.init_meta()Data.set_meta()Data.missing_meta()Data.set_max_optional_metadata_filesize()Data.get_max_optional_metadata_filesize()Data.max_optional_metadata_filesizeData.set_peek()Data.display_peek()Data.to_archive()Data.display_data()Data.display_as_markdown()Data.display_name()Data.display_info()Data.get_mime()Data.add_display_app()Data.remove_display_app()Data.clear_display_apps()Data.add_display_application()Data.get_display_application()Data.get_display_applications_by_dataset()Data.get_display_types()Data.get_display_label()Data.as_display_type()Data.get_display_links()Data.get_converter_types()Data.find_conversion_destination()Data.convert_dataset()Data.after_setting_metadata()Data.before_setting_metadata()Data.add_composite_file()Data.writable_filesData.get_writable_files_for_dataset()Data.get_composite_files()Data.generate_primary_file()Data.has_resolutionData.matches_any()Data.merge()Data.has_dataprovider()Data.dataprovider()Data.validate()Data.base_dataprovider()Data.chunk_dataprovider()Data.chunk64_dataprovider()Data.handle_dataset_as_image()
TextDirectoryGenericAsn1LineCountNewickNexusget_test_fname()get_file_peek()
- galaxy.datatypes.flow module
- galaxy.datatypes.genetics module
GenomeGraphsrgTabListrgSampleListrgFeatureListRgeneticsSNPMatrixLpedPpheFphePheFpedPbedldIndepEigenstratgenoEigenstratpcaSnptestIdeasPrePhenoRexpBaseRexpBase.file_extRexpBase.html_tableRexpBase.composite_typeRexpBase.__init__()RexpBase.generate_primary_file()RexpBase.get_mime()RexpBase.get_phecols()RexpBase.get_pheno()RexpBase.set_peek()RexpBase.get_peek()RexpBase.get_file_peek()RexpBase.regenerate_primary_file()RexpBase.init_meta()RexpBase.set_meta()RexpBase.make_html_table()RexpBase.display_peek()RexpBase.metadata_spec
AffybatchEsetMAlistLinkageStudiesGenotypeMatrixMarkerMapDataInAllegroLOD
- galaxy.datatypes.gis module
- galaxy.datatypes.goldenpath module
- galaxy.datatypes.graph module
- galaxy.datatypes.hdf5 module
HDF5SummarizedExperimentHDF5SummarizedExperiment.file_extHDF5SummarizedExperiment.composite_typeHDF5SummarizedExperiment.allow_datatype_changeHDF5SummarizedExperiment.__init__()HDF5SummarizedExperiment.init_meta()HDF5SummarizedExperiment.generate_primary_file()HDF5SummarizedExperiment.sniff()HDF5SummarizedExperiment.get_mime()HDF5SummarizedExperiment.metadata_spec
- galaxy.datatypes.images module
- galaxy.datatypes.interval module
IntervalInterval.edam_dataInterval.edam_formatInterval.file_extInterval.line_classInterval.track_typeInterval.data_sourcesInterval.__init__()Interval.init_meta()Interval.set_meta()Interval.displayable()Interval.get_estimated_display_viewport()Interval.as_ucsc_display_file()Interval.display_peek()Interval.ucsc_links()Interval.validate()Interval.sniff_prefix()Interval.genomic_region_dataprovider()Interval.genomic_region_dict_dataprovider()Interval.interval_dataprovider()Interval.interval_dict_dataprovider()Interval.dataprovidersInterval.metadata_specInterval.sniff()
BedGraphBedProBedBedStrictBed6Bed12GffGff.edam_dataGff.edam_formatGff.file_extGff.valid_gff_frameGff.column_namesGff.data_sourcesGff.track_typeGff.__init__()Gff.set_attribute_metadata()Gff.set_meta()Gff.display_peek()Gff.get_estimated_display_viewport()Gff.ucsc_links()Gff.gbrowse_links()Gff.sniff_prefix()Gff.genomic_region_dataprovider()Gff.genomic_region_dict_dataprovider()Gff.interval_dataprovider()Gff.interval_dict_dataprovider()Gff.dataprovidersGff.metadata_specGff.sniff()
Gff3GtfWiggleWiggle.edam_formatWiggle.file_extWiggle.track_typeWiggle.data_sourcesWiggle.__init__()Wiggle.get_estimated_display_viewport()Wiggle.gbrowse_links()Wiggle.ucsc_links()Wiggle.display_peek()Wiggle.set_meta()Wiggle.sniff_prefix()Wiggle.wiggle_dataprovider()Wiggle.wiggle_dict_dataprovider()Wiggle.dataprovidersWiggle.metadata_specWiggle.sniff()
