galaxy-lib
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Z
A
abs_path_or_uri() (in module galaxy.tools.cwl.util)
AbstractToolBox (class in galaxy.tools.toolbox)
(class in galaxy.tools.toolbox.base)
AbstractToolTagManager (class in galaxy.tools.toolbox.tags)
acquire() (galaxy.util.filelock.FileLock method)
action_type (in module galaxy.tools.parser.output_actions)
ActionInputError
activate (galaxy.tools.deps.conda_util.CondaContext attribute)
add() (galaxy.util.oset.OrderedSet method)
add_edge() (galaxy.util.simplegraph.SimpleGraph method)
add_node() (galaxy.util.simplegraph.SimpleGraph method)
add_tool_to_cache() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
AdminRequiredException
aggressive_error_checks() (in module galaxy.tools.parser.util)
AliasPickleModule (class in galaxy.util.aliaspickler)
AliasUnpickler (class in galaxy.util.aliaspickler)
allowed_middleware() (galaxy.web.stack.ApplicationStack method)
append() (galaxy.tools.deps.requirements.ToolRequirements method)
append_section() (galaxy.tools.toolbox.panel.ToolPanelElements method)
append_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method)
AppInfo (class in galaxy.tools.deps.containers)
application_stack_class() (in module galaxy.web.stack)
application_stack_instance() (in module galaxy.web.stack)
application_stack_log_filter() (in module galaxy.web.stack)
application_stack_log_formatter() (in module galaxy.web.stack)
ApplicationStack (class in galaxy.web.stack)
ApplicationStackLogFilter (class in galaxy.web.stack)
apply() (galaxy.tools.deps.resolvers.RequirementMapping method)
apply_action() (galaxy.tools.parser.output_actions.FormatToolOutputAction method)
(galaxy.tools.parser.output_actions.MetadataToolOutputAction method)
(galaxy.tools.parser.output_actions.ToolOutputAction method)
(galaxy.tools.parser.output_actions.ToolOutputActionConditional method)
(galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen method)
(galaxy.tools.parser.output_actions.ToolOutputActionGroup method)
argv_to_str() (in module galaxy.tools.deps.commands)
as_dict() (galaxy.util.simplegraph.SimpleGraph method)
asbool() (in module galaxy.util)
assert_attribute_is() (in module galaxy.tools.verify.asserts.xml)
assert_attribute_matches() (in module galaxy.tools.verify.asserts.xml)
assert_element_text() (in module galaxy.tools.verify.asserts.xml)
assert_element_text_is() (in module galaxy.tools.verify.asserts.xml)
assert_element_text_matches() (in module galaxy.tools.verify.asserts.xml)
assert_has_element_with_path() (in module galaxy.tools.verify.asserts.xml)
assert_has_line() (in module galaxy.tools.verify.asserts.text)
assert_has_line_matching() (in module galaxy.tools.verify.asserts.text)
assert_has_n_columns() (in module galaxy.tools.verify.asserts.tabular)
assert_has_n_elements_with_path() (in module galaxy.tools.verify.asserts.xml)
assert_has_text() (in module galaxy.tools.verify.asserts.text)
assert_has_text_matching() (in module galaxy.tools.verify.asserts.text)
assert_is_valid_xml() (in module galaxy.tools.verify.asserts.xml)
assert_not_has_text() (in module galaxy.tools.verify.asserts.text)
attempt_unlink() (in module galaxy.tools.deps.brew_exts)
attempt_unlink_all() (in module galaxy.tools.deps.brew_exts)
AuthenticationFailed
AuthenticationRequired
avg (galaxy.jobs.metrics.collectl.stats.StatisticsTracker attribute)
avsc_names (galaxy.tools.cwl.schema.ProcessDefinition attribute)
AzureBlobObjectStore (class in galaxy.objectstore.azure_blob)
B
Base (class in galaxy.util.inflection)
BaseGalaxyToolBox (class in galaxy.tools.toolbox)
(class in galaxy.tools.toolbox.base)
before_get() (galaxy.util.properties.NicerConfigParser.InterpolateWrapper method)
bind_all_addrs (galaxy.web.stack.UWSGIApplicationStack attribute)
BooleanFilter (class in galaxy.tools.parser.output_actions)
brew_deps() (in module galaxy.tools.deps.brew_exts)
brew_execute() (in module galaxy.tools.deps.brew_exts)
brew_head_at_commit() (in module galaxy.tools.deps.brew_exts)
brew_head_at_version() (in module galaxy.tools.deps.brew_exts)
brew_info() (in module galaxy.tools.deps.brew_exts)
brew_versions_info() (in module galaxy.tools.deps.brew_exts)
BrewContext (class in galaxy.tools.deps.brew_exts)
build (galaxy.tools.deps.mulled.util.Target attribute)
build_cache() (galaxy.tools.deps.CachedDependencyManager method)
build_command() (in module galaxy.tools.deps.docker_util)
build_command_line() (galaxy.jobs.metrics.collectl.cli.CollectlCli method)
build_dependency_manager() (in module galaxy.tools.deps)
build_docker_cache_command() (in module galaxy.tools.deps.docker_util)
build_docker_images_command() (in module galaxy.tools.deps.docker_util)
build_docker_load_command() (in module galaxy.tools.deps.docker_util)
build_docker_run_command() (in module galaxy.tools.deps.docker_util)
build_env() (galaxy.tools.deps.brew_exts.EnvAction static method)
build_env_actions() (in module galaxy.tools.deps.brew_exts)
build_env_statements() (in module galaxy.tools.deps.brew_exts)
build_env_statements_from_recipe_context() (in module galaxy.tools.deps.brew_exts)
build_filter_function() (galaxy.tools.toolbox.filters.FilterFactory method)
build_filters() (galaxy.tools.toolbox.filters.FilterFactory method)
build_index() (galaxy.tools.deps.mulled.mulled_search.QuaySearch method)
build_object_store_from_config() (in module galaxy.objectstore)
build_pull_command() (in module galaxy.tools.deps.docker_util)
build_resolver() (in module galaxy.tools.verify.test_data)
build_save_image_command() (in module galaxy.tools.deps.docker_util)
build_singularity_run_command() (in module galaxy.tools.deps.singularity_util)
build_target() (in module galaxy.tools.deps.mulled.util)
build_tool_hash() (in module galaxy.tools.hash)
build_url() (in module galaxy.util)
BuildMulledDockerContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled)
BuildMulledSingularityContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled)
Bunch (class in galaxy.util.bunch)
C
cacheable (galaxy.tools.deps.resolvers.Dependency attribute)
CachedDependencyManager (class in galaxy.tools.deps)
CachedMulledDockerContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled)
CachedMulledSingularityContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled)
CallableSafeStringWrapper (class in galaxy.util.object_wrapper)
camelize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
can_install() (galaxy.tools.deps.conda_util.CondaContext method)
(galaxy.tools.deps.installable.InstallableContext method)
can_install_conda() (galaxy.tools.deps.conda_util.CondaContext method)
can_uninstall_dependencies (galaxy.tools.deps.resolvers.DependencyResolver attribute)
cellar_path (galaxy.tools.deps.brew_exts.RecipeContext attribute)
check() (galaxy.tools.toolbox.watcher.ToolConfWatcher method)
check_binary() (in module galaxy.util.checkers)
check_bz2() (in module galaxy.util.checkers)
check_gzip() (in module galaxy.util.checkers)
check_html() (in module galaxy.util.checkers)
check_image() (in module galaxy.util.checkers)
check_image_type() (in module galaxy.util.image_util)
check_zip() (in module galaxy.util.checkers)
classify() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
clean() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
(galaxy.tools.deps.views.DependencyResolversView method)
clear() (galaxy.util.odict.odict method)
close_logs() (galaxy.util.heartbeat.Heartbeat method)
cmp() (in module galaxy.util.object_wrapper)
collect_inputs() (galaxy.tools.parser.interface.TestCollectionDef method)
collect_properties() (galaxy.jobs.metrics.JobInstrumenter method)
(galaxy.jobs.metrics.JobMetrics method)
(galaxy.jobs.metrics.NullJobInstrumenter method)
collection_prototype() (galaxy.tools.parser.output_objects.ToolOutputCollectionStructure method)
collection_type (galaxy.tools.cwl.representation.TypeRepresentation attribute)
collection_wrapper_to_array() (in module galaxy.tools.cwl.representation)
collection_wrapper_to_record() (in module galaxy.tools.cwl.representation)
CollectlCli (class in galaxy.jobs.metrics.collectl.cli)
CollectlPlugin (class in galaxy.jobs.metrics.instrumenters.collectl)
ColumnReplaceFilter (class in galaxy.tools.parser.output_actions)
ColumnStripFilter (class in galaxy.tools.parser.output_actions)
commaify() (in module galaxy.util)
command_list() (in module galaxy.tools.deps.docker_util)
command_shell() (in module galaxy.tools.deps.docker_util)
CommandLineException
,
[1]
commit_for_version() (in module galaxy.tools.deps.brew_exts)
compare_endswith() (in module galaxy.tools.parser.output_actions)
compare_eq() (in module galaxy.tools.parser.output_actions)
compare_gt() (in module galaxy.tools.parser.output_actions)
compare_gte() (in module galaxy.tools.parser.output_actions)
compare_in() (in module galaxy.tools.parser.output_actions)
compare_lt() (in module galaxy.tools.parser.output_actions)
compare_lte() (in module galaxy.tools.parser.output_actions)
compare_neq() (in module galaxy.tools.parser.output_actions)
compare_re_search() (in module galaxy.tools.parser.output_actions)
compare_startswith() (in module galaxy.tools.parser.output_actions)
compare_urls() (in module galaxy.util)
CompressedFile (class in galaxy.util.compression_utils)
cond_plural() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
conda_build_available (galaxy.tools.deps.conda_util.CondaContext attribute)
conda_build_target_str() (in module galaxy.tools.deps.mulled.util)
conda_info() (galaxy.tools.deps.conda_util.CondaContext method)
conda_version (galaxy.tools.deps.conda_util.CondaContext attribute)
CondaContext (class in galaxy.tools.deps.conda_util)
CondaDependencyResolver (class in galaxy.tools.deps.resolvers.conda)
CondaTarget (class in galaxy.tools.deps.conda_util)
config_directories_from_setting() (in module galaxy.util)
config_options (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute)
(galaxy.tools.deps.resolvers.DependencyResolver attribute)
ConfigDoesNotAllowException
ConfigurationError
Conflict
connect() (in module galaxy.util.sqlite)
Container (class in galaxy.tools.deps.containers)
container_from_element() (in module galaxy.tools.deps.requirements)
container_type (galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute)
(galaxy.tools.deps.containers.DockerContainer attribute)
(galaxy.tools.deps.containers.SingularityContainer attribute)
ContainerCLIError
ContainerDescription (class in galaxy.tools.deps.requirements)
ContainerFinder (class in galaxy.tools.deps.containers)
ContainerImageNotFound
containerize_command() (galaxy.tools.deps.containers.Container method)
(galaxy.tools.deps.containers.DockerContainer method)
(galaxy.tools.deps.containers.SingularityContainer method)
