Index

_

__init__() (bioblend.galaxy.GalaxyInstance method) (bioblend.toolshed.ToolShedInstance method)

A

add_group_role() (bioblend.galaxy.groups.GroupsClient method) add_group_user() (bioblend.galaxy.groups.GroupsClient method)

API_MODULE (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Library attribute)

B

BASE_ATTRS (bioblend.galaxy.objects.wrappers.ContentInfo attribute) (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) (bioblend.galaxy.objects.wrappers.Folder attribute) (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.HistoryContentInfo attribute) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute) (bioblend.galaxy.objects.wrappers.HistoryPreview attribute) (bioblend.galaxy.objects.wrappers.Library attribute) (bioblend.galaxy.objects.wrappers.Preview attribute) (bioblend.galaxy.objects.wrappers.Step attribute) (bioblend.galaxy.objects.wrappers.Tool attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute) (bioblend.galaxy.objects.wrappers.Wrapper attribute) bioblend (module) bioblend.config (module) bioblend.galaxy.datasets (module) bioblend.galaxy.datatypes (module) bioblend.galaxy.folders (module) bioblend.galaxy.forms (module) bioblend.galaxy.ftpfiles (module) bioblend.galaxy.genomes (module) bioblend.galaxy.groups (module) bioblend.galaxy.histories (module) bioblend.galaxy.jobs (module)

bioblend.galaxy.libraries (module) bioblend.galaxy.objects.client (module) bioblend.galaxy.objects.wrappers (module) bioblend.galaxy.quotas (module) bioblend.galaxy.roles (module) bioblend.galaxy.tool_data (module) bioblend.galaxy.tools (module) bioblend.galaxy.toolshed (module) bioblend.galaxy.users (module) bioblend.galaxy.visual (module) bioblend.galaxy.workflows (module) bioblend.toolshed.repositories (module)

C

clone() (bioblend.galaxy.objects.wrappers.Wrapper method) Config (class in bioblend.config) container_id (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.Folder attribute) CONTENT_INFO_TYPE (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Library attribute) ContentInfo (class in bioblend.galaxy.objects.wrappers) convert_input_map() (bioblend.galaxy.objects.wrappers.Workflow method) copy_from_dataset() (bioblend.galaxy.libraries.LibraryClient method) (bioblend.galaxy.objects.wrappers.Library method) create() (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) create_dataset_collection() (bioblend.galaxy.histories.HistoryClient method) create_folder() (bioblend.galaxy.libraries.LibraryClient method) (bioblend.galaxy.objects.wrappers.Library method)

create_form() (bioblend.galaxy.forms.FormsClient method) create_group() (bioblend.galaxy.groups.GroupsClient method) create_history() (bioblend.galaxy.histories.HistoryClient method) create_history_tag() (bioblend.galaxy.histories.HistoryClient method) create_library() (bioblend.galaxy.libraries.LibraryClient method) create_local_user() (bioblend.galaxy.users.UserClient method) create_remote_user() (bioblend.galaxy.users.UserClient method) create_repository() (bioblend.toolshed.repositories.ToolShedClient method) create_user() (bioblend.galaxy.users.UserClient method) create_user_apikey() (bioblend.galaxy.users.UserClient method)

D

data_input_ids (bioblend.galaxy.objects.wrappers.Workflow attribute) Dataset (class in bioblend.galaxy.objects.wrappers) dataset_ids (bioblend.galaxy.objects.wrappers.DatasetContainer attribute) DatasetClient (class in bioblend.galaxy.datasets) DatasetContainer (class in bioblend.galaxy.objects.wrappers) DatasetStateException DatasetTimeoutException DatatypesClient (class in bioblend.galaxy.datatypes) delete() (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method) (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation method) (bioblend.galaxy.objects.wrappers.Library method) (bioblend.galaxy.objects.wrappers.LibraryDataset method) (bioblend.galaxy.objects.wrappers.Workflow method) delete_data_table() (bioblend.galaxy.tool_data.ToolDataClient method) delete_dataset() (bioblend.galaxy.histories.HistoryClient method) delete_dataset_collection() (bioblend.galaxy.histories.HistoryClient method)

