Index

A

add_arguments() (ephemeris.common_parser.HideUnderscoresHelpFormatter method) add_log_file_argument() (in module ephemeris.common_parser) add_verbosity_argument() (in module ephemeris.common_parser)

already_installed_repos (ephemeris.shed_tools.FilterResults attribute) args_to_repos() (in module ephemeris.shed_tools) ArgumentDefaultsHideUnderscoresHelpFormatter (class in ephemeris.common_parser)

C

cancel() (ephemeris.sleep.SleepCondition method) changeset_revision (ephemeris.shed_tools.InstallRepoDict attribute) check_galaxy_version() (in module ephemeris.get_tool_list_from_galaxy)

check_url() (in module ephemeris) complete_repo_information() (in module ephemeris.shed_tools_methods) create_batch_api() (in module ephemeris.setup_data_libraries) create_legacy() (in module ephemeris.setup_data_libraries)

D

data_table_entry_exists() (ephemeris.run_data_managers.DataManagers method) DataManagers (class in ephemeris.run_data_managers)

disable_external_library_logging() (in module ephemeris.ephemeris_log) dm_is_fetcher() (ephemeris.run_data_managers.DataManagers method) dump_to_yaml_file() (in module ephemeris)

E

ephemeris module ephemeris.common_parser module ephemeris.ephemeris_log module ephemeris.generate_tool_list_from_ga_workflow_files module, [1] ephemeris.get_tool_list_from_galaxy module, [1] ephemeris.install_tool_deps module, [1] ephemeris.run_data_managers module, [1] ephemeris.set_library_permissions module

ephemeris.setup_data_libraries module, [1] ephemeris.shed_tools module, [1] ephemeris.shed_tools_args module ephemeris.shed_tools_methods module ephemeris.sleep module, [1] ephemeris.workflow_install module, [1] errored_repositories (ephemeris.shed_tools.InstallResults attribute) extract_tool_shed_repositories_from_workflow_dict() (in module ephemeris.generate_tool_list_from_ga_workflow_files)

F

filter_installed_repos() (ephemeris.shed_tools.InstallRepositoryManager method) filter_section_name_or_id_or_changeset() (ephemeris.get_tool_list_from_galaxy.GiToToolYaml method)

FilterResults (class in ephemeris.shed_tools) flatten_repo_info() (in module ephemeris.shed_tools_methods) format_tool_shed_url() (in module ephemeris.shed_tools_methods)

G

galaxy_wait() (in module ephemeris.sleep) generate_repo_list_from_workflow() (in module ephemeris.generate_tool_list_from_ga_workflow_files) generate_tool_list_from_workflow() (in module ephemeris.generate_tool_list_from_ga_workflow_files) get_changeset_revisions() (in module ephemeris.shed_tools_methods) get_common_args() (in module ephemeris.common_parser) get_datasets() (in module ephemeris.set_library_permissions) get_dictionary_from_json() (in module ephemeris.generate_tool_list_from_ga_workflow_files)

get_dm_jobs() (ephemeris.run_data_managers.DataManagers method) get_first_valid_entry() (in module ephemeris.run_data_managers) get_galaxy_connection() (in module ephemeris) get_or_create_history() (in module ephemeris) get_repo_from_tool() (in module ephemeris.get_tool_list_from_galaxy) get_tool_panel() (in module ephemeris.get_tool_list_from_galaxy) get_tools() (in module ephemeris.get_tool_list_from_galaxy) GiToToolYaml (class in ephemeris.get_tool_list_from_galaxy)

H

HideUnderscoresHelpFormatter (class in ephemeris.common_parser)

I

import_workflow() (in module ephemeris.workflow_install) initiate_job_lists() (ephemeris.run_data_managers.DataManagers method) input_entries_exist_in_data_tables() (ephemeris.run_data_managers.DataManagers method) install_repositories() (ephemeris.shed_tools.InstallRepositoryManager method) install_repository_dependencies (ephemeris.shed_tools.InstallRepoDict attribute) install_repository_revision() (ephemeris.shed_tools.InstallRepositoryManager method) install_resolver_dependencies (ephemeris.shed_tools.InstallRepoDict attribute)

install_tool_dependencies (ephemeris.shed_tools.InstallRepoDict attribute) installed_repositories (ephemeris.shed_tools.InstallResults attribute) installed_repositories() (ephemeris.shed_tools.InstallRepositoryManager method) installed_tool_list (ephemeris.get_tool_list_from_galaxy.GiToToolYaml property) InstallRepoDict (class in ephemeris.shed_tools) InstallRepositoryManager (class in ephemeris.shed_tools) InstallResults (class in ephemeris.shed_tools)