ContainerNotFound
ContainerRegistry (class in galaxy.tools.deps.containers)
ContainerResolver (class in galaxy.tools.deps.container_resolvers)
ContainerRunError
convert_bytes() (in module galaxy.objectstore)
copy() (galaxy.tools.deps.requirements.ToolRequirement method)
(galaxy.tools.toolbox.ToolSection method)
(galaxy.tools.toolbox.panel.ToolSection method)
(galaxy.util.odict.odict method)
CorePlugin (class in galaxy.jobs.metrics.instrumenters.core)
CpuInfoPlugin (class in galaxy.jobs.metrics.instrumenters.cpuinfo)
create() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.DistributedObjectStore method)
(galaxy.objectstore.HierarchicalObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
create_section() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
create_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
CwlPageSource (class in galaxy.tools.parser.cwl)
CwlToolSource (class in galaxy.tools.parser.cwl)
CycleError
D
dataset_collection_description() (in module galaxy.tools.parser.output_collection_def)
dataset_collector_descriptions (galaxy.tools.parser.output_objects.ToolOutputCollection attribute)
dataset_collector_descriptions_from_elem() (in module galaxy.tools.parser.output_collection_def)
dataset_collector_descriptions_from_list() (in module galaxy.tools.parser.output_collection_def)
dataset_wrapper_to_directory_json() (in module galaxy.tools.cwl.representation)
dataset_wrapper_to_file_json() (in module galaxy.tools.cwl.representation)
DatasetCollectionDescription (class in galaxy.tools.parser.output_collection_def)
DatatypeIsInstanceToolOutputActionConditionalWhen (class in galaxy.tools.parser.output_actions)
deactivate (galaxy.tools.deps.conda_util.CondaContext attribute)
default_app_name (galaxy.web.stack.ApplicationStack attribute)
default_is_multi_byte (galaxy.tools.parser.interface.ToolSource attribute)
(galaxy.tools.parser.ToolSource attribute)
default_optional (galaxy.tools.parser.interface.InputSource attribute)
defaults() (galaxy.util.properties.NicerConfigParser method)
delete() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
demodulize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
DependenciesDescription (class in galaxy.tools.deps.dependencies)
Dependency (class in galaxy.tools.deps.resolvers)
dependency_resolvers (galaxy.tools.deps.NullDependencyManager attribute)
dependency_shell_commands() (galaxy.tools.deps.CachedDependencyManager method)
(galaxy.tools.deps.DependencyManager method)
(galaxy.tools.deps.NullDependencyManager method)
dependency_type (galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute)
(galaxy.tools.deps.resolvers.NullDependency attribute)
(galaxy.tools.deps.resolvers.galaxy_packages.ToolShedDependency attribute)
(galaxy.tools.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute)
DependencyException
DependencyManager (class in galaxy.tools.deps)
DependencyResolver (class in galaxy.tools.deps.resolvers)
DependencyResolversView (class in galaxy.tools.deps.views)
DeprecatedMethod
deregister_message_handler() (galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.MessageApplicationStack method)
dict() (galaxy.util.bunch.Bunch method)
dict_collection_visible_keys (galaxy.tools.deps.container_resolvers.ContainerResolver attribute)
(galaxy.tools.deps.resolvers.Dependency attribute)
(galaxy.tools.deps.resolvers.DependencyResolver attribute)
(galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute)
(galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute)
(galaxy.tools.deps.resolvers.lmod.LmodDependencyResolver attribute)
(galaxy.tools.deps.resolvers.modules.ModuleDependencyResolver attribute)
(galaxy.tools.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute)
(galaxy.tools.parser.output_objects.ToolOutput attribute)
(galaxy.tools.parser.output_objects.ToolOutputCollection attribute)
(galaxy.tools.toolbox.ToolSection attribute)
(galaxy.tools.toolbox.ToolSectionLabel attribute)
(galaxy.tools.toolbox.panel.ToolSection attribute)
(galaxy.tools.toolbox.panel.ToolSectionLabel attribute)
Dictifiable (class in galaxy.util.dictifiable)
directory_hash_id() (in module galaxy.util)
DirectoryUploadTarget (class in galaxy.tools.cwl.util)
disabled (galaxy.tools.deps.resolvers.DependencyResolver attribute)
discard() (galaxy.util.oset.OrderedSet method)
discover_via (galaxy.tools.parser.output_collection_def.FilePatternDatasetCollectionDescription attribute)
(galaxy.tools.parser.output_collection_def.ToolProvidedMetadataDatasetCollection attribute)
DiskObjectStore (class in galaxy.objectstore)
DistributedObjectStore (class in galaxy.objectstore)
docker_cache_path() (in module galaxy.tools.deps.containers)
docker_host_args() (in module galaxy.tools.deps.dockerfiles)
DockerContainer (class in galaxy.tools.deps.containers)
dockerfile_build() (in module galaxy.tools.deps.dockerfiles)
DockStoreResolver (class in galaxy.tools.locations.dockstore)
docstring_trim() (in module galaxy.util)
document_loader (galaxy.tools.cwl.schema.ProcessDefinition attribute)
download_command() (in module galaxy.tools.deps.commands)
download_to_file() (in module galaxy.util)
dump() (galaxy.util.aliaspickler.AliasPickleModule method)
(galaxy.util.heartbeat.Heartbeat method)
dump_signal_handler() (galaxy.util.heartbeat.Heartbeat method)
dumps() (galaxy.util.aliaspickler.AliasPickleModule method)
DuplicatedIdentifierException
DuplicatedSlugException
dynamic_conf_filenames() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
dynamic_confs() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
dynamic_structure (galaxy.tools.parser.output_objects.ToolOutputCollection attribute)
E
effective_output_name (galaxy.tools.parser.output_objects.ToolOutputCollectionPart attribute)
(galaxy.tools.parser.ToolOutputCollectionPart attribute)
elapsed (galaxy.util.ExecutionTimer attribute)
elem() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
empty() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
English (class in galaxy.util.inflection)
ensure_brew_on_path() (in module galaxy.tools.deps.brew_exts)
ensure_conda_build_installed_if_needed() (galaxy.tools.deps.conda_util.CondaContext method)
ensure_cwltool_available() (in module galaxy.tools.cwl.cwltool_deps)
ensure_installed() (in module galaxy.tools.deps.installable)
ensure_tool_conf_item() (in module galaxy.tools.toolbox.parser)
env_path() (galaxy.tools.deps.conda_util.CondaContext method)
EnvAction (class in galaxy.tools.deps.brew_exts)
EnvPlugin (class in galaxy.jobs.metrics.instrumenters.env)
envs_path (galaxy.tools.deps.conda_util.CondaContext attribute)
err_code (galaxy.exceptions.ActionInputError attribute)
(galaxy.exceptions.AdminRequiredException attribute)
(galaxy.exceptions.AuthenticationFailed attribute)
(galaxy.exceptions.AuthenticationRequired attribute)
(galaxy.exceptions.ConfigDoesNotAllowException attribute)
(galaxy.exceptions.ConfigurationError attribute)
(galaxy.exceptions.Conflict attribute)
(galaxy.exceptions.DeprecatedMethod attribute)
(galaxy.exceptions.DuplicatedIdentifierException attribute)
(galaxy.exceptions.DuplicatedSlugException attribute)
(galaxy.exceptions.InconsistentDatabase attribute)
(galaxy.exceptions.InsufficientPermissionsException attribute)
(galaxy.exceptions.InternalServerError attribute)
(galaxy.exceptions.ItemAccessibilityException attribute)
(galaxy.exceptions.ItemOwnershipException attribute)
(galaxy.exceptions.MalformedContents attribute)
(galaxy.exceptions.MalformedId attribute)
(galaxy.exceptions.MessageException attribute)
(galaxy.exceptions.NotImplemented attribute)
(galaxy.exceptions.ObjectAttributeInvalidException attribute)
(galaxy.exceptions.ObjectAttributeMissingException attribute)
(galaxy.exceptions.ObjectNotFound attribute)
(galaxy.exceptions.RequestParameterInvalidException attribute)
(galaxy.exceptions.RequestParameterMissingException attribute)
(galaxy.exceptions.ToolMetaParameterException attribute)
(galaxy.exceptions.ToolMissingException attribute)
(galaxy.exceptions.UnknownContentsType attribute)
error() (galaxy.tools.lint.LintContext method)
error_on_exit_code() (in module galaxy.tools.parser.util)
ErrorCode (class in galaxy.exceptions.error_codes)
exact (galaxy.tools.deps.resolvers.Dependency attribute)
(galaxy.tools.deps.resolvers.NullDependency attribute)
(galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency attribute)
(galaxy.tools.deps.resolvers.resolver_mixins.HomebrewDependency attribute)
exec_clean() (galaxy.tools.deps.conda_util.CondaContext method)
exec_command() (galaxy.tools.deps.conda_util.CondaContext method)
exec_create() (galaxy.tools.deps.conda_util.CondaContext method)
exec_install() (galaxy.tools.deps.conda_util.CondaContext method)
exec_remove() (galaxy.tools.deps.conda_util.CondaContext method)
execute() (galaxy.tools.verify.test_data.GitDataResolver method)
(in module galaxy.tools.deps.brew_exts)
(in module galaxy.tools.deps.commands)
ExecutionTimer (class in galaxy.util)
exists() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.HierarchicalObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
(galaxy.tools.verify.test_data.FileDataResolver method)
(galaxy.tools.verify.test_data.GitDataResolver method)
ExplicitContainerResolver (class in galaxy.tools.deps.container_resolvers.explicit)
export_list() (galaxy.tools.deps.conda_util.CondaContext method)
ExpressionContext (class in galaxy.util.expressions)
extended_brew_info() (in module galaxy.tools.deps.brew_exts)
extract() (galaxy.util.compression_utils.CompressedFile method)
F
facts (galaxy.web.stack.ApplicationStack attribute)
(galaxy.web.stack.UWSGIApplicationStack attribute)
failed() (galaxy.tools.lint.LintContext method)
field_to_field_type() (in module galaxy.tools.cwl.representation)
file_iter() (in module galaxy.util)
file_reader() (in module galaxy.util)
file_ready() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
FileDataResolver (class in galaxy.tools.verify.test_data)
FileLock (class in galaxy.util.filelock)
FileLockException
FilePatternDatasetCollectionDescription (class in galaxy.tools.parser.output_collection_def)
files_contains() (in module galaxy.tools.verify)
files_diff() (in module galaxy.tools.verify)
files_re_match() (in module galaxy.tools.verify)
files_re_match_multiline() (in module galaxy.tools.verify)
FileUploadTarget (class in galaxy.tools.cwl.util)
filter() (galaxy.web.stack.ApplicationStackLogFilter method)
(galaxy.web.stack.UWSGILogFilter method)
filter_options() (galaxy.tools.parser.output_actions.BooleanFilter method)
(galaxy.tools.parser.output_actions.ColumnReplaceFilter method)
(galaxy.tools.parser.output_actions.ColumnStripFilter method)
(galaxy.tools.parser.output_actions.InsertColumnToolOutputActionOptionFilter method)