delete_folder() (bioblend.galaxy.folders.FoldersClient method) delete_group_role() (bioblend.galaxy.groups.GroupsClient method) delete_group_user() (bioblend.galaxy.groups.GroupsClient method) delete_history() (bioblend.galaxy.histories.HistoryClient method) delete_library() (bioblend.galaxy.libraries.LibraryClient method) delete_library_dataset() (bioblend.galaxy.libraries.LibraryClient method) delete_workflow() (bioblend.galaxy.workflows.WorkflowClient method) download() (bioblend.galaxy.objects.wrappers.Dataset method) (bioblend.galaxy.objects.wrappers.History method) download_dataset() (bioblend.galaxy.datasets.DatasetClient method) (bioblend.galaxy.histories.HistoryClient method) download_history() (bioblend.galaxy.histories.HistoryClient method) DS_TYPE (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Library attribute)

E

emit() (bioblend.NullHandler method) export() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.objects.wrappers.Workflow method) export_history() (bioblend.galaxy.histories.HistoryClient method)

export_workflow_json() (bioblend.galaxy.workflows.WorkflowClient method) export_workflow_to_local_path() (bioblend.galaxy.workflows.WorkflowClient method)

F

Folder (class in bioblend.galaxy.objects.wrappers) folder_ids (bioblend.galaxy.objects.wrappers.Library attribute) FoldersClient (class in bioblend.galaxy.folders)

FormsClient (class in bioblend.galaxy.forms) from_json() (bioblend.galaxy.objects.wrappers.Wrapper class method) FTPFilesClient (class in bioblend.galaxy.ftpfiles)

G

GalaxyInstance (class in bioblend.galaxy) (class in bioblend.galaxy.objects.galaxy_instance) GenomeClient (class in bioblend.galaxy.genomes) get() (bioblend.config.Config method) (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) (bioblend.galaxy.objects.client.ObjToolClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method) get_categories() (bioblend.toolshed.repositories.ToolShedClient method) get_contents() (bioblend.galaxy.objects.wrappers.Dataset method) get_current_history() (bioblend.galaxy.histories.HistoryClient method) get_current_user() (bioblend.galaxy.users.UserClient method) get_data_tables() (bioblend.galaxy.tool_data.ToolDataClient method) get_dataset() (bioblend.galaxy.objects.wrappers.DatasetContainer method) get_datasets() (bioblend.galaxy.objects.wrappers.DatasetContainer method) get_datatypes() (bioblend.galaxy.datatypes.DatatypesClient method) get_folder() (bioblend.galaxy.objects.wrappers.Library method) get_folders() (bioblend.galaxy.libraries.LibraryClient method) get_forms() (bioblend.galaxy.forms.FormsClient method) get_ftp_files() (bioblend.galaxy.ftpfiles.FTPFilesClient method) get_genomes() (bioblend.galaxy.genomes.GenomeClient method) get_group_roles() (bioblend.galaxy.groups.GroupsClient method) get_group_users() (bioblend.galaxy.groups.GroupsClient method) get_groups() (bioblend.galaxy.groups.GroupsClient method) get_histories() (bioblend.galaxy.histories.HistoryClient method) get_jobs() (bioblend.galaxy.jobs.JobsClient method) get_libraries() (bioblend.galaxy.libraries.LibraryClient method) get_library_permissions() (bioblend.galaxy.libraries.LibraryClient method) get_most_recently_used_history() (bioblend.galaxy.histories.HistoryClient method)

