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()
MockApp
MockApp.config
MockApp.amqp_type
MockApp.job_search
MockApp.tool_cache
MockApp.watchers
MockApp.dataset_collection_manager
MockApp.hda_manager
MockApp.workflow_manager
MockApp.history_manager
MockApp.job_metrics
MockApp.stop
MockApp.is_webapp
MockApp.__init__()
MockApp.install_model
MockApp.toolbox
MockApp.wait_for_toolbox_reload()
MockApp.reindex_tool_search()
MockApp.setup_test_vault()
MockLock
MockAppConfig
MockWebapp
mock_url_builder()
MockTrans
MockTrans.__init__()
MockTrans.tag_handler
MockTrans.check_csrf_token()
MockTrans.handle_user_login()
MockTrans.log_event()
MockTrans.get_user()
MockTrans.set_user()
MockTrans.user
MockTrans.get_history()
MockTrans.set_history()
MockTrans.fill_template()
MockTrans.username
MockTrans.email
MockTrans.init_user_in_database()
MockTrans.user_vault
MockVisualizationsRegistry
MockDir
MockTemplateHelpers
- galaxy.app_unittest_utils.tools_support module
- galaxy.auth package
- galaxy.authnz package
IdentityProvider
- Submodules
- galaxy.authnz.custos_authnz module
InvalidAuthnzConfigException
CustosAuthnzConfiguration
CustosAuthnzConfiguration.provider
CustosAuthnzConfiguration.verify_ssl
CustosAuthnzConfiguration.url
CustosAuthnzConfiguration.label
CustosAuthnzConfiguration.client_id
CustosAuthnzConfiguration.client_secret
CustosAuthnzConfiguration.require_create_confirmation
CustosAuthnzConfiguration.redirect_uri
CustosAuthnzConfiguration.ca_bundle
CustosAuthnzConfiguration.pkce_support
CustosAuthnzConfiguration.accepted_audiences
CustosAuthnzConfiguration.extra_params
CustosAuthnzConfiguration.extra_scopes
CustosAuthnzConfiguration.authorization_endpoint
CustosAuthnzConfiguration.token_endpoint
CustosAuthnzConfiguration.end_session_endpoint
CustosAuthnzConfiguration.well_known_oidc_config_uri
CustosAuthnzConfiguration.iam_client_secret
CustosAuthnzConfiguration.userinfo_endpoint
CustosAuthnzConfiguration.credential_url
CustosAuthnzConfiguration.issuer
CustosAuthnzConfiguration.jwks_uri
CustosAuthnzConfiguration.__init__()
OIDCAuthnzBase
OIDCAuthnzBaseKeycloak
OIDCAuthnzBaseCiLogon
CustosAuthFactory
OIDCAuthnzBaseCustos
- galaxy.authnz.managers module
AuthnzManager
AuthnzManager.__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
PSAAuthnz
Strategy
Strategy.__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()
Storage
on_the_fly_config()
contains_required_data()
verify()
allowed_to_disconnect()
disconnect()
- galaxy.celery package
- galaxy.config package
LOGGING_CONFIG_DEFAULT
DEPENDENT_CONFIG_DEFAULTS
configure_logging()
find_root()
expand_pretty_datetime_format()
BaseAppConfiguration
BaseAppConfiguration.renamed_options
BaseAppConfiguration.deprecated_dirs
BaseAppConfiguration.paths_to_check_against_root
BaseAppConfiguration.add_sample_file_to_defaults
BaseAppConfiguration.listify_options
BaseAppConfiguration.object_store_store_by
BaseAppConfiguration.shed_tools_dir
BaseAppConfiguration.__init__()
BaseAppConfiguration.is_set()
BaseAppConfiguration.resolve_path()
CommonConfigurationMixin
GalaxyAppConfiguration
GalaxyAppConfiguration.renamed_options
GalaxyAppConfiguration.deprecated_options
GalaxyAppConfiguration.default_config_file_name
GalaxyAppConfiguration.deprecated_dirs
GalaxyAppConfiguration.paths_to_check_against_root