(galaxy.tools.parser.output_actions.MetadataValueFilter method)
(galaxy.tools.parser.output_actions.MultipleSplitterFilter method)
(galaxy.tools.parser.output_actions.ParamValueToolOutputActionOptionFilter method)
(galaxy.tools.parser.output_actions.StringFunctionFilter method)
(galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter method)
filter_type (in module galaxy.tools.parser.output_actions)
FilterFactory (class in galaxy.tools.toolbox.filters)
find_best_container_description() (galaxy.tools.deps.containers.ContainerFinder method)
(galaxy.tools.deps.containers.ContainerRegistry method)
find_class() (galaxy.util.aliaspickler.AliasUnpickler method)
find_config_file() (in module galaxy.util.properties)
find_container() (galaxy.tools.deps.containers.ContainerFinder method)
(galaxy.tools.deps.containers.NullContainerFinder method)
find_dep() (galaxy.tools.deps.DependencyManager method)
(galaxy.tools.deps.NullDependencyManager method)
find_possible_tools_from_path() (in module galaxy.tools.loader_directory)
find_section_id() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
flatten() (galaxy.util.Params method)
force_symlink() (in module galaxy.util)
foreignKey() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
format() (galaxy.jobs.metrics.formatting.JobMetricFormatter method)
(galaxy.jobs.metrics.JobMetrics method)
formatter (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin attribute)
(galaxy.jobs.metrics.instrumenters.InstrumentPlugin attribute)
(galaxy.jobs.metrics.instrumenters.core.CorePlugin attribute)
(galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute)
(galaxy.jobs.metrics.instrumenters.env.EnvPlugin attribute)
(galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin attribute)
(galaxy.jobs.metrics.instrumenters.uname.UnamePlugin attribute)
FormatToolOutputAction (class in galaxy.tools.parser.output_actions)
from_args() (galaxy.tools.deps.brew_exts.RecipeContext static method)
from_dict() (galaxy.tools.deps.dependencies.DependenciesDescription static method)
(galaxy.tools.deps.requirements.ContainerDescription static method)
(galaxy.tools.deps.requirements.RequirementSpecification static method)
(galaxy.tools.deps.requirements.ToolRequirement static method)
(galaxy.tools.deps.resolvers.RequirementMapping static method)
(galaxy.tools.parser.interface.TestCollectionDef static method)
(galaxy.tools.parser.interface.TestCollectionOutputDef static method)
from_elem() (galaxy.tools.parser.output_actions.ToolOutputAction class method)
(galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen class method)
(galaxy.tools.parser.output_actions.ToolOutputActionOption class method)
(galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter class method)
from_file() (galaxy.jobs.metrics.JobInstrumenter static method)
from_list() (galaxy.tools.deps.requirements.ToolRequirements static method)
from_tool() (galaxy.tools.toolbox.lineages.interface.ToolLineage static method)
(galaxy.tools.toolbox.lineages.ToolLineage static method)
from_xml() (galaxy.tools.parser.interface.TestCollectionDef static method)
FromDataTableOutputActionOption (class in galaxy.tools.parser.output_actions)
FromFileToolOutputActionOption (class in galaxy.tools.parser.output_actions)
FromParamToolOutputActionOption (class in galaxy.tools.parser.output_actions)
G
galactic_job_json() (in module galaxy.tools.cwl.util)
galaxy (module)
galaxy.exceptions (module)
galaxy.exceptions.error_codes (module)
galaxy.jobs (module)
galaxy.jobs.metrics (module)
galaxy.jobs.metrics.collectl (module)
galaxy.jobs.metrics.collectl.cli (module)
galaxy.jobs.metrics.collectl.processes (module)
galaxy.jobs.metrics.collectl.stats (module)
galaxy.jobs.metrics.collectl.subsystems (module)
galaxy.jobs.metrics.formatting (module)
galaxy.jobs.metrics.instrumenters (module)
galaxy.jobs.metrics.instrumenters.collectl (module)
galaxy.jobs.metrics.instrumenters.core (module)
galaxy.jobs.metrics.instrumenters.cpuinfo (module)
galaxy.jobs.metrics.instrumenters.env (module)
galaxy.jobs.metrics.instrumenters.meminfo (module)
galaxy.jobs.metrics.instrumenters.uname (module)
galaxy.objectstore (module)
galaxy.objectstore.azure_blob (module)
galaxy.objectstore.pithos (module)
galaxy.objectstore.pulsar (module)
galaxy.objectstore.rods (module)
galaxy.objectstore.s3 (module)
galaxy.objectstore.s3_multipart_upload (module)
galaxy.tools (module)
galaxy.tools.cwl (module)
galaxy.tools.cwl.cwltool_deps (module)
galaxy.tools.cwl.parser (module)
galaxy.tools.cwl.representation (module)
galaxy.tools.cwl.runtime_actions (module)
galaxy.tools.cwl.schema (module)
galaxy.tools.cwl.util (module)
galaxy.tools.deps (module)
galaxy.tools.deps.brew_exts (module)
galaxy.tools.deps.brew_util (module)
galaxy.tools.deps.commands (module)
galaxy.tools.deps.conda_compat (module)
galaxy.tools.deps.conda_util (module)
galaxy.tools.deps.container_resolvers (module)
galaxy.tools.deps.container_resolvers.explicit (module)
galaxy.tools.deps.container_resolvers.mulled (module)
galaxy.tools.deps.containers (module)
galaxy.tools.deps.dependencies (module)
galaxy.tools.deps.docker_util (module)
galaxy.tools.deps.dockerfiles (module)
galaxy.tools.deps.installable (module)
galaxy.tools.deps.mulled (module)
galaxy.tools.deps.mulled.mulled_build (module)
galaxy.tools.deps.mulled.mulled_build_channel (module)
galaxy.tools.deps.mulled.mulled_build_files (module)
galaxy.tools.deps.mulled.mulled_build_tool (module)
galaxy.tools.deps.mulled.mulled_search (module)
galaxy.tools.deps.mulled.util (module)
galaxy.tools.deps.requirements (module)
galaxy.tools.deps.resolvers (module)
galaxy.tools.deps.resolvers.brewed_tool_shed_packages (module)
galaxy.tools.deps.resolvers.conda (module)
galaxy.tools.deps.resolvers.galaxy_packages (module)
galaxy.tools.deps.resolvers.homebrew (module)
galaxy.tools.deps.resolvers.lmod (module)
galaxy.tools.deps.resolvers.modules (module)
galaxy.tools.deps.resolvers.resolver_mixins (module)
galaxy.tools.deps.resolvers.tool_shed_packages (module)
galaxy.tools.deps.resolvers.unlinked_tool_shed_packages (module)
galaxy.tools.deps.singularity_util (module)
galaxy.tools.deps.views (module)
galaxy.tools.fetcher (module)
galaxy.tools.hash (module)
galaxy.tools.lint (module)
galaxy.tools.lint_util (module)
galaxy.tools.linters (module)
galaxy.tools.linters.citations (module)
galaxy.tools.linters.command (module)
galaxy.tools.linters.cwl (module)
galaxy.tools.linters.general (module)
galaxy.tools.linters.help (module)
galaxy.tools.linters.inputs (module)
galaxy.tools.linters.outputs (module)
galaxy.tools.linters.stdio (module)
galaxy.tools.linters.tests (module)
galaxy.tools.linters.xml_order (module)
galaxy.tools.loader (module)
galaxy.tools.loader_directory (module)
galaxy.tools.locations (module)
galaxy.tools.locations.dockstore (module)
galaxy.tools.locations.file (module)
galaxy.tools.locations.http (module)
galaxy.tools.parser (module)
galaxy.tools.parser.cwl (module)
galaxy.tools.parser.factory (module)
galaxy.tools.parser.interface (module)
galaxy.tools.parser.output_actions (module)
galaxy.tools.parser.output_collection_def (module)
galaxy.tools.parser.output_objects (module)
galaxy.tools.parser.util (module)
galaxy.tools.parser.xml (module)
galaxy.tools.parser.yaml (module)
galaxy.tools.toolbox (module)
galaxy.tools.toolbox.base (module)
galaxy.tools.toolbox.filters (module)
galaxy.tools.toolbox.integrated_panel (module)
galaxy.tools.toolbox.lineages (module)
galaxy.tools.toolbox.lineages.factory (module)
galaxy.tools.toolbox.lineages.interface (module)
galaxy.tools.toolbox.panel (module)
galaxy.tools.toolbox.parser (module)
galaxy.tools.toolbox.tags (module)
galaxy.tools.toolbox.watcher (module)
galaxy.tools.verify (module)
galaxy.tools.verify.asserts (module)
galaxy.tools.verify.asserts.tabular (module)
galaxy.tools.verify.asserts.text (module)
galaxy.tools.verify.asserts.xml (module)
galaxy.tools.verify.test_data (module)
galaxy.util (module)
galaxy.util.aliaspickler (module)
galaxy.util.bunch (module)
galaxy.util.checkers (module)
galaxy.util.compression_utils (module)
galaxy.util.dictifiable (module)
galaxy.util.expressions (module)
galaxy.util.filelock (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.lazy_process (module)
galaxy.util.object_wrapper (module)
galaxy.util.odict (module)
galaxy.util.oset (module)
galaxy.util.plugin_config (module)
galaxy.util.properties (module)
galaxy.util.simplegraph (module)
galaxy.util.sleeper (module)
galaxy.util.sockets (module)
galaxy.util.specs (module)
galaxy.util.sqlite (module)
galaxy.util.submodules (module)
galaxy.util.tool_version (module)
galaxy.util.topsort (module)
galaxy.util.xml_macros (module)
galaxy.web (module)
galaxy.web.stack (module)
galaxy_directory() (in module galaxy.util)
galaxy_param_type (galaxy.tools.cwl.representation.TypeRepresentation attribute)
GalaxyOutput (class in galaxy.tools.cwl.util)
GalaxyPackageDependency (class in galaxy.tools.deps.resolvers.galaxy_packages)
GalaxyPackageDependencyResolver (class in galaxy.tools.deps.resolvers.galaxy_packages)
gen_edge_dicts() (galaxy.util.simplegraph.SimpleGraph method)
gen_node_dicts() (galaxy.util.simplegraph.SimpleGraph method)
generate_process_statistics() (in module galaxy.jobs.metrics.collectl.processes)
get() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.yaml.YamlInputSource method)
(galaxy.tools.toolbox.lineages.LineageMap method)
(galaxy.tools.toolbox.lineages.factory.LineageMap method)
(galaxy.util.Params method)
(galaxy.util.bunch.Bunch method)
get_additional_repository_information() (galaxy.tools.deps.mulled.mulled_search.QuaySearch method)
get_app_kwds() (galaxy.web.stack.ApplicationStack class method)
(galaxy.web.stack.UWSGIApplicationStack class method)
(in module galaxy.web.stack)
get_app_option() (galaxy.tools.deps.DependencyManager method)
get_bool() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.yaml.YamlInputSource method)
get_charset_from_http_headers() (in module galaxy.util)
get_command() (in module galaxy.tools.linters.command)
get_current_thread_object_dict() (in module galaxy.util.heartbeat)
get_data() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
get_elements() (galaxy.util.topsort.CycleError method)
get_file_size() (in module galaxy.util)
get_filename() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
(galaxy.tools.verify.test_data.TestDataResolver method)
get_fileobj() (in module galaxy.util.compression_utils)
get_fileobj_raw() (in module galaxy.util.compression_utils)
get_first_line() (in module galaxy.tools.verify.asserts.tabular)
get_hashed_dependencies_path() (galaxy.tools.deps.CachedDependencyManager method)
