Ephemeris
latest
Introduction
Installation
Commands
Code of conduct
Contributing
Project Governance
Release Checklist
History
Ephemeris
Index
Edit on GitHub
Index
A
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
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
emit() (ephemeris.ephemeris_log.ProgressConsoleHandler method)
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_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)
get_workflow_dictionary() (in module ephemeris.generate_tool_list_from_ga_workflow_files)
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
on_same_line (ephemeris.ephemeris_log.ProgressConsoleHandler attribute)
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)
ProgressConsoleHandler (class in ephemeris.ephemeris_log)
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)
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)
Read the Docs
v: latest
Versions
master
latest
stable
Downloads
On Read the Docs
Project Home
Builds