Index

_

__init__() (bioblend.galaxy.GalaxyInstance method)

A

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

autoscaling_enabled() (bioblend.cloudman.CloudManInstance method)

B

bioblend (module) bioblend.cloudman (module) bioblend.config (module) bioblend.galaxy.datasets (module) bioblend.galaxy.histories (module)

bioblend.galaxy.libraries (module) bioblend.galaxy.users (module) bioblend.galaxy.workflows (module) block_till_vm_ready() (in module bioblend.cloudman)

C

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)

create_cm_security_group() (bioblend.cloudman.launch.CloudManLauncher method) create_folder() (bioblend.galaxy.libraries.LibraryClient method) create_history() (bioblend.galaxy.histories.HistoryClient method) create_key_pair() (bioblend.cloudman.launch.CloudManLauncher method) create_library() (bioblend.galaxy.libraries.LibraryClient method) create_user() (bioblend.galaxy.users.UserClient method) CustomTypeDecoder() (bioblend.cloudman.CloudManConfig static method)

D

DatasetClient (class in bioblend.galaxy.datasets) DatasetStateException DatasetTimeoutException default() (bioblend.cloudman.CloudManConfig.CustomTypeEncoder method)

delete_history() (bioblend.galaxy.histories.HistoryClient method) disable_autoscaling() (bioblend.cloudman.CloudManInstance method) download_dataset() (bioblend.galaxy.datasets.DatasetClient method) (bioblend.galaxy.histories.HistoryClient method)

E

emit() (bioblend.NullHandler method) enable_autoscaling() (bioblend.cloudman.CloudManInstance method)

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

G

galaxy_url (bioblend.cloudman.CloudManInstance attribute) GalaxyInstance (class in bioblend.galaxy) GenericVMInstance (class in bioblend.cloudman) get() (bioblend.config.Config method) get_cluster_size() (bioblend.cloudman.CloudManInstance method) get_cluster_type() (bioblend.cloudman.CloudManInstance method) get_current_history() (bioblend.galaxy.histories.HistoryClient method) get_current_user() (bioblend.galaxy.users.UserClient method) get_galaxy_state() (bioblend.cloudman.CloudManInstance 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_nodes() (bioblend.cloudman.CloudManInstance method) get_static_state() (bioblend.cloudman.CloudManInstance method) get_status() (bioblend.cloudman.CloudManInstance method) (bioblend.cloudman.launch.CloudManLauncher method) (bioblend.galaxy.histories.HistoryClient method) get_users() (bioblend.galaxy.users.UserClient method) get_value() (bioblend.config.Config method) get_version() (in module bioblend) get_workflows() (bioblend.galaxy.workflows.WorkflowClient method) getbool() (bioblend.config.Config method) getfloat() (bioblend.config.Config method) getint() (bioblend.config.Config method)

H

HistoryClient (class in bioblend.galaxy.histories)

I

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) instance_id (bioblend.cloudman.GenericVMInstance 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)

LibraryClient (class in bioblend.galaxy.libraries) load_config() (bioblend.cloudman.CloudManConfig static method)

M

make_delete_request() (bioblend.galaxy.GalaxyInstance method) make_get_request() (bioblend.galaxy.GalaxyInstance method)

make_post_request() (bioblend.galaxy.GalaxyInstance method)

N

NullHandler (class in bioblend)

R

reboot_node() (bioblend.cloudman.CloudManInstance method) remove_node() (bioblend.cloudman.CloudManInstance method) remove_nodes() (bioblend.cloudman.CloudManInstance method)

rule_exists() (bioblend.cloudman.launch.CloudManLauncher 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_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) show_history() (bioblend.galaxy.histories.HistoryClient method) show_library() (bioblend.galaxy.libraries.LibraryClient method) show_user() (bioblend.galaxy.users.UserClient method) show_workflow() (bioblend.galaxy.workflows.WorkflowClient method)

T

terminate() (bioblend.cloudman.CloudManInstance method)

U

undelete_history() (bioblend.galaxy.histories.HistoryClient method) update() (bioblend.cloudman.CloudManInstance method) upload_dataset_from_library() (bioblend.galaxy.histories.HistoryClient 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) UserClient (class in bioblend.galaxy.users)

V

validate() (bioblend.cloudman.CloudManConfig method)

VMLaunchException

W

wait_till_instance_ready() (bioblend.cloudman.GenericVMInstance method)

WorkflowClient (class in bioblend.galaxy.workflows)