get_input_source() (in module galaxy.tools.parser)
(in module galaxy.tools.parser.factory)
get_integrated_section_for_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_interesting_stack_frame() (galaxy.util.heartbeat.Heartbeat method)
get_loaded_tools_by_lineage() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_object_url() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
get_observer_class() (in module galaxy.tools.toolbox.watcher)
get_pairlist() (galaxy.util.topsort.CycleError method)
get_partial() (galaxy.util.topsort.CycleError method)
get_pred_counts() (galaxy.util.topsort.CycleError method)
get_preds() (galaxy.util.topsort.CycleError method)
get_ref() (galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen method)
get_requirements_status() (galaxy.tools.deps.views.DependencyResolversView method)
get_resolver_option() (galaxy.tools.deps.DependencyManager method)
get_section() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_sections() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_shed_config_dict_by_filename() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_stack_facts() (in module galaxy.web.stack)
get_store_usage_percent() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
get_subsystem() (in module galaxy.jobs.metrics.collectl.subsystems)
get_succs() (galaxy.util.topsort.CycleError method)
get_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_tool_conf_watcher() (in module galaxy.tools.toolbox.watcher)
get_tool_data_dir_watcher() (in module galaxy.tools.toolbox.watcher)
get_tool_id() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_tool_repository_from_xml_item() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_tool_source() (in module galaxy.tools.parser)
(in module galaxy.tools.parser.factory)
get_tool_source_path() (galaxy.tools.locations.dockstore.DockStoreResolver method)
(galaxy.tools.locations.ToolLocationResolver method)
(galaxy.tools.locations.file.HttpToolResolver method)
(galaxy.tools.locations.http.HttpToolResolver method)
get_tool_to_dict() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
get_tool_watcher() (in module galaxy.tools.toolbox.watcher)
get_tool_with_id() (galaxy.tools.toolbox.panel.ToolPanelElements method)
get_toolbox_parser() (in module galaxy.tools.toolbox.parser)
get_value() (galaxy.tools.parser.output_actions.FromDataTableOutputActionOption method)
(galaxy.tools.parser.output_actions.FromFileToolOutputActionOption method)
(galaxy.tools.parser.output_actions.FromParamToolOutputActionOption method)
(galaxy.tools.parser.output_actions.NullToolOutputActionOption method)
(galaxy.tools.parser.output_actions.ToolOutputActionOption method)
get_version_ids() (galaxy.tools.toolbox.lineages.interface.ToolLineage method)
(galaxy.tools.toolbox.lineages.ToolLineage method)
get_versions() (galaxy.tools.toolbox.lineages.interface.ToolLineage method)
(galaxy.tools.toolbox.lineages.ToolLineage method)
getmember() (galaxy.util.compression_utils.CompressedFile method)
getmembers() (galaxy.util.compression_utils.CompressedFile method)
getmembers_tar() (galaxy.util.compression_utils.CompressedFile method)
getmembers_zip() (galaxy.util.compression_utils.CompressedFile method)
getname() (galaxy.util.compression_utils.CompressedFile method)
getname_tar() (galaxy.util.compression_utils.CompressedFile method)
getname_zip() (galaxy.util.compression_utils.CompressedFile method)
git_execute() (in module galaxy.tools.deps.brew_exts)
GitDataResolver (class in galaxy.tools.verify.test_data)
H
handle_outputs() (in module galaxy.tools.cwl)
(in module galaxy.tools.cwl.runtime_actions)
handle_panel_update() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
handle_tags() (galaxy.tools.toolbox.tags.AbstractToolTagManager method)
(galaxy.tools.toolbox.tags.NullToolTagManager method)
(galaxy.tools.toolbox.tags.PersistentToolTagManager method)
has_env() (galaxy.tools.deps.conda_util.CondaContext method)
has_pool() (galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.UWSGIApplicationStack method)
has_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
has_tool_with_id() (galaxy.tools.toolbox.panel.ToolPanelElements method)
HasDockerLikeVolumes (class in galaxy.tools.deps.containers)
hash_dependencies() (galaxy.tools.deps.CachedDependencyManager method)
HasPanelItems (class in galaxy.tools.toolbox.panel)
Heartbeat (class in galaxy.util.heartbeat)
HierarchicalObjectStore (class in galaxy.objectstore)
history_content_id (galaxy.tools.cwl.util.GalaxyOutput attribute)
history_content_type (galaxy.tools.cwl.util.GalaxyOutput attribute)
history_id (galaxy.tools.cwl.util.GalaxyOutput attribute)
hmac_new() (in module galaxy.util.hash_util)
HomebrewDependency (class in galaxy.tools.deps.resolvers.resolver_mixins)
HomebrewDependencyResolver (class in galaxy.tools.deps.resolvers.homebrew)
HomebrewRecipe (class in galaxy.tools.deps.brew_util)
HomebrewToolShedDependencyResolver (class in galaxy.tools.deps.resolvers.brewed_tool_shed_packages)
HttpsToolResolver (class in galaxy.tools.locations.http)
HttpToolResolver (class in galaxy.tools.locations.file)
(class in galaxy.tools.locations.http)
humanize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
I
id_based (galaxy.tools.toolbox.lineages.interface.ToolLineageVersion attribute)
image_name() (in module galaxy.tools.deps.mulled.util)
image_type() (in module galaxy.util.image_util)
imported_macro_paths() (in module galaxy.tools.loader)
(in module galaxy.util.xml_macros)
in_directory() (in module galaxy.util)
in_pool() (galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.UWSGIApplicationStack method)
InconsistentDatabase
index() (galaxy.tools.deps.views.DependencyResolversView method)
index_of_tool_id() (galaxy.tools.toolbox.panel.ToolPanelElements method)
Inflector (class in galaxy.util.inflection)
info() (galaxy.tools.lint.LintContext method)
inputs_defined (galaxy.tools.parser.interface.PagesSource attribute)
(galaxy.tools.parser.xml.XmlPagesSource attribute)
InputSource (class in galaxy.tools.parser.interface)
insert() (galaxy.util.odict.odict method)
insert_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method)
InsertColumnToolOutputActionOptionFilter (class in galaxy.tools.parser.output_actions)
install_all() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
install_conda() (in module galaxy.tools.deps.conda_util)
install_conda_target() (in module galaxy.tools.deps.conda_util)
install_dependencies() (galaxy.tools.deps.views.DependencyResolversView method)
install_dependency() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
(galaxy.tools.deps.resolvers.InstallableDependencyResolver method)
(galaxy.tools.deps.views.DependencyResolversView method)
install_environment (galaxy.tools.deps.conda_util.CondaTarget attribute)
installable_description (galaxy.tools.deps.conda_util.CondaContext attribute)
(galaxy.tools.deps.installable.InstallableContext attribute)
installable_resolvers (galaxy.tools.deps.views.DependencyResolversView attribute)
InstallableContext (class in galaxy.tools.deps.installable)
InstallableDependencyResolver (class in galaxy.tools.deps.resolvers)
instance_id (galaxy.web.stack.UWSGIApplicationStack attribute)
InstrumentPlugin (class in galaxy.jobs.metrics.instrumenters)
InsufficientPermissionsException
InternalServerError
invocation_to_output() (in module galaxy.tools.cwl.util)
IRODSObjectStore (class in galaxy.objectstore.rods)
is_a_yaml_with_class() (in module galaxy.tools.loader_directory)
is_binary() (in module galaxy.util)
is_bz2() (in module galaxy.util.checkers)
is_case() (galaxy.tools.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen method)
(galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen method)
(galaxy.tools.parser.output_actions.ValueToolOutputActionConditionalWhen method)
is_conda_installed() (galaxy.tools.deps.conda_util.CondaContext method)
is_datasource() (in module galaxy.tools.lint_util)
is_gzip() (in module galaxy.util.checkers)
is_hashable() (in module galaxy.util.hash_util)
is_in() (in module galaxy.util.specs)
is_installed() (galaxy.tools.deps.conda_util.CondaContext method)
(galaxy.tools.deps.installable.InstallableContext method)
is_missing_shed_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
is_named_collection_part_name() (galaxy.tools.parser.output_objects.ToolOutputCollectionPart static method)
(galaxy.tools.parser.ToolOutputCollectionPart static method)
is_read_only_query() (in module galaxy.util.sqlite)
is_tool_load_error() (in module galaxy.tools.loader_directory)
is_uuid() (in module galaxy.util)
is_zip() (in module galaxy.util.checkers)
isdir() (galaxy.util.compression_utils.CompressedFile method)
isdir_tar() (galaxy.util.compression_utils.CompressedFile method)
isdir_zip() (galaxy.util.compression_utils.CompressedFile method)
isfile() (galaxy.util.compression_utils.CompressedFile method)
ItemAccessibilityException
ItemDeletionException
ItemOwnershipException
items() (galaxy.util.bunch.Bunch method)
(galaxy.util.odict.odict method)
iteritems() (galaxy.util.odict.odict method)
iterkeys() (galaxy.util.odict.odict method)
itervalues() (galaxy.util.odict.odict method)
J
job_properties() (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin method)
(galaxy.jobs.metrics.instrumenters.InstrumentPlugin method)
(galaxy.jobs.metrics.instrumenters.core.CorePlugin method)
(galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin method)
(galaxy.jobs.metrics.instrumenters.env.EnvPlugin method)
(galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin method)
(galaxy.jobs.metrics.instrumenters.uname.UnamePlugin method)
JobInfo (class in galaxy.tools.deps.containers)
JobInstrumenter (class in galaxy.jobs.metrics)
JobMetricFormatter (class in galaxy.jobs.metrics.formatting)
JobMetrics (class in galaxy.jobs.metrics)
jsonrpc_request() (in module galaxy.util.json)
jsonrpc_response() (in module galaxy.util.json)
K
keys() (galaxy.util.bunch.Bunch method)
(galaxy.util.odict.odict method)
kill_command() (in module galaxy.tools.deps.docker_util)
known_outputs() (galaxy.tools.parser.output_objects.ToolOutputCollection method)
L
label (galaxy.tools.cwl.representation.TypeRepresentation attribute)
LazyProcess (class in galaxy.util.lazy_process)
LineageMap (class in galaxy.tools.toolbox.lineages)
(class in galaxy.tools.toolbox.lineages.factory)
lineages_by_id (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute)
(galaxy.tools.toolbox.lineages.ToolLineage attribute)
lint() (galaxy.tools.lint.LintContext method)
lint_citations() (in module galaxy.tools.linters.citations)
lint_command() (in module galaxy.tools.linters.command)
lint_cwl_validation() (in module galaxy.tools.linters.cwl)
lint_description() (in module galaxy.tools.linters.cwl)