CustomTrackENCODEPeakChromatinInteractionsScIdxIntervalTabixJuicerMediumTabixBedTabixGffTabix
- galaxy.datatypes.isa module
- galaxy.datatypes.media module
- galaxy.datatypes.metacyto module
- galaxy.datatypes.metadata module
StatementMetadataCollectionMetadataCollection.__init__()MetadataCollection.get_parent()MetadataCollection.set_parent()MetadataCollection.parentMetadataCollection.specMetadataCollection.remove_key()MetadataCollection.element_is_set()MetadataCollection.get_metadata_parameter()MetadataCollection.make_dict_copy()MetadataCollection.requires_dataset_idMetadataCollection.from_JSON_dict()MetadataCollection.to_JSON_dict()
MetadataSpecCollectionMetadataParameterMetadataParameter.__init__()MetadataParameter.get_field()MetadataParameter.to_string()MetadataParameter.to_safe_string()MetadataParameter.make_copy()MetadataParameter.marshal()MetadataParameter.validate()MetadataParameter.unwrap()MetadataParameter.wrap()MetadataParameter.from_external_value()MetadataParameter.to_external_value()
MetadataElementSpecSelectParameterDBKeyParameterRangeParameterColumnParameterColumnTypesParameterListParameterDictParameterPythonObjectParameterFileParameterMetadataTempFile
- 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
WiffWiff2MzTabMzTab2KroenikPepListPSMSPEFFPepXmlReportProtXmlReportDtaDta2dEdtaProteomicsXmlParamXmlPepXmlMascotXMLMzMLNmrMLProtXMLMzXMLMzDataMzIdentMLTraMLTrafoXMLMzQuantMLConsensusXMLFeatureXMLIdXMLTandemXMLUniProtXMLXquestXMLXquestSpecXMLQCMLMgfMascotDatThermoRAWMspSPLibNoIndexSPLibMs2XHunterAslFormatSf3ImzML
- galaxy.datatypes.qiime2 module
- galaxy.datatypes.qualityscore module
- galaxy.datatypes.registry module
ConfigurationErrorRegistryRegistry.__init__()Registry.load_datatypes()Registry.get_legacy_sites_by_build()Registry.get_display_sites()Registry.load_datatype_sniffers()Registry.get_datatype_from_filename()Registry.is_extension_unsniffable_binary()Registry.get_datatype_class_by_name()Registry.get_available_tracks()Registry.get_mimetype_by_extension()Registry.get_datatype_by_extension()Registry.change_datatype()Registry.load_datatype_converters()Registry.load_display_applications()Registry.reload_display_applications()Registry.load_external_metadata_tool()Registry.set_default_values()Registry.get_converters_by_datatype()Registry.get_converter_by_target_type()Registry.find_conversion_destination_for_dataset_by_extensions()Registry.get_composite_extensions()Registry.get_upload_metadata_params()Registry.edam_formatsRegistry.edam_dataRegistry.to_xml_file()Registry.get_extension()
upload_warning()example_datatype_registry_for_sample()
- galaxy.datatypes.sequence module
SequenceSplitLocationsSequenceAlignmentFastacsFastaFastgBaseFastqBaseFastq.edam_formatBaseFastq.file_extBaseFastq.bases_regexpBaseFastq.set_meta()BaseFastq.sniff_prefix()BaseFastq.display_data()BaseFastq.split()BaseFastq.process_split_file()BaseFastq.quality_check()BaseFastq.check_first_block()BaseFastq.check_block()BaseFastq.validate()BaseFastq.metadata_specBaseFastq.sniff()
FastqFastqSangerFastqSolexaFastqIlluminaFastqCSSangerMafMafCustomTrackAxtLavRNADotPlotMatrixDotBracketGenbankMemePsp
- galaxy.datatypes.sniff module
get_test_fname()sniff_with_cls()handle_composite_file()ConvertResultConvertFunctionconvert_newlines()convert_sep2tabs()convert_newlines_sep2tabs()iter_headers()validate_tabular()get_headers()is_column_based()guess_ext()guess_ext_from_file_name()FilePrefixrun_sniffers_raw()zip_single_fileobj()build_sniff_from_prefix()disable_parent_class_sniffing()HandleCompressedFileResponsehandle_compressed_file()handle_uploaded_dataset_file()HandleUploadedDatasetFileInternalResponseconvert_function()handle_uploaded_dataset_file_internal()InappropriateDatasetContentError
- galaxy.datatypes.spaln module
- galaxy.datatypes.speech module
- galaxy.datatypes.tabular module