get_ordered_installable_revisions() (bioblend.toolshed.repositories.ToolShedClient method) get_previews() (bioblend.galaxy.objects.client.ObjClient method) (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) (bioblend.galaxy.objects.client.ObjToolClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method) get_quotas() (bioblend.galaxy.quotas.QuotaClient method) get_repositories() (bioblend.galaxy.toolshed.ToolShedClient method) (bioblend.toolshed.repositories.ToolShedClient method) get_repository_revision_install_info() (bioblend.toolshed.repositories.ToolShedClient method) get_retry_delay (bioblend.galaxy.GalaxyInstance attribute) get_roles() (bioblend.galaxy.roles.RolesClient method) get_sniffers() (bioblend.galaxy.datatypes.DatatypesClient method) get_state() (bioblend.galaxy.jobs.JobsClient method) get_status() (bioblend.galaxy.histories.HistoryClient method) get_stream() (bioblend.galaxy.objects.wrappers.Dataset method) get_tool_panel() (bioblend.galaxy.tools.ToolClient method) get_tools() (bioblend.galaxy.tools.ToolClient method) get_users() (bioblend.galaxy.users.UserClient method) get_value() (bioblend.config.Config method) get_version() (in module bioblend) get_visualizations() (bioblend.galaxy.visual.VisualClient method) get_workflow_inputs() (bioblend.galaxy.workflows.WorkflowClient method) get_workflows() (bioblend.galaxy.workflows.WorkflowClient method) getbool() (bioblend.config.Config method) getfloat() (bioblend.config.Config method) getint() (bioblend.config.Config method) gi_module (bioblend.galaxy.objects.wrappers.Folder attribute) (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.HistoryContentInfo attribute) (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute) (bioblend.galaxy.objects.wrappers.HistoryPreview attribute) (bioblend.galaxy.objects.wrappers.Library attribute) (bioblend.galaxy.objects.wrappers.LibraryContentInfo attribute) (bioblend.galaxy.objects.wrappers.LibraryPreview attribute) (bioblend.galaxy.objects.wrappers.Step attribute) (bioblend.galaxy.objects.wrappers.Tool attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute) (bioblend.galaxy.objects.wrappers.WorkflowPreview attribute) (bioblend.galaxy.objects.wrappers.Wrapper attribute) GroupsClient (class in bioblend.galaxy.groups)

H

histories (bioblend.galaxy.objects.galaxy_instance.GalaxyInstance attribute) History (class in bioblend.galaxy.objects.wrappers) HistoryClient (class in bioblend.galaxy.histories)

HistoryContentInfo (class in bioblend.galaxy.objects.wrappers) HistoryDatasetAssociation (class in bioblend.galaxy.objects.wrappers) HistoryPreview (class in bioblend.galaxy.objects.wrappers)

I

import_dataset() (bioblend.galaxy.objects.wrappers.History method) import_new() (bioblend.galaxy.objects.client.ObjWorkflowClient method) import_shared() (bioblend.galaxy.objects.client.ObjWorkflowClient method) import_shared_workflow() (bioblend.galaxy.workflows.WorkflowClient method) import_workflow_from_local_path() (bioblend.galaxy.workflows.WorkflowClient method) import_workflow_json() (bioblend.galaxy.workflows.WorkflowClient method)

init_logging() (in module bioblend) input_labels (bioblend.galaxy.objects.wrappers.Workflow attribute) install_genome() (bioblend.galaxy.genomes.GenomeClient method) install_repository_revision() (bioblend.galaxy.toolshed.ToolShedClient method) is_mapped (bioblend.galaxy.objects.wrappers.Wrapper attribute) is_runnable (bioblend.galaxy.objects.wrappers.Workflow attribute)

J

JobsClient (class in bioblend.galaxy.jobs)

L

libraries (bioblend.galaxy.objects.galaxy_instance.GalaxyInstance attribute) Library (class in bioblend.galaxy.objects.wrappers) LibraryClient (class in bioblend.galaxy.libraries) LibraryContentInfo (class in bioblend.galaxy.objects.wrappers)