lint_docker_image() (in module galaxy.tools.linters.cwl)
lint_general() (in module galaxy.tools.linters.general)
lint_help() (in module galaxy.tools.linters.help)
lint_inputs() (in module galaxy.tools.linters.inputs)
lint_new_draft() (in module galaxy.tools.linters.cwl)
lint_output() (in module galaxy.tools.linters.outputs)
lint_repeats() (in module galaxy.tools.linters.inputs)
lint_stdio() (in module galaxy.tools.linters.stdio)
lint_tool_source() (in module galaxy.tools.lint)
lint_tool_source_with() (in module galaxy.tools.lint)
lint_tsts() (in module galaxy.tools.linters.tests)
lint_xml() (in module galaxy.tools.lint)
lint_xml_order() (in module galaxy.tools.linters.xml_order)
lint_xml_with() (in module galaxy.tools.lint)
LintContext (class in galaxy.tools.lint)
list_dependencies() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
(galaxy.tools.deps.resolvers.ListableDependencyResolver method)
(galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method)
ListableDependencyResolver (class in galaxy.tools.deps.resolvers)
listify() (in module galaxy.util)
LmodDependencyResolver (class in galaxy.tools.deps.resolvers.lmod)
load() (galaxy.util.aliaspickler.AliasPickleModule method)
(in module galaxy.util.xml_macros)
load_app_properties() (in module galaxy.util.properties)
load_hidden_lib_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
load_hidden_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
load_item() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
load_job_proxy() (in module galaxy.tools.cwl.parser)
load_plugins() (in module galaxy.util.plugin_config)
load_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
(in module galaxy.tools.loader)
load_tool_elements_from_path() (in module galaxy.tools.loader_directory)
load_tool_from_cache() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
load_tool_sources_from_path() (in module galaxy.tools.loader_directory)
load_tool_with_refereces() (in module galaxy.tools.loader)
load_versioned_deps() (in module galaxy.tools.deps.brew_exts)
load_with_references() (in module galaxy.util.xml_macros)
loads() (galaxy.util.aliaspickler.AliasPickleModule method)
local_extra_dirs() (in module galaxy.objectstore)
localhost_addrs (galaxy.web.stack.UWSGIApplicationStack attribute)
LocFileEventHandler (class in galaxy.tools.toolbox.watcher)
lock (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute)
(galaxy.tools.toolbox.lineages.ToolLineage attribute)
log_filter() (galaxy.web.stack.ApplicationStack class method)
log_filter_class (galaxy.web.stack.ApplicationStack attribute)
(galaxy.web.stack.UWSGIApplicationStack attribute)
log_format (galaxy.web.stack.ApplicationStack attribute)
(galaxy.web.stack.UWSGIApplicationStack attribute)
log_startup() (galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.UWSGIApplicationStack method)
logs_command() (in module galaxy.tools.deps.docker_util)
looks_like_a_cwl_artifact() (in module galaxy.tools.loader_directory)
looks_like_a_tool_cwl() (in module galaxy.tools.loader_directory)
looks_like_a_tool_xml() (in module galaxy.tools.loader_directory)
looks_like_a_tool_yaml() (in module galaxy.tools.loader_directory)
M
macro_paths() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
main() (in module galaxy.tools.deps.brew_exts)
(in module galaxy.tools.deps.mulled.mulled_build)
(in module galaxy.tools.deps.mulled.mulled_build_channel)
(in module galaxy.tools.deps.mulled.mulled_build_files)
(in module galaxy.tools.deps.mulled.mulled_build_tool)
(in module galaxy.tools.deps.mulled.mulled_search)
make_temp_fname() (in module galaxy.tools.verify)
MalformedContents
MalformedId
manager_dependency() (galaxy.tools.deps.views.DependencyResolversView method)
manager_requirements() (galaxy.tools.deps.views.DependencyResolversView method)
ManagesIntegratedToolPanelMixin (class in galaxy.tools.toolbox.integrated_panel)
map_wrap() (in module galaxy.objectstore.s3_multipart_upload)
MappableDependencyResolver (class in galaxy.tools.deps.resolvers)
mask_password_from_url() (in module galaxy.util)
matches_requirement() (galaxy.tools.deps.resolvers.RequirementMapping method)
md5() (in module galaxy.util.hash_util)
MemInfoPlugin (class in galaxy.jobs.metrics.instrumenters.meminfo)
merge_sorted_iterables() (in module galaxy.util)
merged_environment_name() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
MessageApplicationStack (class in galaxy.web.stack)
MessageException
metadata (galaxy.tools.cwl.schema.ProcessDefinition attribute)
MetaData (in module galaxy.tools.deps.conda_compat)
MetadataToolOutputAction (class in galaxy.tools.parser.output_actions)
MetadataValueFilter (class in galaxy.tools.parser.output_actions)
mkstemp_ln() (in module galaxy.util)
modify_environ() (galaxy.tools.deps.brew_exts.EnvAction method)
ModuleDependencyResolver (class in galaxy.tools.deps.resolvers.modules)
modulize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
monitor() (galaxy.tools.toolbox.watcher.NullToolConfWatcher method)
(galaxy.tools.toolbox.watcher.ToolConfWatcher method)
(galaxy.tools.toolbox.watcher.ToolDataWatcher method)
(galaxy.tools.toolbox.watcher.ToolWatcher method)
move_merge() (in module galaxy.util)
mp_from_ids() (in module galaxy.objectstore.s3_multipart_upload)
mulled_tags_for() (in module galaxy.tools.deps.mulled.util)
MulledDockerContainerResolver (class in galaxy.tools.deps.container_resolvers.mulled)
multimap() (in module galaxy.objectstore.s3_multipart_upload)
multipart_upload() (in module galaxy.objectstore.s3_multipart_upload)
MultipleDependencyResolver (class in galaxy.tools.deps.resolvers)
MultipleSplitterFilter (class in galaxy.tools.parser.output_actions)
N
name (galaxy.tools.cwl.representation.TypeRepresentation attribute)
(galaxy.web.stack.ApplicationStack attribute)
(galaxy.web.stack.PasteApplicationStack attribute)
(galaxy.web.stack.UWSGIApplicationStack attribute)
(galaxy.web.stack.WeblessApplicationStack attribute)
needs_shell_quoting() (in module galaxy.tools.cwl)
(in module galaxy.tools.cwl.cwltool_deps)
NestedObjectStore (class in galaxy.objectstore)
NEVER_SANITIZE (galaxy.util.Params attribute)
new_secure_hash() (in module galaxy.util.hash_util)
nice_size() (in module galaxy.util)
NicerConfigParser (class in galaxy.util.properties)
NicerConfigParser.InterpolateWrapper (class in galaxy.util.properties)
NoOpLazyProcess (class in galaxy.util.lazy_process)
NotImplemented
NullContainer (class in galaxy.tools.deps.containers)
NullContainerFinder (class in galaxy.tools.deps.containers)
NullDependency (class in galaxy.tools.deps.resolvers)
NullDependencyManager (class in galaxy.tools.deps)
NullJobInstrumenter (class in galaxy.jobs.metrics)
NullToolConfWatcher (class in galaxy.tools.toolbox.watcher)
NullToolOutputActionOption (class in galaxy.tools.parser.output_actions)
NullToolTagManager (class in galaxy.tools.toolbox.tags)
NullWatcher (class in galaxy.tools.toolbox.watcher)
O
object_to_string() (in module galaxy.util)
ObjectAttributeInvalidException
ObjectAttributeMissingException
ObjectInvalid
ObjectNotFound
ObjectStore (class in galaxy.objectstore)
ObjectStorePopulator (class in galaxy.objectstore)
ObjectUploadTarget (class in galaxy.tools.cwl.util)
odict (class in galaxy.util.odict)
on_any_event() (galaxy.tools.toolbox.watcher.LocFileEventHandler method)
(galaxy.tools.toolbox.watcher.ToolFileEventHandler method)
open_logs() (galaxy.util.heartbeat.Heartbeat method)
open_tar() (galaxy.util.compression_utils.CompressedFile method)
open_zip() (galaxy.util.compression_utils.CompressedFile method)
option_type (in module galaxy.tools.parser.output_actions)
OrderedSet (class in galaxy.util.oset)
ordinalize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
output_properties() (in module galaxy.tools.cwl.util)
output_to_cwl_json() (in module galaxy.tools.cwl.util)
P
package_name (galaxy.tools.deps.mulled.util.Target attribute)
package_specifier (galaxy.tools.deps.conda_util.CondaTarget attribute)
package_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
packages (galaxy.tools.deps.requirements.ToolRequirements attribute)
PageSource (class in galaxy.tools.parser.interface)
PagesSource (class in galaxy.tools.parser.interface)
panel_items() (galaxy.tools.toolbox.panel.HasPanelItems method)
(galaxy.tools.toolbox.ToolSection method)
(galaxy.tools.toolbox.panel.ToolPanelElements method)
(galaxy.tools.toolbox.panel.ToolSection method)
panel_items_iter() (galaxy.tools.toolbox.panel.HasPanelItems method)
Params (class in galaxy.util)
ParamsWithSpecs (class in galaxy.util)
ParamValueToolOutputActionOptionFilter (class in galaxy.tools.parser.output_actions)
parent_path (galaxy.tools.deps.conda_util.CondaContext attribute)
(galaxy.tools.deps.installable.InstallableContext attribute)
parse_action_module() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_cast_attribute() (in module galaxy.tools.parser.output_actions)
parse_command() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_compare_type() (in module galaxy.tools.parser.output_actions)
parse_config_xml() (in module galaxy.objectstore.pithos)
parse_conversion_tuples() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
parse_description() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_display() (galaxy.tools.parser.interface.PageSource method)
(galaxy.tools.parser.xml.XmlPageSource method)
parse_display_interface() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_docker_env_pass_through() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_dynamic_options_elem() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
parse_edam_operations() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_edam_topics() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_environment_variables() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_error_level() (galaxy.tools.parser.xml.StdioParser method)
parse_help() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_hidden() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_home_target() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_id() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_input_pages() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_input_sources() (galaxy.tools.parser.cwl.CwlPageSource method)
(galaxy.tools.parser.interface.PageSource method)
(galaxy.tools.parser.xml.XmlPageSource method)
(galaxy.tools.parser.yaml.YamlPageSource method)
parse_input_type() (galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.yaml.YamlInputSource method)
parse_int() (in module galaxy.util)
parse_interpreter() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_is_multi_byte() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_label() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