GalaxyAppConfiguration.add_sample_file_to_defaults
GalaxyAppConfiguration.listify_options
GalaxyAppConfiguration.allowed_origin_hostnames
GalaxyAppConfiguration.builds_file_path
GalaxyAppConfiguration.container_resolvers_config_file
GalaxyAppConfiguration.database_connection
GalaxyAppConfiguration.drmaa_external_runjob_script
GalaxyAppConfiguration.email_from
GalaxyAppConfiguration.enable_tool_shed_check
GalaxyAppConfiguration.galaxy_data_manager_data_path
GalaxyAppConfiguration.galaxy_infrastructure_url
GalaxyAppConfiguration.hours_between_check
GalaxyAppConfiguration.integrated_tool_panel_config
GalaxyAppConfiguration.involucro_path
GalaxyAppConfiguration.len_file_path
GalaxyAppConfiguration.manage_dependency_relationships
GalaxyAppConfiguration.monitor_thread_join_timeout
GalaxyAppConfiguration.mulled_channels
GalaxyAppConfiguration.new_file_path
GalaxyAppConfiguration.nginx_upload_store
GalaxyAppConfiguration.password_expiration_period
GalaxyAppConfiguration.preserve_python_environment
GalaxyAppConfiguration.pretty_datetime_format
GalaxyAppConfiguration.sanitize_allowlist_file
GalaxyAppConfiguration.shed_tool_data_path
GalaxyAppConfiguration.themes
GalaxyAppConfiguration.themes_by_host
GalaxyAppConfiguration.tool_data_path
GalaxyAppConfiguration.tool_dependency_dir
GalaxyAppConfiguration.tool_filters
GalaxyAppConfiguration.tool_label_filters
GalaxyAppConfiguration.tool_path
GalaxyAppConfiguration.tool_section_filters
GalaxyAppConfiguration.toolbox_filter_base_modules
GalaxyAppConfiguration.track_jobs_in_database
GalaxyAppConfiguration.trust_jupyter_notebook_conversion
GalaxyAppConfiguration.tus_upload_store
GalaxyAppConfiguration.use_remote_user
GalaxyAppConfiguration.user_library_import_dir_auto_creation
GalaxyAppConfiguration.user_library_import_symlink_allowlist
GalaxyAppConfiguration.user_tool_filters
GalaxyAppConfiguration.user_tool_label_filters
GalaxyAppConfiguration.user_tool_section_filters
GalaxyAppConfiguration.visualization_plugins_directory
GalaxyAppConfiguration.workflow_resource_params_mapper
GalaxyAppConfiguration.__init__()
GalaxyAppConfiguration.config_value_for_host()
GalaxyAppConfiguration.reload_sanitize_allowlist()
GalaxyAppConfiguration.ensure_tempdir()
GalaxyAppConfiguration.check()
GalaxyAppConfiguration.is_fetch_with_celery_enabled()
Configuration
reload_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
Binary
Ab1
Idat
Cel
MashSketch
CompressedArchive
Meryldb
Visium
Bref3
DynamicCompressedArchive
GzDynamicCompressedArchive
Bz2DynamicCompressedArchive
CompressedZipArchive
GenericAsn1Binary
BamNative
BamNative.edam_format
BamNative.edam_data
BamNative.file_ext
BamNative.sort_flag
BamNative.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
Bam
Bam.edam_format
Bam.edam_data
Bam.file_ext
Bam.track_type
Bam.data_sources
Bam.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.dataproviders
Bam.metadata_spec
ProBam
BamInputSorted
BamQuerynameSorted
CRAM
BaseBcf
Bcf
BcfUncompressed
H5
Loom
Anndata
Grib
GmxBinary
Trr
Cpt
Xtc
Edr
Biom2
Cool
MCool
H5MLM
H5MLM.file_ext
H5MLM.TARGET_URL
H5MLM.max_peek_size
H5MLM.max_preview_size
H5MLM.CONFIG
H5MLM.HTTP_REPR
H5MLM.HYPERPARAMETER
H5MLM.REPR
H5MLM.URL
H5MLM.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
LudwigModel
HexrdMaterials
Scf
Sff
BigWig
BigBed
TwoBit
SQlite
GeminiSQLite
ChiraSQLite