TabularDataTabularData.edam_formatTabularData.CHUNKABLETabularData.data_line_offsetTabularData.max_peek_columnsTabularData.set_meta()TabularData.set_peek()TabularData.displayable()TabularData.get_chunk()TabularData.display_data()TabularData.display_as_markdown()TabularData.make_html_table()TabularData.make_html_peek_header()TabularData.make_html_peek_rows()TabularData.display_peek()TabularData.is_int()TabularData.is_float()TabularData.guess_type()TabularData.column_dataprovider()TabularData.dataset_column_dataprovider()TabularData.dict_dataprovider()TabularData.dataset_dict_dataprovider()TabularData.dataprovidersTabularData.metadata_spec
TabularSraManifestTaxonomySamSam.edam_formatSam.edam_dataSam.file_extSam.track_typeSam.data_sourcesSam.__init__()Sam.display_peek()Sam.sniff_prefix()Sam.set_meta()Sam.merge()Sam.line_dataprovider()Sam.regex_line_dataprovider()Sam.column_dataprovider()Sam.dataset_column_dataprovider()Sam.dict_dataprovider()Sam.dataset_dict_dataprovider()Sam.header_dataprovider()Sam.id_seq_qual_dataprovider()Sam.genomic_region_dataprovider()Sam.genomic_region_dict_dataprovider()Sam.dataprovidersSam.metadata_specSam.sniff()
PileupBaseVcfVcfVcfGzElandElandMultiFeatureLocationIndexBaseCSVCSVTSVConnectivityTableConnectivityTable.edam_formatConnectivityTable.file_extConnectivityTable.header_regexpConnectivityTable.structure_regexpConnectivityTable.__init__()ConnectivityTable.set_meta()ConnectivityTable.sniff_prefix()ConnectivityTable.get_chunk()ConnectivityTable.metadata_specConnectivityTable.sniff()
MatrixMarketCMAPPsl
- 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
ConditionalDependenciesConditionalDependencies.__init__()ConditionalDependencies.parse_configs()ConditionalDependencies.get_conditional_requirements()ConditionalDependencies.check()ConditionalDependencies.check_psycopg2_binary()ConditionalDependencies.check_mysqlclient()ConditionalDependencies.check_drmaa()ConditionalDependencies.check_galaxycloudrunner()ConditionalDependencies.check_total_perspective_vortex()ConditionalDependencies.check_pbs_python()ConditionalDependencies.check_pykube_ng()ConditionalDependencies.check_chronos_python()ConditionalDependencies.check_boto3_python()ConditionalDependencies.check_fluent_logger()ConditionalDependencies.check_sentry_sdk()ConditionalDependencies.check_statsd()ConditionalDependencies.check_python_ldap()ConditionalDependencies.check_ldap3()ConditionalDependencies.check_python_pam()ConditionalDependencies.check_azure_storage()ConditionalDependencies.check_boto3()ConditionalDependencies.check_kamaki()ConditionalDependencies.check_python_irodsclient()ConditionalDependencies.check_fs_dropboxfs()ConditionalDependencies.check_fs_webdavfs()ConditionalDependencies.check_fs_anvilfs()ConditionalDependencies.check_fs_sshfs()ConditionalDependencies.check_fs_googledrivefs()ConditionalDependencies.check_fs_gcsfs()ConditionalDependencies.check_google_cloud_storage()ConditionalDependencies.check_onedatafilerestclient()ConditionalDependencies.check_fs_onedatarestfs()ConditionalDependencies.check_fs_basespace()ConditionalDependencies.check_watchdog()ConditionalDependencies.check_python_gitlab()ConditionalDependencies.check_pygithub()ConditionalDependencies.check_influxdb()ConditionalDependencies.check_tensorflow()ConditionalDependencies.check_weasyprint()ConditionalDependencies.check_pydyf()ConditionalDependencies.check_custos_sdk()ConditionalDependencies.check_hvac()ConditionalDependencies.check_pkce()ConditionalDependencies.check_rucio_clients()
optional()
- galaxy.exceptions package