L

load_yaml_file() (in module ephemeris) log_repository_install_error() (in module ephemeris.shed_tools)

log_repository_install_skip() (in module ephemeris.shed_tools) log_repository_install_start() (in module ephemeris.shed_tools) log_repository_install_success() (in module ephemeris.shed_tools)

M

main() (in module ephemeris.generate_tool_list_from_ga_workflow_files) (in module ephemeris.get_tool_list_from_galaxy) (in module ephemeris.install_tool_deps) (in module ephemeris.run_data_managers) (in module ephemeris.set_library_permissions) (in module ephemeris.setup_data_libraries) (in module ephemeris.shed_tools) (in module ephemeris.sleep) (in module ephemeris.workflow_install) merge_repository_changeset_revisions() (in module ephemeris.get_tool_list_from_galaxy) module ephemeris ephemeris.common_parser ephemeris.ephemeris_log ephemeris.generate_tool_list_from_ga_workflow_files, [1] ephemeris.get_tool_list_from_galaxy, [1] ephemeris.install_tool_deps, [1] ephemeris.run_data_managers, [1] ephemeris.set_library_permissions ephemeris.setup_data_libraries, [1] ephemeris.shed_tools, [1] ephemeris.shed_tools_args ephemeris.shed_tools_methods ephemeris.sleep, [1] ephemeris.workflow_install, [1]

N

name (ephemeris.shed_tools.InstallRepoDict attribute)

not_installed_repos (ephemeris.shed_tools.FilterResults attribute)

O

owner (ephemeris.shed_tools.InstallRepoDict attribute)

P

parse_items() (ephemeris.run_data_managers.DataManagers method)

parser() (in module ephemeris.shed_tools_args) print_yaml_tool_list() (in module ephemeris.generate_tool_list_from_ga_workflow_files)

R

RawDescriptionHideUnderscoresHelpFormatter (class in ephemeris.common_parser) reduce_tool_list() (in module ephemeris.generate_tool_list_from_ga_workflow_files)

repository_list (ephemeris.get_tool_list_from_galaxy.GiToToolYaml property) revisions (ephemeris.shed_tools.InstallRepoDict attribute) run() (ephemeris.run_data_managers.DataManagers method)

S

set_permissions() (in module ephemeris.set_library_permissions) setup_data_libraries() (in module ephemeris.setup_data_libraries)

setup_global_logger() (in module ephemeris.ephemeris_log) skipped_repositories (ephemeris.shed_tools.InstallResults attribute) SleepCondition (class in ephemeris.sleep)

T

test_tools() (ephemeris.shed_tools.InstallRepositoryManager method) the_same_repository() (in module ephemeris.get_tool_list_from_galaxy) tool_list (ephemeris.get_tool_list_from_galaxy.GiToToolYaml property) tool_panel_section_id (ephemeris.shed_tools.InstallRepoDict attribute) tool_panel_section_label (ephemeris.shed_tools.InstallRepoDict attribute)

tool_shed_url (ephemeris.shed_tools.InstallRepoDict attribute) toolbox (ephemeris.get_tool_list_from_galaxy.GiToToolYaml property) ToolInstallationException tools_for_repository() (in module ephemeris.get_tool_list_from_galaxy) translate_workflow_dictionary_to_tool_list() (in module ephemeris.generate_tool_list_from_ga_workflow_files)

U

update_repositories() (ephemeris.shed_tools.InstallRepositoryManager method)

W

wait() (in module ephemeris.run_data_managers) wait_for_install() (ephemeris.shed_tools.InstallRepositoryManager method)

walk_tools() (in module ephemeris.get_tool_list_from_galaxy) write_to_yaml() (ephemeris.get_tool_list_from_galaxy.GiToToolYaml method)