parse_name() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_nested_inputs_source() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.yaml.YamlInputSource method)
parse_non_hex_float() (in module galaxy.util)
parse_optional() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
parse_outputs() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_parallelism() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_profile() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_provided_metadata_file() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_provided_metadata_style() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_redirect_url_params_elem() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_refresh() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_request_param_translation_elem() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_require_login() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_requirements_and_containers() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_requirements_from_dict() (in module galaxy.tools.deps.requirements)
parse_requirements_from_xml() (in module galaxy.tools.deps.requirements)
parse_resource_parameters() (in module galaxy.util)
parse_sanitize() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_sanitizer_elem() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
parse_static_options() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.yaml.YamlInputSource method)
parse_stdio() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_stdio_exit_codes() (galaxy.tools.parser.xml.StdioParser method)
parse_stdio_regexes() (galaxy.tools.parser.xml.StdioParser method)
parse_strict_shell() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_test_input_source() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.yaml.YamlInputSource method)
parse_tests_to_dict() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_tmp_directory_vars() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
parse_tmp_target() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_tool_module() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_tool_type() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
parse_validator_elems() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
parse_version() (galaxy.tools.parser.cwl.CwlToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_version_command() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_version_command_interpreter() (galaxy.tools.parser.interface.ToolSource method)
(galaxy.tools.parser.ToolSource method)
(galaxy.tools.parser.xml.XmlToolSource method)
(galaxy.tools.parser.yaml.YamlToolSource method)
parse_when_input_sources() (galaxy.tools.parser.interface.InputSource method)
(galaxy.tools.parser.xml.XmlInputSource method)
(galaxy.tools.parser.yaml.YamlInputSource method)
parse_xml() (in module galaxy.util)
parse_xml_string() (in module galaxy.util)
PasteApplicationStack (class in galaxy.web.stack)
path() (galaxy.tools.verify.test_data.FileDataResolver method)
path_or_uri_to_uri() (in module galaxy.tools.cwl.util)
PersistentToolTagManager (class in galaxy.tools.toolbox.tags)
pick_a_cycle() (galaxy.util.topsort.CycleError method)
pickle_SafeStringWrapper() (in module galaxy.util.object_wrapper)
PithosObjectStore (class in galaxy.objectstore.pithos)
plugin_source_from_path() (in module galaxy.util.plugin_config)
plugin_type (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin attribute)
(galaxy.jobs.metrics.instrumenters.InstrumentPlugin attribute)
(galaxy.jobs.metrics.instrumenters.core.CorePlugin attribute)
(galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin attribute)
(galaxy.jobs.metrics.instrumenters.env.EnvPlugin attribute)
(galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin attribute)
(galaxy.jobs.metrics.instrumenters.uname.UnamePlugin attribute)
plugins_dict() (in module galaxy.util.plugin_config)
pluralize() (galaxy.util.inflection.English method)
(galaxy.util.inflection.Inflector method)
pool_name (galaxy.web.stack.ApplicationStack attribute)
pools (galaxy.web.stack.ApplicationStack attribute)
pop() (galaxy.util.oset.OrderedSet method)
popitem() (galaxy.util.odict.odict method)
post_execute_commands() (galaxy.jobs.metrics.JobInstrumenter method)
(galaxy.jobs.metrics.NullJobInstrumenter method)
post_execute_instrument() (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin method)
(galaxy.jobs.metrics.instrumenters.InstrumentPlugin method)
(galaxy.jobs.metrics.instrumenters.core.CorePlugin method)
(galaxy.jobs.metrics.instrumenters.env.EnvPlugin method)
postfork_functions (galaxy.web.stack.UWSGIApplicationStack attribute)
pre_execute_commands() (galaxy.jobs.metrics.JobInstrumenter method)
(galaxy.jobs.metrics.NullJobInstrumenter method)
pre_execute_instrument() (galaxy.jobs.metrics.instrumenters.collectl.CollectlPlugin method)
(galaxy.jobs.metrics.instrumenters.InstrumentPlugin method)
(galaxy.jobs.metrics.instrumenters.core.CorePlugin method)
(galaxy.jobs.metrics.instrumenters.cpuinfo.CpuInfoPlugin method)
(galaxy.jobs.metrics.instrumenters.env.EnvPlugin method)
(galaxy.jobs.metrics.instrumenters.meminfo.MemInfoPlugin method)
(galaxy.jobs.metrics.instrumenters.uname.UnamePlugin method)
prefix (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute)
preprocess_volumes() (in module galaxy.tools.deps.containers)
pretty_print_json() (in module galaxy.util)
pretty_print_time_interval() (in module galaxy.util)
pretty_print_xml() (in module galaxy.util)
print_nonsleeping() (galaxy.util.heartbeat.Heartbeat method)
print_versioned_deps() (in module galaxy.tools.deps.brew_exts)
process_definition() (galaxy.tools.cwl.schema.SchemaLoader method)
process_object (galaxy.tools.cwl.schema.ProcessDefinition attribute)
(galaxy.tools.cwl.schema.RawProcessReference attribute)
ProcessDefinition (class in galaxy.tools.cwl.schema)
prohibited_middleware (galaxy.web.stack.ApplicationStack attribute)
(galaxy.web.stack.UWSGIApplicationStack attribute)
PulsarObjectStore (class in galaxy.objectstore.pulsar)
Q
quay_versions() (in module galaxy.tools.deps.mulled.util)
QuaySearch (class in galaxy.tools.deps.mulled.mulled_search)
R
raw_document_loader (galaxy.tools.cwl.schema.SchemaLoader attribute)
raw_metadata() (in module galaxy.tools.deps.conda_compat)
raw_process_reference (galaxy.tools.cwl.schema.ProcessDefinition attribute)
raw_process_reference() (galaxy.tools.cwl.schema.SchemaLoader method)
raw_process_reference_for_object() (galaxy.tools.cwl.schema.SchemaLoader method)
raw_tool_xml_tree() (in module galaxy.tools.loader)
raw_xml_tree() (in module galaxy.util.xml_macros)
RawProcessReference (class in galaxy.tools.cwl.schema)
read_build_sites() (in module galaxy.util)
read_dbnames() (in module galaxy.util)
read_file() (galaxy.util.properties.NicerConfigParser method)
ready_name_for_url() (in module galaxy.util)
recipe_cellar_path() (in module galaxy.tools.deps.brew_exts)
RecipeContext (class in galaxy.tools.deps.brew_exts)
redirect_aware_commmunicate() (in module galaxy.tools.deps.commands)
redirecting_io() (in module galaxy.tools.deps.commands)
register() (galaxy.tools.toolbox.lineages.factory.LineageMap method)
(galaxy.tools.toolbox.lineages.LineageMap method)
register_message_handler() (galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.MessageApplicationStack method)
register_postfork_function() (galaxy.web.stack.ApplicationStack class method)
(galaxy.web.stack.UWSGIApplicationStack class method)
(in module galaxy.web.stack)
register_tool() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
register_version() (galaxy.tools.toolbox.lineages.interface.ToolLineage method)
(galaxy.tools.toolbox.lineages.ToolLineage method)
relativize_symlinks() (in module galaxy.util)
release() (galaxy.util.filelock.FileLock method)
reload() (galaxy.tools.deps.views.DependencyResolversView method)
reload_dependency_manager() (galaxy.tools.toolbox.base.BaseGalaxyToolBox method)
(galaxy.tools.toolbox.BaseGalaxyToolBox method)
reload_tool_by_id() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
remove_protocol_from_url() (in module galaxy.util)
remove_tool_by_id() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
remove_unused_dependency_paths() (galaxy.tools.deps.views.DependencyResolversView method)
remove_version_from_guid() (in module galaxy.util.tool_version)
replace_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method)
RequestParameterInvalidException
RequestParameterMissingException
requirement_to_recipe() (in module galaxy.tools.deps.brew_util)
RequirementMapping (class in galaxy.tools.deps.resolvers)
requirements_to_conda_targets() (in module galaxy.tools.deps.conda_util)
requirements_to_dependencies() (galaxy.tools.deps.DependencyManager method)
requirements_to_mulled_targets() (in module galaxy.tools.deps.mulled.mulled_build_tool)
requirements_to_recipe_contexts() (in module galaxy.tools.deps.brew_util)
requirements_to_recipes() (in module galaxy.tools.deps.brew_util)
RequirementSpecification (class in galaxy.tools.deps.requirements)
reset_tags() (galaxy.tools.toolbox.tags.AbstractToolTagManager method)
(galaxy.tools.toolbox.tags.NullToolTagManager method)
(galaxy.tools.toolbox.tags.PersistentToolTagManager method)
resolvable (galaxy.tools.deps.requirements.ToolRequirements attribute)
resolve() (galaxy.tools.deps.container_resolvers.ContainerResolver method)
(galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver method)
(galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver method)
(galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver method)
(galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver method)
(galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver method)
(galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver method)
(galaxy.tools.deps.resolvers.DependencyResolver method)
(galaxy.tools.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver method)
(galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
(galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver method)
(galaxy.tools.deps.resolvers.homebrew.HomebrewDependencyResolver method)
(galaxy.tools.deps.resolvers.lmod.LmodDependencyResolver method)
(galaxy.tools.deps.resolvers.modules.ModuleDependencyResolver method)
resolve_all() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
(galaxy.tools.deps.resolvers.MultipleDependencyResolver method)
resolve_dependencies (galaxy.tools.deps.containers.Container attribute)
resolver_dependency() (galaxy.tools.deps.views.DependencyResolversView method)
resolver_msg (galaxy.tools.deps.resolvers.Dependency attribute)