MessageExceptionItemDeletionExceptionObjectInvalidAcceptedRetryLaterNoContentExceptionActionInputErrorDuplicatedSlugExceptionDuplicatedIdentifierExceptionObjectAttributeInvalidExceptionObjectAttributeMissingExceptionMalformedIdUserInvalidRunAsExceptionMalformedContentsUnknownContentsTypeRequestParameterMissingExceptionToolMetaParameterExceptionToolMissingExceptionRequestParameterInvalidExceptionToolInputsNotReadyExceptionToolInputsNotOKExceptionRealUserRequiredExceptionAuthenticationFailedAuthenticationRequiredItemAccessibilityExceptionItemOwnershipExceptionItemImmutableExceptionConfigDoesNotAllowExceptionInsufficientPermissionsExceptionUserCannotRunAsExceptionUserRequiredExceptionAdminRequiredExceptionUserActivationRequiredExceptionObjectNotFoundConflictDeprecatedMethodConfigurationErrorInconsistentDatabaseInternalServerErrorToolExecutionErrorNotImplementedInvalidFileFormatErrorReferenceDataErrorServerNotConfiguredForRequestHandlerAssignmentError- Submodules
- galaxy.exceptions.error_codes module
- galaxy.files package
FileSourcePathFileSourceScoreNoMatchingFileSourceUserDefinedFileSourcesNullUserDefinedFileSourcesConfiguredFileSourcesConfConfiguredFileSourcesConfiguredFileSources.__init__()ConfiguredFileSources.find_best_match()ConfiguredFileSources.get_file_source_path()ConfiguredFileSources.validate_uri_root()ConfiguredFileSources.looks_like_uri()ConfiguredFileSources.plugins_to_dict()ConfiguredFileSources.to_dict()ConfiguredFileSources.from_dict()
NullConfiguredFileSourcesDictifiableFilesSourceContextFileSourceDictifiableFileSourcesUserContextProvidesFileSourcesUserContextProvidesFileSourcesUserContext.__init__()ProvidesFileSourcesUserContext.emailProvidesFileSourcesUserContext.usernameProvidesFileSourcesUserContext.ftp_dirProvidesFileSourcesUserContext.preferencesProvidesFileSourcesUserContext.role_namesProvidesFileSourcesUserContext.group_namesProvidesFileSourcesUserContext.is_adminProvidesFileSourcesUserContext.user_vaultProvidesFileSourcesUserContext.app_vaultProvidesFileSourcesUserContext.file_sourcesProvidesFileSourcesUserContext.anonymous
DictFileSourcesUserContextDictFileSourcesUserContext.__init__()DictFileSourcesUserContext.emailDictFileSourcesUserContext.usernameDictFileSourcesUserContext.ftp_dirDictFileSourcesUserContext.preferencesDictFileSourcesUserContext.role_namesDictFileSourcesUserContext.group_namesDictFileSourcesUserContext.is_adminDictFileSourcesUserContext.user_vaultDictFileSourcesUserContext.app_vaultDictFileSourcesUserContext.file_sourcesDictFileSourcesUserContext.anonymous
- Subpackages
- galaxy.files.sources package
PluginKindFileSourceSupportsFilesSourcePropertiesFilesSourceOptionsEntryDataEntryRemoteEntryTDirectoryClassTFileClassRemoteDirectoryRemoteFileSingleFileSourceSupportsBrowsingFilesSourcefile_source_type_is_browsable()BaseFilesSourceuri_join()slash_join()- Submodules
- galaxy.files.sources.anvil module
- galaxy.files.sources.basespace module
- galaxy.files.sources.dropbox module
- galaxy.files.sources.ftp module
- galaxy.files.sources.galaxy module
- galaxy.files.sources.googlecloudstorage module
- galaxy.files.sources.googledrive module
- galaxy.files.sources.onedata module
- galaxy.files.sources.posix module
- galaxy.files.sources.s3 module
- galaxy.files.sources.s3fs module
- galaxy.files.sources.ssh module
- galaxy.files.sources.webdav module
- galaxy.files.unittest_utils package
- galaxy.files.sources package
- Submodules
- galaxy.files.uris module
- galaxy.forms package
- Submodules
- galaxy.forms.forms module
- galaxy.job_execution package
- Subpackages
- Submodules
- galaxy.job_execution.compute_environment module
dataset_path_to_extra_path()ComputeEnvironmentComputeEnvironment.output_names()ComputeEnvironment.input_path_rewrite()ComputeEnvironment.output_path_rewrite()ComputeEnvironment.input_extra_files_rewrite()ComputeEnvironment.output_extra_files_rewrite()ComputeEnvironment.input_metadata_rewrite()ComputeEnvironment.unstructured_path_rewrite()ComputeEnvironment.working_directory()ComputeEnvironment.config_directory()ComputeEnvironment.env_config_directory()ComputeEnvironment.sep()ComputeEnvironment.new_file_path()ComputeEnvironment.tool_directory()ComputeEnvironment.version_path()ComputeEnvironment.home_directory()ComputeEnvironment.tmp_directory()ComputeEnvironment.galaxy_url()ComputeEnvironment.get_file_sources_dict()
