Index

_

__init__() (bioblend.galaxy.GalaxyInstance method)

A

add_nodes() (bioblend.cloudman.CloudManInstance method) adjust_autoscaling() (bioblend.cloudman.CloudManInstance method)

API_MODULE (bioblend.galaxy.objects.wrappers.History attribute) (bioblend.galaxy.objects.wrappers.Library attribute) autoscaling_enabled() (bioblend.cloudman.CloudManInstance method)

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.cloudman (module) bioblend.config (module) bioblend.galaxy.datasets (module) bioblend.galaxy.genomes (module) bioblend.galaxy.histories (module) bioblend.galaxy.libraries (module) bioblend.galaxy.objects.client (module)

bioblend.galaxy.objects.wrappers (module) bioblend.galaxy.quotas (module) bioblend.galaxy.tools (module) bioblend.galaxy.toolshed (module) bioblend.galaxy.users (module) bioblend.galaxy.visual (module) bioblend.galaxy.workflows (module) block_until_vm_ready() (in module bioblend.cloudman)

C

clone() (bioblend.galaxy.objects.wrappers.Wrapper method) cloudman_url (bioblend.cloudman.CloudManInstance attribute) CloudManConfig (class in bioblend.cloudman) CloudManConfig.CustomTypeEncoder (class in bioblend.cloudman) CloudManInstance (class in bioblend.cloudman) CloudManLauncher (class in bioblend.cloudman.launch) Config (class in bioblend.config) connect_ec2() (bioblend.cloudman.launch.CloudManLauncher method) connect_s3() (bioblend.cloudman.launch.CloudManLauncher method) container_id (bioblend.galaxy.objects.wrappers.Dataset 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_cm_security_group() (bioblend.cloudman.launch.CloudManLauncher method) create_dataset_collection() (bioblend.galaxy.histories.HistoryClient method) create_folder() (bioblend.galaxy.libraries.LibraryClient method) (bioblend.galaxy.objects.wrappers.Library method) create_history() (bioblend.galaxy.histories.HistoryClient method) create_history_tag() (bioblend.galaxy.histories.HistoryClient method) create_key_pair() (bioblend.cloudman.launch.CloudManLauncher 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_user() (bioblend.galaxy.users.UserClient method) create_user_apikey() (bioblend.galaxy.users.UserClient method) CustomTypeDecoder() (bioblend.cloudman.CloudManConfig static method)

D

dag (bioblend.galaxy.objects.wrappers.Workflow attribute) 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 default() (bioblend.cloudman.CloudManConfig.CustomTypeEncoder method) 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_dataset() (bioblend.galaxy.histories.HistoryClient method)

delete_dataset_collection() (bioblend.galaxy.histories.HistoryClient 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) disable_autoscaling() (bioblend.cloudman.CloudManInstance 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) enable_autoscaling() (bioblend.cloudman.CloudManInstance 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

find_placements() (bioblend.cloudman.launch.CloudManLauncher method) Folder (class in bioblend.galaxy.objects.wrappers)

folder_ids (bioblend.galaxy.objects.wrappers.Library attribute) from_json() (bioblend.galaxy.objects.wrappers.Wrapper class method)

G

galaxy_url (bioblend.cloudman.CloudManInstance attribute) GalaxyInstance (class in bioblend.galaxy) (class in bioblend.galaxy.objects.galaxy_instance) GenericVMInstance (class in bioblend.cloudman) 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_cloudman_version() (bioblend.cloudman.CloudManInstance method) get_cluster_pd() (bioblend.cloudman.launch.CloudManLauncher method) get_cluster_size() (bioblend.cloudman.CloudManInstance method) get_cluster_type() (bioblend.cloudman.CloudManInstance method) get_clusters_pd() (bioblend.cloudman.launch.CloudManLauncher 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_dataset() (bioblend.galaxy.objects.wrappers.DatasetContainer method) get_datasets() (bioblend.galaxy.objects.wrappers.DatasetContainer method) get_folder() (bioblend.galaxy.objects.wrappers.Library method) get_folders() (bioblend.galaxy.libraries.LibraryClient method) get_galaxy_state() (bioblend.cloudman.CloudManInstance method) get_genomes() (bioblend.galaxy.genomes.GenomeClient method) get_histories() (bioblend.galaxy.histories.HistoryClient method) get_libraries() (bioblend.galaxy.libraries.LibraryClient method) get_machine_status() (bioblend.cloudman.GenericVMInstance method) get_master_id() (bioblend.cloudman.CloudManInstance method)