(galaxy.tools.deps.resolvers.NullDependency attribute)
resolver_requirements() (galaxy.tools.deps.views.DependencyResolversView method)
resolver_type (galaxy.tools.deps.container_resolvers.ContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver attribute)
(galaxy.tools.deps.container_resolvers.mulled.MulledDockerContainerResolver attribute)
(galaxy.tools.deps.resolvers.brewed_tool_shed_packages.HomebrewToolShedDependencyResolver attribute)
(galaxy.tools.deps.resolvers.conda.CondaDependencyResolver attribute)
(galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependencyResolver attribute)
(galaxy.tools.deps.resolvers.homebrew.HomebrewDependencyResolver attribute)
(galaxy.tools.deps.resolvers.lmod.LmodDependencyResolver attribute)
(galaxy.tools.deps.resolvers.modules.ModuleDependencyResolver attribute)
(galaxy.tools.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute)
(galaxy.tools.deps.resolvers.unlinked_tool_shed_packages.UnlinkedToolShedPackageDependencyResolver attribute)
resolves_simple_dependencies (galaxy.tools.deps.resolvers.DependencyResolver attribute)
(galaxy.tools.deps.resolvers.tool_shed_packages.ToolShedPackageDependencyResolver attribute)
restore_text() (in module galaxy.util)
reverse() (galaxy.util.odict.odict method)
rods_connect() (in module galaxy.objectstore.rods)
roundify() (in module galaxy.util)
rst_invalid() (in module galaxy.tools.linters.help)
rst_to_html() (in module galaxy.util)
run() (galaxy.jobs.metrics.collectl.cli.CollectlCli method)
(galaxy.util.heartbeat.Heartbeat method)
running (galaxy.util.lazy_process.LazyProcess attribute)
(galaxy.util.lazy_process.NoOpLazyProcess attribute)
S
S3ObjectStore (class in galaxy.objectstore.s3)
sa_session (galaxy.tools.toolbox.base.BaseGalaxyToolBox attribute)
(galaxy.tools.toolbox.BaseGalaxyToolBox attribute)
safe_dumps() (in module galaxy.util.json)
safe_str_cmp() (in module galaxy.util)
SafeStringWrapper (class in galaxy.util.object_wrapper)
sanitize_for_filename() (in module galaxy.util)
sanitize_lists_to_string() (in module galaxy.util)
(in module galaxy.util.object_wrapper)
sanitize_param() (in module galaxy.util)
sanitize_text() (in module galaxy.util)
SchemaLoader (class in galaxy.tools.cwl.schema)
scheme (galaxy.tools.locations.dockstore.DockStoreResolver attribute)
(galaxy.tools.locations.ToolLocationResolver attribute)
(galaxy.tools.locations.file.HttpToolResolver attribute)
(galaxy.tools.locations.http.HttpToolResolver attribute)
(galaxy.tools.locations.http.HttpsToolResolver attribute)
search_repository() (galaxy.tools.deps.mulled.mulled_search.QuaySearch method)
seconds_to_str() (in module galaxy.jobs.metrics.formatting)
send_mail() (in module galaxy.util)
send_message() (galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.MessageApplicationStack method)
server_name_template (galaxy.web.stack.ApplicationStack attribute)
(galaxy.web.stack.UWSGIApplicationStack attribute)
set_basename_and_derived_properties() (in module galaxy.tools.cwl.util)
set_destination_conf_element() (galaxy.jobs.metrics.JobMetrics method)
set_destination_conf_file() (galaxy.jobs.metrics.JobMetrics method)
set_destination_instrumenter() (galaxy.jobs.metrics.JobMetrics method)
set_object_store_id() (galaxy.objectstore.ObjectStorePopulator method)
set_postfork_server_name() (galaxy.web.stack.ApplicationStack method)
setdefault() (galaxy.util.odict.odict method)
sha() (in module galaxy.util.hash_util)
sha1() (in module galaxy.util.hash_util)
shell (galaxy.tools.deps.containers.Container attribute)
shell() (in module galaxy.tools.deps.commands)
shell_commands() (galaxy.tools.deps.resolvers.Dependency method)
(galaxy.tools.deps.resolvers.NullDependency method)
(galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency method)
(galaxy.tools.deps.resolvers.resolver_mixins.HomebrewDependency method)
shell_process() (in module galaxy.tools.deps.commands)
short_name (galaxy.tools.deps.requirements.RequirementSpecification attribute)
show() (galaxy.tools.deps.views.DependencyResolversView method)
show_dependencies() (galaxy.tools.deps.views.DependencyResolversView method)
shrink_stream_by_size() (in module galaxy.util)
shrink_string_by_size() (in module galaxy.util)
shutdown() (galaxy.objectstore.DistributedObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.tools.toolbox.watcher.NullToolConfWatcher method)
(galaxy.tools.toolbox.watcher.NullWatcher method)
(galaxy.tools.toolbox.watcher.ToolConfWatcher method)
(galaxy.tools.toolbox.watcher.ToolDataWatcher method)
(galaxy.tools.toolbox.watcher.ToolWatcher method)
(galaxy.util.heartbeat.Heartbeat method)
(galaxy.util.lazy_process.LazyProcess method)
(galaxy.util.lazy_process.NoOpLazyProcess method)
(galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.MessageApplicationStack method)
(galaxy.web.stack.UWSGIApplicationStack method)
SimpleGraph (class in galaxy.util.simplegraph)
SimpleGraphEdge (class in galaxy.util.simplegraph)
SimpleGraphNode (class in galaxy.util.simplegraph)
SingularityContainer (class in galaxy.tools.deps.containers)
singularize() (galaxy.util.inflection.English method)
(galaxy.util.inflection.Inflector method)
size() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
size_to_bytes() (in module galaxy.util)
sleep() (galaxy.util.sleeper.Sleeper method)
Sleeper (class in galaxy.util.sleeper)
smart_str() (in module galaxy.util)
SpecificationAwareDependencyResolver (class in galaxy.tools.deps.resolvers)
SpecificationPatternDependencyResolver (class in galaxy.tools.deps.resolvers)
specifies_version (galaxy.tools.deps.requirements.RequirementSpecification attribute)
split_output_name() (galaxy.tools.parser.output_objects.ToolOutputCollectionPart static method)
(galaxy.tools.parser.ToolOutputCollectionPart static method)
split_tag() (in module galaxy.tools.deps.mulled.util)
start() (galaxy.tools.toolbox.watcher.NullToolConfWatcher method)
(galaxy.tools.toolbox.watcher.NullWatcher method)
(galaxy.tools.toolbox.watcher.ToolConfWatcher method)
(galaxy.tools.toolbox.watcher.ToolDataWatcher method)
(galaxy.tools.toolbox.watcher.ToolWatcher method)
(galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.MessageApplicationStack method)
(galaxy.web.stack.UWSGIApplicationStack method)
start_process() (galaxy.util.lazy_process.LazyProcess method)
(galaxy.util.lazy_process.NoOpLazyProcess method)
StatisticsTracker (class in galaxy.jobs.metrics.collectl.stats)
status_code (galaxy.exceptions.ActionInputError attribute)
(galaxy.exceptions.AdminRequiredException attribute)
(galaxy.exceptions.AuthenticationFailed attribute)
(galaxy.exceptions.AuthenticationRequired attribute)
(galaxy.exceptions.ConfigDoesNotAllowException attribute)
(galaxy.exceptions.ConfigurationError attribute)
(galaxy.exceptions.Conflict attribute)
(galaxy.exceptions.DeprecatedMethod attribute)
(galaxy.exceptions.DuplicatedIdentifierException attribute)
(galaxy.exceptions.DuplicatedSlugException attribute)
(galaxy.exceptions.InconsistentDatabase attribute)
(galaxy.exceptions.InsufficientPermissionsException attribute)
(galaxy.exceptions.InternalServerError attribute)
(galaxy.exceptions.ItemAccessibilityException attribute)
(galaxy.exceptions.ItemOwnershipException attribute)
(galaxy.exceptions.MalformedContents attribute)
(galaxy.exceptions.MalformedId attribute)
(galaxy.exceptions.MessageException attribute)
(galaxy.exceptions.NotImplemented attribute)
(galaxy.exceptions.ObjectAttributeInvalidException attribute)
(galaxy.exceptions.ObjectAttributeMissingException attribute)
(galaxy.exceptions.ObjectNotFound attribute)
(galaxy.exceptions.RequestParameterInvalidException attribute)
(galaxy.exceptions.RequestParameterMissingException attribute)
(galaxy.exceptions.ToolMetaParameterException attribute)
(galaxy.exceptions.ToolMissingException attribute)
(galaxy.exceptions.UnknownContentsType attribute)
StdioParser (class in galaxy.tools.parser.xml)
string_as_bool() (in module galaxy.util)
string_as_bool_or_none() (in module galaxy.util)
string_replace() (galaxy.util.inflection.Base method)
string_to_object() (in module galaxy.util)
StringFunctionFilter (class in galaxy.tools.parser.output_actions)
stringify_dictionary_keys() (in module galaxy.util)
strip_control_characters() (in module galaxy.util)
stub_label() (galaxy.tools.toolbox.panel.ToolPanelElements method)
stub_tool() (galaxy.tools.toolbox.panel.ToolPanelElements method)
stub_workflow() (galaxy.tools.toolbox.panel.ToolPanelElements method)
submodules() (in module galaxy.util.submodules)
SwiftObjectStore (class in galaxy.objectstore.s3)
synchronized() (in module galaxy.util)
T
tableize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
tag (galaxy.tools.parser.output_actions.BooleanFilter attribute)
(galaxy.tools.parser.output_actions.ColumnReplaceFilter attribute)
(galaxy.tools.parser.output_actions.ColumnStripFilter attribute)
(galaxy.tools.parser.output_actions.DatatypeIsInstanceToolOutputActionConditionalWhen attribute)
(galaxy.tools.parser.output_actions.FormatToolOutputAction attribute)
(galaxy.tools.parser.output_actions.FromDataTableOutputActionOption attribute)
(galaxy.tools.parser.output_actions.FromFileToolOutputActionOption attribute)
(galaxy.tools.parser.output_actions.FromParamToolOutputActionOption attribute)
(galaxy.tools.parser.output_actions.InsertColumnToolOutputActionOptionFilter attribute)
(galaxy.tools.parser.output_actions.MetadataToolOutputAction attribute)
(galaxy.tools.parser.output_actions.MetadataValueFilter attribute)
(galaxy.tools.parser.output_actions.MultipleSplitterFilter attribute)
(galaxy.tools.parser.output_actions.NullToolOutputActionOption attribute)
(galaxy.tools.parser.output_actions.ParamValueToolOutputActionOptionFilter attribute)
(galaxy.tools.parser.output_actions.StringFunctionFilter attribute)
(galaxy.tools.parser.output_actions.ToolOutputAction attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionConditional attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionGroup attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionOption attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter attribute)
(galaxy.tools.parser.output_actions.ValueToolOutputActionConditionalWhen attribute)
tap_path (galaxy.tools.deps.brew_exts.RecipeContext attribute)
Target (class in galaxy.tools.deps.mulled.util)
template_macro_params() (in module galaxy.tools.loader)
(in module galaxy.util.xml_macros)
TestCollectionDef (class in galaxy.tools.parser.interface)
TestCollectionOutputDef (class in galaxy.tools.parser.interface)
TestDataResolver (class in galaxy.tools.verify.test_data)
thread_is_sleeping() (galaxy.util.heartbeat.Heartbeat method)
titleize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