CuffDiffSQlite
MzSQlite
PQP
OSW
SQmass
BlibSQlite
DlibSQlite
ElibSQlite
IdpDB
GAFASQLite
NcbiTaxonomySQlite
Xlsx
ExcelXls
Sra
RData
RDS
OxliBinary
OxliCountGraph
OxliNodeGraph
OxliTagSet
OxliStopTags
OxliSubset
OxliGraphLabels
PostgresqlArchive
MongoDBArchive
GeneNoteBook
Fast5Archive
Fast5ArchiveGz
Fast5ArchiveXz
Fast5ArchiveBz2
Pod5
SearchGuiArchive
NetCDF
Dcd
Vel
DAA
RMA6
DMND
ICM
Parquet
BafTar
YepTar
TdfTar
MassHunterTar
MassLynxTar
WiffTar
Wiff2Tar
Pretext
JP2
Npz
HexrdImagesNpz
HexrdEtaOmeNpz
FITS
Numpy
- 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
DatatypeConverterNotFoundException
DatatypeValidation
validate()
get_params_and_input_name()
DataMeta
Data
Data.edam_data
Data.edam_format
Data.file_ext
Data.CHUNKABLE
Data.metadata_spec
Data.is_binary
Data.composite_type
Data.primary_file_name
Data.allow_datatype_change
Data.track_type
Data.data_sources
Data.dataproviders
Data.__init__()
Data.supported_display_apps
Data.composite_files
Data.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_filesize
Data.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_files
Data.get_writable_files_for_dataset()
Data.get_composite_files()
Data.generate_primary_file()
Data.has_resolution
Data.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()
Text
Directory
GenericAsn1
LineCount
Newick
Nexus
get_test_fname()
get_file_peek()
- galaxy.datatypes.flow module
- galaxy.datatypes.genetics module
GenomeGraphs
rgTabList
rgSampleList
rgFeatureList
Rgenetics
SNPMatrix
Lped
Pphe
Fphe
Phe
Fped
Pbed
ldIndep
Eigenstratgeno
Eigenstratpca
Snptest
IdeasPre
Pheno
RexpBase
RexpBase.file_ext
RexpBase.html_table
RexpBase.composite_type
RexpBase.__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
Affybatch
Eset
MAlist
LinkageStudies
GenotypeMatrix
MarkerMap
DataIn
AllegroLOD
- galaxy.datatypes.gis module
- galaxy.datatypes.goldenpath module
- galaxy.datatypes.graph module
- galaxy.datatypes.hdf5 module
HDF5SummarizedExperiment
HDF5SummarizedExperiment.file_ext
HDF5SummarizedExperiment.composite_type
HDF5SummarizedExperiment.allow_datatype_change
HDF5SummarizedExperiment.__init__()
HDF5SummarizedExperiment.init_meta()
HDF5SummarizedExperiment.generate_primary_file()
HDF5SummarizedExperiment.sniff()
HDF5SummarizedExperiment.get_mime()
HDF5SummarizedExperiment.metadata_spec
- galaxy.datatypes.images module
- galaxy.datatypes.interval module
Interval
Interval.edam_data
Interval.edam_format
Interval.file_ext
Interval.line_class
Interval.track_type
Interval.data_sources
Interval.__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.dataproviders
Interval.metadata_spec
Interval.sniff()
BedGraph
Bed
ProBed
BedStrict
Bed6
Bed12
Gff
Gff.edam_data
Gff.edam_format
Gff.file_ext
Gff.valid_gff_frame
Gff.column_names
Gff.data_sources
Gff.track_type
Gff.__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.dataproviders
Gff.metadata_spec
Gff.sniff()
Gff3
Gtf
Wiggle
Wiggle.edam_format
Wiggle.file_ext
Wiggle.track_type
Wiggle.data_sources
Wiggle.__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.dataproviders
Wiggle.metadata_spec
Wiggle.sniff()
CustomTrack
ENCODEPeak
ChromatinInteractions
ScIdx
IntervalTabix
JuicerMediumTabix
BedTabix
GffTabix
- galaxy.datatypes.isa module
- galaxy.datatypes.media module
- galaxy.datatypes.metacyto module
- galaxy.datatypes.metadata module
Statement