LibraryDataset (class in bioblend.galaxy.objects.wrappers) LibraryDatasetDatasetAssociation (class in bioblend.galaxy.objects.wrappers) LibraryPreview (class in bioblend.galaxy.objects.wrappers) list() (bioblend.galaxy.objects.client.ObjHistoryClient method) (bioblend.galaxy.objects.client.ObjLibraryClient method) (bioblend.galaxy.objects.client.ObjToolClient method) (bioblend.galaxy.objects.client.ObjWorkflowClient method)

M

max_get_attempts (bioblend.galaxy.GalaxyInstance attribute)

N

NullHandler (class in bioblend)

O

ObjClient (class in bioblend.galaxy.objects.client) ObjDatasetClient (class in bioblend.galaxy.objects.client) ObjHistoryClient (class in bioblend.galaxy.objects.client)

ObjLibraryClient (class in bioblend.galaxy.objects.client) ObjToolClient (class in bioblend.galaxy.objects.client) ObjWorkflowClient (class in bioblend.galaxy.objects.client)

P

parent (bioblend.galaxy.objects.wrappers.Folder attribute) (bioblend.galaxy.objects.wrappers.Wrapper attribute) paste_content() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.tools.ToolClient method) peek() (bioblend.galaxy.objects.wrappers.Dataset method) POLLING_INTERVAL (bioblend.galaxy.objects.wrappers.Dataset attribute) (bioblend.galaxy.objects.wrappers.Tool attribute) (bioblend.galaxy.objects.wrappers.Workflow attribute)

Preview (class in bioblend.galaxy.objects.wrappers) preview() (bioblend.galaxy.objects.wrappers.DatasetContainer method) (bioblend.galaxy.objects.wrappers.Workflow method) put_url() (bioblend.galaxy.tools.ToolClient method)

Q

QuotaClient (class in bioblend.galaxy.quotas)

R

refresh() (bioblend.galaxy.objects.wrappers.Dataset method) (bioblend.galaxy.objects.wrappers.DatasetContainer method) (bioblend.galaxy.objects.wrappers.Folder method) repository_revisions() (bioblend.toolshed.repositories.ToolShedClient method) RolesClient (class in bioblend.galaxy.roles) root_folder (bioblend.galaxy.objects.wrappers.Library attribute)

run() (bioblend.galaxy.objects.wrappers.Tool method) (bioblend.galaxy.objects.wrappers.Workflow method) run_tool() (bioblend.galaxy.tools.ToolClient method) run_workflow() (bioblend.galaxy.workflows.WorkflowClient method)

S

search_jobs() (bioblend.galaxy.jobs.JobsClient method) set_file_logger() (in module bioblend) set_library_permissions() (bioblend.galaxy.libraries.LibraryClient method) set_stream_logger() (in module bioblend) show_data_table() (bioblend.galaxy.tool_data.ToolDataClient method) show_dataset() (bioblend.galaxy.datasets.DatasetClient method) (bioblend.galaxy.histories.HistoryClient method) (bioblend.galaxy.libraries.LibraryClient method) show_dataset_collection() (bioblend.galaxy.histories.HistoryClient method) show_dataset_provenance() (bioblend.galaxy.histories.HistoryClient method) show_folder() (bioblend.galaxy.folders.FoldersClient method) (bioblend.galaxy.libraries.LibraryClient method) show_form() (bioblend.galaxy.forms.FormsClient method) show_genome() (bioblend.galaxy.genomes.GenomeClient method) show_group() (bioblend.galaxy.groups.GroupsClient method) show_history() (bioblend.galaxy.histories.HistoryClient method) show_job() (bioblend.galaxy.jobs.JobsClient method) show_library() (bioblend.galaxy.libraries.LibraryClient method)