SimpleComputeEnvironmentSharedComputeEnvironmentSharedComputeEnvironment.job_idSharedComputeEnvironment.__init__()SharedComputeEnvironment.jobSharedComputeEnvironment.get_file_sources_dict()SharedComputeEnvironment.output_names()SharedComputeEnvironment.output_paths()SharedComputeEnvironment.input_path_rewrite()SharedComputeEnvironment.output_path_rewrite()SharedComputeEnvironment.input_extra_files_rewrite()SharedComputeEnvironment.output_extra_files_rewrite()SharedComputeEnvironment.input_metadata_rewrite()SharedComputeEnvironment.unstructured_path_rewrite()SharedComputeEnvironment.working_directory()SharedComputeEnvironment.env_config_directory()SharedComputeEnvironment.new_file_path()SharedComputeEnvironment.version_path()SharedComputeEnvironment.tool_directory()SharedComputeEnvironment.home_directory()SharedComputeEnvironment.tmp_directory()SharedComputeEnvironment.galaxy_url()
- galaxy.job_execution.datasets module
- galaxy.job_execution.output_collect module
PermissionProviderMetadataSourceProvidercollect_dynamic_outputs()BaseJobContextJobContextJobContext.__init__()JobContext.job_working_directoryJobContext.tool_provided_metadataJobContext.discovered_file_countJobContext.change_datatype_actionsJobContext.tag_handlerJobContext.work_contextJobContext.sa_sessionJobContext.permission_providerJobContext.metadata_source_providerJobContext.jobJobContext.flush_per_n_datasetsJobContext.input_dbkeyJobContext.object_storeJobContext.userJobContext.persist_object()JobContext.flush()JobContext.get_library_folder()JobContext.get_hdca()JobContext.create_library_folder()JobContext.create_hdca()JobContext.add_output_dataset_association()JobContext.add_library_dataset_to_folder()JobContext.add_datasets_to_history()JobContext.output_collection_def()JobContext.output_def()JobContext.job_id()JobContext.get_job_id()JobContext.get_implicit_collection_jobs_association_id()
SessionlessJobContextSessionlessJobContext.__init__()SessionlessJobContext.tool_provided_metadataSessionlessJobContext.discovered_file_countSessionlessJobContext.change_datatype_actionsSessionlessJobContext.output_collection_def()SessionlessJobContext.output_def()SessionlessJobContext.job_id()SessionlessJobContext.get_hdca()SessionlessJobContext.add_dataset_collection()SessionlessJobContext.add_output_dataset_association()SessionlessJobContext.get_job_id()SessionlessJobContext.get_implicit_collection_jobs_association_id()SessionlessJobContext.job_working_directory
collect_primary_datasets()discover_files()walk_over_file_collectors()walk_over_extra_files()dataset_collector()ToolMetadataDatasetCollectorDatasetCollectorread_exit_code_from()default_exit_code_file()collect_extra_files()collect_shrinked_content_from_path()
- galaxy.job_execution.setup module
JobOutputJobOutputsJobIOJobIO.dict_collection_visible_keysJobIO.__init__()JobIO.jobJobIO.from_json()JobIO.from_dict()JobIO.to_dict()JobIO.to_json()JobIO.file_sourcesJobIO.dataset_path_rewriterJobIO.output_pathsJobIO.output_hdas_and_pathsJobIO.get_input_dataset_fnames()JobIO.get_input_datasets()JobIO.get_input_fnames()JobIO.get_input_paths()JobIO.get_input_path()JobIO.get_output_basenames()JobIO.get_output_fnames()JobIO.get_output_path()JobIO.get_mutable_output_fnames()JobIO.get_output_hdas_and_fnames()JobIO.compute_outputs()JobIO.get_output_file_id()
ensure_configs_directory()create_working_directory_for_job()
- galaxy.job_metrics package
JobInstrumenterSafety- Subpackages
- galaxy.job_metrics.instrumenters package