MetadataCollection
MetadataCollection.__init__()
MetadataCollection.get_parent()
MetadataCollection.set_parent()
MetadataCollection.parent
MetadataCollection.spec
MetadataCollection.remove_key()
MetadataCollection.element_is_set()
MetadataCollection.get_metadata_parameter()
MetadataCollection.make_dict_copy()
MetadataCollection.requires_dataset_id
MetadataCollection.from_JSON_dict()
MetadataCollection.to_JSON_dict()
MetadataSpecCollection
MetadataParameter
MetadataParameter.__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()
MetadataElementSpec
SelectParameter
DBKeyParameter
RangeParameter
ColumnParameter
ColumnTypesParameter
ListParameter
DictParameter
PythonObjectParameter
FileParameter
MetadataTempFile
- 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
Wiff
Wiff2
MzTab
MzTab2
Kroenik
PepList
PSMS
PEFF
PepXmlReport
ProtXmlReport
Dta
Dta2d
Edta
ProteomicsXml
ParamXml
PepXml
MascotXML
MzML
NmrML
ProtXML
MzXML
MzData
MzIdentML
TraML
TrafoXML
MzQuantML
ConsensusXML
FeatureXML
IdXML
TandemXML
UniProtXML
XquestXML
XquestSpecXML
QCML
Mgf
MascotDat
ThermoRAW
Msp
SPLibNoIndex
SPLib
Ms2
XHunterAslFormat
Sf3
ImzML
- galaxy.datatypes.qiime2 module
- galaxy.datatypes.qualityscore module
- galaxy.datatypes.registry module
ConfigurationError
Registry
Registry.__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_formats
Registry.edam_data
Registry.to_xml_file()
Registry.get_extension()
upload_warning()
example_datatype_registry_for_sample()
- galaxy.datatypes.sequence module
SequenceSplitLocations
Sequence
Alignment
Fasta
csFasta
Fastg
BaseFastq
BaseFastq.edam_format
BaseFastq.file_ext
BaseFastq.bases_regexp
BaseFastq.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_spec
BaseFastq.sniff()
Fastq
FastqSanger
FastqSolexa
FastqIllumina
FastqCSSanger
Maf
MafCustomTrack
Axt
Lav
RNADotPlotMatrix
DotBracket
Genbank
MemePsp
- galaxy.datatypes.sniff module
get_test_fname()
sniff_with_cls()
handle_composite_file()
ConvertResult
ConvertFunction
convert_newlines()
convert_sep2tabs()
convert_newlines_sep2tabs()
iter_headers()
validate_tabular()
get_headers()
is_column_based()
guess_ext()
guess_ext_from_file_name()
FilePrefix
run_sniffers_raw()
zip_single_fileobj()
build_sniff_from_prefix()
disable_parent_class_sniffing()
HandleCompressedFileResponse
handle_compressed_file()
handle_uploaded_dataset_file()
HandleUploadedDatasetFileInternalResponse
convert_function()
handle_uploaded_dataset_file_internal()
InappropriateDatasetContentError
- galaxy.datatypes.spaln module
- galaxy.datatypes.speech module
- galaxy.datatypes.tabular module
TabularData
TabularData.edam_format
TabularData.CHUNKABLE
TabularData.data_line_offset
TabularData.max_peek_columns
TabularData.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.dataproviders
TabularData.metadata_spec
Tabular
SraManifest
Taxonomy
Sam
Sam.edam_format
Sam.edam_data
Sam.file_ext
Sam.track_type
Sam.data_sources
Sam.__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.dataproviders
Sam.metadata_spec
Sam.sniff()
Pileup
BaseVcf
Vcf
VcfGz
Eland
ElandMulti
FeatureLocationIndex
BaseCSV
CSV
TSV
ConnectivityTable
ConnectivityTable.edam_format
ConnectivityTable.file_ext
ConnectivityTable.header_regexp
ConnectivityTable.structure_regexp
ConnectivityTable.__init__()
ConnectivityTable.set_meta()
ConnectivityTable.sniff_prefix()