show_matching_datasets() (bioblend.galaxy.histories.HistoryClient method) show_quota() (bioblend.galaxy.quotas.QuotaClient method) show_repository() (bioblend.galaxy.toolshed.ToolShedClient method) (bioblend.toolshed.repositories.ToolShedClient method) show_repository_revision() (bioblend.toolshed.repositories.ToolShedClient method) show_role() (bioblend.galaxy.roles.RolesClient method) show_stderr() (bioblend.galaxy.datasets.DatasetClient method) show_stdout() (bioblend.galaxy.datasets.DatasetClient method) show_tool() (bioblend.galaxy.tools.ToolClient method) show_user() (bioblend.galaxy.users.UserClient method) show_visualization() (bioblend.galaxy.visual.VisualClient method) show_workflow() (bioblend.galaxy.workflows.WorkflowClient method) sorted_step_ids() (bioblend.galaxy.objects.wrappers.Workflow method) SRC (bioblend.galaxy.objects.wrappers.HistoryDatasetAssociation attribute) (bioblend.galaxy.objects.wrappers.LibraryDataset attribute) (bioblend.galaxy.objects.wrappers.LibraryDatasetDatasetAssociation attribute) Step (class in bioblend.galaxy.objects.wrappers)

T

to_json() (bioblend.galaxy.objects.wrappers.Wrapper method) Tool (class in bioblend.galaxy.objects.wrappers) tool_ids (bioblend.galaxy.objects.wrappers.Workflow attribute) ToolClient (class in bioblend.galaxy.tools) ToolDataClient (class in bioblend.galaxy.tool_data)

tools (bioblend.galaxy.objects.galaxy_instance.GalaxyInstance attribute) ToolShedClient (class in bioblend.galaxy.toolshed) (class in bioblend.toolshed.repositories) ToolShedInstance (class in bioblend.toolshed) touch() (bioblend.galaxy.objects.wrappers.Wrapper method)

U

undelete_history() (bioblend.galaxy.histories.HistoryClient method) unmap() (bioblend.galaxy.objects.wrappers.Wrapper method) update() (bioblend.galaxy.objects.wrappers.History method) update_dataset() (bioblend.galaxy.histories.HistoryClient method) update_dataset_collection() (bioblend.galaxy.histories.HistoryClient method) update_group() (bioblend.galaxy.groups.GroupsClient method) update_history() (bioblend.galaxy.histories.HistoryClient method) update_repository() (bioblend.toolshed.repositories.ToolShedClient method) upload_data() (bioblend.galaxy.objects.wrappers.Library method) upload_dataset() (bioblend.galaxy.objects.wrappers.History method) upload_dataset_from_library() (bioblend.galaxy.histories.HistoryClient method)

upload_file() (bioblend.galaxy.objects.wrappers.History method) (bioblend.galaxy.tools.ToolClient method) upload_file_contents() (bioblend.galaxy.libraries.LibraryClient method) upload_file_from_local_path() (bioblend.galaxy.libraries.LibraryClient method) upload_file_from_server() (bioblend.galaxy.libraries.LibraryClient method) upload_file_from_url() (bioblend.galaxy.libraries.LibraryClient method) upload_from_galaxy_filesystem() (bioblend.galaxy.libraries.LibraryClient method) upload_from_galaxy_fs() (bioblend.galaxy.objects.wrappers.Library method) upload_from_local() (bioblend.galaxy.objects.wrappers.Library method) upload_from_url() (bioblend.galaxy.objects.wrappers.Library method) UserClient (class in bioblend.galaxy.users)

V

VisualClient (class in bioblend.galaxy.visual)

W

wait() (bioblend.galaxy.objects.wrappers.Dataset method) Workflow (class in bioblend.galaxy.objects.wrappers) WorkflowClient (class in bioblend.galaxy.workflows)

WorkflowPreview (class in bioblend.galaxy.objects.wrappers) workflows (bioblend.galaxy.objects.galaxy_instance.GalaxyInstance attribute) Wrapper (class in bioblend.galaxy.objects.wrappers)