get_master_ip() (bioblend.cloudman.CloudManInstance method) get_most_recently_used_history() (bioblend.galaxy.histories.HistoryClient method) get_nodes() (bioblend.cloudman.CloudManInstance 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) get_retry_delay (bioblend.galaxy.GalaxyInstance attribute) get_static_state() (bioblend.cloudman.CloudManInstance method) get_status() (bioblend.cloudman.CloudManInstance method) (bioblend.cloudman.launch.CloudManLauncher method) (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)

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) initialize() (bioblend.cloudman.CloudManInstance method)

input_labels (bioblend.galaxy.objects.wrappers.Workflow attribute) install_genome() (bioblend.galaxy.genomes.GenomeClient method) install_repository_revision() (bioblend.galaxy.toolshed.ToolShedClient method) instance_id (bioblend.cloudman.GenericVMInstance attribute) inv_dag (bioblend.galaxy.objects.wrappers.Workflow attribute) is_mapped (bioblend.galaxy.objects.wrappers.Wrapper attribute) is_master_execution_host() (bioblend.cloudman.CloudManInstance method) is_runnable (bioblend.galaxy.objects.wrappers.Workflow attribute)

K

key_pair_material (bioblend.cloudman.GenericVMInstance attribute)

key_pair_name (bioblend.cloudman.GenericVMInstance attribute)

L

launch() (bioblend.cloudman.launch.CloudManLauncher method) launch_instance() (bioblend.cloudman.CloudManInstance static method) 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) load_config() (bioblend.cloudman.CloudManConfig static 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

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

reboot_node() (bioblend.cloudman.CloudManInstance method) refresh() (bioblend.galaxy.objects.wrappers.Dataset method) (bioblend.galaxy.objects.wrappers.DatasetContainer method) remove_node() (bioblend.cloudman.CloudManInstance method) remove_nodes() (bioblend.cloudman.CloudManInstance method)

rule_exists() (bioblend.cloudman.launch.CloudManLauncher method) 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

save_config() (bioblend.cloudman.CloudManConfig method) set_connection_parameters() (bioblend.cloudman.CloudManConfig method) set_extra_parameters() (bioblend.cloudman.CloudManConfig method) set_file_logger() (in module bioblend) set_library_permissions() (bioblend.galaxy.libraries.LibraryClient method) set_master_as_execution_host() (bioblend.cloudman.CloudManInstance method) set_post_launch_parameters() (bioblend.cloudman.CloudManConfig method) set_pre_launch_parameters() (bioblend.cloudman.CloudManConfig method) set_stream_logger() (in module bioblend) 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.libraries.LibraryClient method) show_genome() (bioblend.galaxy.genomes.GenomeClient method)

show_history() (bioblend.galaxy.histories.HistoryClient 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) 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

terminate() (bioblend.cloudman.CloudManInstance method) 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) tools (bioblend.galaxy.objects.galaxy_instance.GalaxyInstance attribute) ToolShedClient (class in bioblend.galaxy.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.cloudman.CloudManInstance method) (bioblend.galaxy.objects.wrappers.History method) update_dataset() (bioblend.galaxy.histories.HistoryClient method) update_dataset_collection() (bioblend.galaxy.histories.HistoryClient method) update_history() (bioblend.galaxy.histories.HistoryClient 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

validate() (bioblend.cloudman.CloudManConfig method) VisualClient (class in bioblend.galaxy.visual)

VMLaunchException

W

wait() (bioblend.galaxy.objects.wrappers.Dataset method) wait_until_instance_ready() (bioblend.cloudman.GenericVMInstance 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)