ConnectivityTable.get_chunk()
ConnectivityTable.metadata_spec
ConnectivityTable.sniff()
MatrixMarket
CMAP
Psl
- 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
ConditionalDependencies
ConditionalDependencies.__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
MessageException
ItemDeletionException
ObjectInvalid
AcceptedRetryLater
NoContentException
ActionInputError
DuplicatedSlugException
DuplicatedIdentifierException
ObjectAttributeInvalidException
ObjectAttributeMissingException
MalformedId
UserInvalidRunAsException
MalformedContents
UnknownContentsType
RequestParameterMissingException
ToolMetaParameterException
ToolMissingException
RequestParameterInvalidException
ToolInputsNotReadyException
ToolInputsNotOKException
RealUserRequiredException
AuthenticationFailed
AuthenticationRequired
ItemAccessibilityException
ItemOwnershipException
ItemImmutableException
ConfigDoesNotAllowException
InsufficientPermissionsException
UserCannotRunAsException
UserRequiredException
AdminRequiredException
UserActivationRequiredException
ObjectNotFound
Conflict
DeprecatedMethod
ConfigurationError
InconsistentDatabase
InternalServerError
ToolExecutionError
NotImplemented
InvalidFileFormatError
ReferenceDataError
ServerNotConfiguredForRequest
HandlerAssignmentError
- Submodules
- galaxy.exceptions.error_codes module
- galaxy.files package
FileSourcePath
FileSourceScore
NoMatchingFileSource
UserDefinedFileSources
NullUserDefinedFileSources
ConfiguredFileSourcesConf
ConfiguredFileSources
ConfiguredFileSources.__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()
NullConfiguredFileSources
DictifiableFilesSourceContext
FileSourceDictifiable
FileSourcesUserContext
ProvidesFileSourcesUserContext
ProvidesFileSourcesUserContext.__init__()
ProvidesFileSourcesUserContext.email
ProvidesFileSourcesUserContext.username
ProvidesFileSourcesUserContext.ftp_dir
ProvidesFileSourcesUserContext.preferences
ProvidesFileSourcesUserContext.role_names
ProvidesFileSourcesUserContext.group_names
ProvidesFileSourcesUserContext.is_admin
ProvidesFileSourcesUserContext.user_vault
ProvidesFileSourcesUserContext.app_vault
ProvidesFileSourcesUserContext.file_sources
ProvidesFileSourcesUserContext.anonymous
DictFileSourcesUserContext
DictFileSourcesUserContext.__init__()
DictFileSourcesUserContext.email
DictFileSourcesUserContext.username
DictFileSourcesUserContext.ftp_dir
DictFileSourcesUserContext.preferences
DictFileSourcesUserContext.role_names
DictFileSourcesUserContext.group_names
DictFileSourcesUserContext.is_admin
DictFileSourcesUserContext.user_vault
DictFileSourcesUserContext.app_vault
DictFileSourcesUserContext.file_sources
DictFileSourcesUserContext.anonymous
- Subpackages
- galaxy.files.sources package
PluginKind
FileSourceSupports
FilesSourceProperties
FilesSourceOptions
EntryData
Entry
RemoteEntry
TDirectoryClass
TFileClass
RemoteDirectory
RemoteFile
SingleFileSource
SupportsBrowsing
FilesSource
file_source_type_is_browsable()
BaseFilesSource
uri_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()
ComputeEnvironment
ComputeEnvironment.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()
SimpleComputeEnvironment
SharedComputeEnvironment
SharedComputeEnvironment.job_id
SharedComputeEnvironment.__init__()
SharedComputeEnvironment.job
SharedComputeEnvironment.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