to_bool() (in module galaxy.util.specs)
to_bool_or_none() (in module galaxy.util.specs)
to_cwl_job() (in module galaxy.tools.cwl)
(in module galaxy.tools.cwl.representation)
to_dict() (galaxy.tools.deps.dependencies.DependenciesDescription method)
(galaxy.tools.deps.requirements.ContainerDescription method)
(galaxy.tools.deps.requirements.RequirementSpecification method)
(galaxy.tools.deps.requirements.ToolRequirement method)
(galaxy.tools.parser.interface.TestCollectionDef method)
(galaxy.tools.parser.interface.TestCollectionOutputDef method)
(galaxy.tools.parser.output_objects.ToolOutput method)
(galaxy.tools.parser.output_objects.ToolOutputBase method)
(galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.ToolSection method)
(galaxy.tools.toolbox.ToolSectionLabel method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
(galaxy.tools.toolbox.lineages.ToolLineage method)
(galaxy.tools.toolbox.lineages.interface.ToolLineage method)
(galaxy.tools.toolbox.lineages.interface.ToolLineageVersion method)
(galaxy.tools.toolbox.panel.ToolSection method)
(galaxy.tools.toolbox.panel.ToolSectionLabel method)
(galaxy.util.dictifiable.Dictifiable method)
to_float_or_none() (in module galaxy.util.specs)
to_galaxy_parameters() (in module galaxy.tools.cwl)
(in module galaxy.tools.cwl.representation)
to_list() (galaxy.tools.deps.requirements.ToolRequirements method)
to_statements() (galaxy.tools.deps.brew_exts.EnvAction method)
to_str_or_none() (in module galaxy.util.specs)
to_tool_path() (galaxy.tools.fetcher.ToolLocationFetcher method)
to_xml() (in module galaxy.tools.verify.asserts.xml)
tool (galaxy.tools.parser.output_actions.ToolOutputAction attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionConditional attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionGroup attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionOption attribute)
(galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter attribute)
tool() (galaxy.tools.cwl.schema.SchemaLoader method)
tool_ids (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute)
(galaxy.tools.toolbox.lineages.ToolLineage attribute)
tool_ids_by_requirements (galaxy.tools.deps.views.DependencyResolversView attribute)
tool_panel_contents() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
tool_proxy (galaxy.tools.parser.cwl.CwlToolSource attribute)
tool_proxy() (in module galaxy.tools.cwl)
(in module galaxy.tools.cwl.parser)
tool_proxy_from_persistent_representation() (in module galaxy.tools.cwl)
tool_response_to_output() (in module galaxy.tools.cwl.util)
tool_tag_manager() (in module galaxy.tools.toolbox.tags)
tool_versions (galaxy.tools.toolbox.lineages.interface.ToolLineage attribute)
(galaxy.tools.toolbox.lineages.ToolLineage attribute)
toolbox_requirements_status (galaxy.tools.deps.views.DependencyResolversView attribute)
ToolConfWatcher (class in galaxy.tools.toolbox.watcher)
ToolDataWatcher (class in galaxy.tools.toolbox.watcher)
ToolFileEventHandler (class in galaxy.tools.toolbox.watcher)
ToolInfo (class in galaxy.tools.deps.containers)
ToolLineage (class in galaxy.tools.toolbox.lineages)
(class in galaxy.tools.toolbox.lineages.interface)
ToolLineageVersion (class in galaxy.tools.toolbox.lineages.interface)
ToolLocationFetcher (class in galaxy.tools.fetcher)
ToolLocationResolver (class in galaxy.tools.locations)
ToolMetaParameterException
ToolMissingException
ToolOutput (class in galaxy.tools.parser.output_objects)
ToolOutputAction (class in galaxy.tools.parser.output_actions)
ToolOutputActionConditional (class in galaxy.tools.parser.output_actions)
ToolOutputActionConditionalWhen (class in galaxy.tools.parser.output_actions)
ToolOutputActionGroup (class in galaxy.tools.parser.output_actions)
ToolOutputActionOption (class in galaxy.tools.parser.output_actions)
ToolOutputActionOptionFilter (class in galaxy.tools.parser.output_actions)
ToolOutputBase (class in galaxy.tools.parser.output_objects)
ToolOutputCollection (class in galaxy.tools.parser.output_objects)
ToolOutputCollectionPart (class in galaxy.tools.parser)
(class in galaxy.tools.parser.output_objects)
ToolOutputCollectionStructure (class in galaxy.tools.parser.output_objects)
ToolPanelElements (class in galaxy.tools.toolbox.panel)
ToolProvidedMetadataDatasetCollection (class in galaxy.tools.parser.output_collection_def)
ToolRequirement (class in galaxy.tools.deps.requirements)
ToolRequirements (class in galaxy.tools.deps.requirements)
ToolRequirementsException
tools() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
ToolSection (class in galaxy.tools.toolbox)
(class in galaxy.tools.toolbox.panel)
ToolSectionLabel (class in galaxy.tools.toolbox)
(class in galaxy.tools.toolbox.panel)
ToolShedDependency (class in galaxy.tools.deps.resolvers.galaxy_packages)
ToolShedPackageDependencyResolver (class in galaxy.tools.deps.resolvers.tool_shed_packages)
ToolSource (class in galaxy.tools.parser)
(class in galaxy.tools.parser.interface)
ToolStdioExitCode (class in galaxy.tools.parser.interface)
ToolStdioRegex (class in galaxy.tools.parser.interface)
ToolWatcher (class in galaxy.tools.toolbox.watcher)
topsort() (in module galaxy.util.topsort)
topsort_levels() (in module galaxy.util.topsort)
track() (galaxy.jobs.metrics.collectl.stats.StatisticsTracker method)
transfer_part() (in module galaxy.objectstore.s3_multipart_upload)
transport_class (galaxy.web.stack.ApplicationStack attribute)
(galaxy.web.stack.UWSGIApplicationStack attribute)
type_descriptions_for_field_types() (in module galaxy.tools.cwl.representation)
type_representation_from_name() (in module galaxy.tools.cwl.representation)
TypeRepresentation (class in galaxy.tools.cwl.representation)
U
umask_fix_perms() (in module galaxy.util)
unaccent() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
UnamePlugin (class in galaxy.jobs.metrics.instrumenters.uname)
underscore() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
unicodify() (in module galaxy.util)
uninstall() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
uninstall_dependencies() (galaxy.tools.deps.views.DependencyResolversView method)
uninstall_environments() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
uninstallable_resolvers (galaxy.tools.deps.views.DependencyResolversView attribute)
unique_id() (in module galaxy.util)
UnknownContentsType
UnlinkedToolShedPackageDependencyResolver (class in galaxy.tools.deps.resolvers.unlinked_tool_shed_packages)
unused_dependency_paths (galaxy.tools.deps.views.DependencyResolversView attribute)
unused_dependency_paths() (galaxy.tools.deps.resolvers.conda.CondaDependencyResolver method)
unused_port() (in module galaxy.util.sockets)
unversioned_install() (in module galaxy.tools.deps.brew_exts)
update() (galaxy.util.odict.odict method)
(galaxy.util.Params method)
update_from_file() (galaxy.objectstore.azure_blob.AzureBlobObjectStore method)
(galaxy.objectstore.DiskObjectStore method)
(galaxy.objectstore.NestedObjectStore method)
(galaxy.objectstore.ObjectStore method)
(galaxy.objectstore.pithos.PithosObjectStore method)
(galaxy.objectstore.pulsar.PulsarObjectStore method)
(galaxy.objectstore.rods.IRODSObjectStore method)
(galaxy.objectstore.s3.S3ObjectStore method)
update_or_append() (galaxy.tools.toolbox.panel.ToolPanelElements method)
update_repository() (galaxy.tools.verify.test_data.GitDataResolver method)
update_shed_config() (galaxy.tools.toolbox.AbstractToolBox method)
(galaxy.tools.toolbox.base.AbstractToolBox method)
uri (galaxy.tools.cwl.schema.RawProcessReference attribute)
url_get() (in module galaxy.util)
urlize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
uses_param() (galaxy.tools.cwl.representation.TypeRepresentation method)
uses_tool_shed_dependencies() (galaxy.tools.deps.DependencyManager method)
(galaxy.tools.deps.NullDependencyManager method)
UsesHomebrewMixin (class in galaxy.tools.deps.resolvers.resolver_mixins)
UsesInstalledRepositoriesMixin (class in galaxy.tools.deps.resolvers.resolver_mixins)
UsesToolDependencyDirMixin (class in galaxy.tools.deps.resolvers.resolver_mixins)
UWSGIApplicationStack (class in galaxy.web.stack)
UWSGILogFilter (class in galaxy.web.stack)
V
v1_image_name() (in module galaxy.tools.deps.mulled.util)
v2_image_name() (in module galaxy.tools.deps.mulled.util)
valid() (galaxy.tools.lint.LintContext method)
validate_jsonrpc_request() (in module galaxy.util.json)
validate_jsonrpc_response() (in module galaxy.util.json)
values() (galaxy.util.bunch.Bunch method)
(galaxy.util.odict.odict method)
ValueToolOutputActionConditionalWhen (class in galaxy.tools.parser.output_actions)
variablize() (galaxy.util.inflection.Base method)
(galaxy.util.inflection.Inflector method)
verify() (in module galaxy.tools.verify)
verify_assertion() (in module galaxy.tools.verify.asserts)
verify_assertions() (in module galaxy.tools.verify.asserts)
version (galaxy.tools.deps.mulled.util.Target attribute)
version_sorted() (in module galaxy.tools.deps.mulled.util)
versioned_install() (in module galaxy.tools.deps.brew_exts)
W
wake() (galaxy.util.sleeper.Sleeper method)
warn() (galaxy.tools.lint.LintContext method)
watch_directory() (galaxy.tools.toolbox.watcher.NullWatcher method)
(galaxy.tools.toolbox.watcher.ToolDataWatcher method)
(galaxy.tools.toolbox.watcher.ToolWatcher method)
watch_file() (galaxy.tools.toolbox.watcher.NullToolConfWatcher method)
(galaxy.tools.toolbox.watcher.NullWatcher method)
(galaxy.tools.toolbox.watcher.ToolConfWatcher method)
(galaxy.tools.toolbox.watcher.ToolWatcher method)
WeblessApplicationStack (class in galaxy.web.stack)
which() (in module galaxy.tools.deps.brew_exts)
(in module galaxy.tools.deps.commands)
(in module galaxy.util)
workers() (galaxy.web.stack.ApplicationStack method)
(galaxy.web.stack.UWSGIApplicationStack method)
workflow_proxy() (in module galaxy.tools.cwl)
wrap_with_safe_string() (in module galaxy.util.object_wrapper)
X
xml_element_compare() (in module galaxy.util)
xml_element_list_compare() (in module galaxy.util)
xml_element_to_dict() (in module galaxy.util)
xml_find() (in module galaxy.tools.verify.asserts.xml)
xml_find_text() (in module galaxy.tools.verify.asserts.xml)
xml_text() (in module galaxy.util)
xml_to_string() (in module galaxy.util)
XmlInputSource (class in galaxy.tools.parser.xml)
XmlPageSource (class in galaxy.tools.parser.xml)
XmlPagesSource (class in galaxy.tools.parser.xml)
XmlToolSource (class in galaxy.tools.parser.xml)
Y
YamlInputSource (class in galaxy.tools.parser.yaml)
YamlPageSource (class in galaxy.tools.parser.yaml)
YamlToolSource (class in galaxy.tools.parser.yaml)
Z
zipfile_ok() (galaxy.util.compression_utils.CompressedFile method)
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