InstrumentPlugin- Submodules
- galaxy.job_metrics.instrumenters.cgroup 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
- galaxy.job_metrics.instrumenters package
- Submodules
- galaxy.job_metrics.formatting module
- galaxy.job_metrics.safety module
- galaxy.jobs package
JobDestinationNoopQueueJobToolConfigurationJobConfigurationJobConfiguration.DEFAULT_BASE_HANDLER_POOLSJobConfiguration.DEFAULT_NWORKERSJobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZEJobConfiguration.JOB_RESOURCE_CONDITIONAL_XMLJobConfiguration.__init__()JobConfiguration.runner_pluginsJobConfiguration.handlersJobConfiguration.handler_runner_pluginsJobConfiguration.destinationsJobConfiguration.toolsJobConfiguration.tool_classesJobConfiguration.resource_groupsJobConfiguration.resource_parametersJobConfiguration.get_tool_resource_xml()JobConfiguration.get_params()JobConfiguration.get_envs()JobConfiguration.get_resubmits()JobConfiguration.default_job_tool_configurationJobConfiguration.get_job_tool_configurations()JobConfiguration.get_destination()JobConfiguration.get_destinations()JobConfiguration.get_job_runner_plugins()JobConfiguration.is_id()JobConfiguration.is_tag()JobConfiguration.convert_legacy_destinations()
JobWrapperTaskWrapperTaskWrapper.is_taskTaskWrapper.__init__()TaskWrapper.can_split()TaskWrapper.get_job()TaskWrapper.get_task()TaskWrapper.get_id_tag()TaskWrapper.prepare()TaskWrapper.fail()TaskWrapper.change_state()TaskWrapper.get_state()TaskWrapper.get_exit_code()TaskWrapper.set_runner()TaskWrapper.finish()TaskWrapper.cleanup()TaskWrapper.get_command_line()TaskWrapper.get_session_id()TaskWrapper.get_output_file_id()TaskWrapper.get_tool_provided_job_metadata()TaskWrapper.get_dataset_finish_context()TaskWrapper.setup_external_metadata()TaskWrapper.get_output_destination()
- Subpackages
- galaxy.jobs.rules package
- galaxy.jobs.runners package
RunnerParamsBaseJobRunnerJobStateAsynchronousJobStateAsynchronousJobRunner- Subpackages
- 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
- galaxy.jobs.splitters package
- Submodules
- galaxy.jobs.command_factory module
- galaxy.jobs.dynamic_tool_destination module
priority_listdestination_listmax_edit_distMalformedYMLExceptionScannerErrorget_keys_from_dict()RuleValidatorparse_yaml()validate_destination()validate_config()bytes_to_str()str_to_bytes()importer()map_tool_to_destination()get_destination_list_from_job_config()get_edit_distance()get_typo_correction()verbose
- galaxy.jobs.handler module
JobHandlerIJobHandlerItemGrabberInvocationGrabberJobGrabberStopSignalExceptionBaseJobHandlerQueueJobHandlerQueueJobHandlerQueue.__init__()JobHandlerQueue.start()JobHandlerQueue.job_wrapper()JobHandlerQueue.job_pair_for_id()JobHandlerQueue.get_user_job_count()JobHandlerQueue.get_user_job_count_per_destination()JobHandlerQueue.increase_running_job_count()JobHandlerQueue.get_total_job_count_per_destination()JobHandlerQueue.put()JobHandlerQueue.shutdown()JobHandlerQueue.queue
JobHandlerStopQueueDefaultJobDispatcher
- galaxy.jobs.manager module
- galaxy.jobs.mapper module
- galaxy.jobs.rule_helper module
- galaxy.jobs.stock_rules module
- galaxy.managers package
- Submodules
- galaxy.managers.annotatable module
- galaxy.managers.api_keys module
- galaxy.managers.base module
ParsedFilterparsed_filtersecurity_check()get_class()decode_id()decode_with_security()encode_with_security()get_object()ModelManagerModelManager.model_classModelManager.foreign_key_nameModelManager.__init__()ModelManager.appModelManager.session()ModelManager.query()ModelManager.one()ModelManager.by_id()ModelManager.list()ModelManager.count()ModelManager.by_ids()ModelManager.create()ModelManager.copy()ModelManager.update()ModelManager.associate()ModelManager.query_associated()
HasAModelManagerModelSerializingErrorModelDeserializingErrorSkipAttributeSerializer