PermissionProvider
MetadataSourceProvider
collect_dynamic_outputs()
BaseJobContext
JobContext
JobContext.__init__()
JobContext.job_working_directory
JobContext.tool_provided_metadata
JobContext.discovered_file_count
JobContext.change_datatype_actions
JobContext.tag_handler
JobContext.work_context
JobContext.sa_session
JobContext.permission_provider
JobContext.metadata_source_provider
JobContext.job
JobContext.flush_per_n_datasets
JobContext.input_dbkey
JobContext.object_store
JobContext.user
JobContext.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()
SessionlessJobContext
SessionlessJobContext.__init__()
SessionlessJobContext.tool_provided_metadata
SessionlessJobContext.discovered_file_count
SessionlessJobContext.change_datatype_actions
SessionlessJobContext.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()
ToolMetadataDatasetCollector
DatasetCollector
read_exit_code_from()
default_exit_code_file()
collect_extra_files()
collect_shrinked_content_from_path()
- galaxy.job_execution.setup module
JobOutput
JobOutputs
JobIO
JobIO.dict_collection_visible_keys
JobIO.__init__()
JobIO.job
JobIO.from_json()
JobIO.from_dict()
JobIO.to_dict()
JobIO.to_json()
JobIO.file_sources
JobIO.dataset_path_rewriter
JobIO.output_paths
JobIO.output_hdas_and_paths
JobIO.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
JobInstrumenter
Safety
- 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
JobDestination
NoopQueue
JobToolConfiguration
JobConfiguration
JobConfiguration.DEFAULT_BASE_HANDLER_POOLS
JobConfiguration.DEFAULT_NWORKERS
JobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZE
JobConfiguration.JOB_RESOURCE_CONDITIONAL_XML
JobConfiguration.__init__()
JobConfiguration.runner_plugins
JobConfiguration.handlers
JobConfiguration.handler_runner_plugins
JobConfiguration.destinations
JobConfiguration.tools
JobConfiguration.tool_classes
JobConfiguration.resource_groups
JobConfiguration.resource_parameters
JobConfiguration.get_tool_resource_xml()
JobConfiguration.get_params()
JobConfiguration.get_envs()
JobConfiguration.get_resubmits()
JobConfiguration.default_job_tool_configuration
JobConfiguration.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()
JobWrapper
TaskWrapper
TaskWrapper.is_task
TaskWrapper.__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
RunnerParams
BaseJobRunner
JobState
AsynchronousJobState
AsynchronousJobRunner
- 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_list
destination_list
max_edit_dist
MalformedYMLException
ScannerError
get_keys_from_dict()
RuleValidator
parse_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
JobHandlerI
JobHandler
ItemGrabber
InvocationGrabber
JobGrabber
StopSignalException
BaseJobHandlerQueue
JobHandlerQueue
JobHandlerQueue.__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
JobHandlerStopQueue
DefaultJobDispatcher
- 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
ParsedFilter
parsed_filter
security_check()
get_class()
decode_id()
decode_with_security()
encode_with_security()
get_object()
ModelManager
ModelManager.model_class
ModelManager.foreign_key_name
ModelManager.__init__()
ModelManager.app
ModelManager.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()
HasAModelManager
ModelSerializingError
ModelDeserializingError
SkipAttribute
Serializer