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galaxy.tool_shed package¶
Subpackages¶
- galaxy.tool_shed.galaxy_install package
- Subpackages
- Submodules
- galaxy.tool_shed.galaxy_install.install_manager module
InstallRepositoryManager
InstallRepositoryManager.__init__()
InstallRepositoryManager.app
InstallRepositoryManager.tpm
InstallRepositoryManager.handle_tool_shed_repositories()
InstallRepositoryManager.initiate_repository_installation()
InstallRepositoryManager.install()
InstallRepositoryManager.install_repositories()
InstallRepositoryManager.install_tool_shed_repository()
InstallRepositoryManager.update_tool_shed_repository()
InstallRepositoryManager.order_components_for_installation()
InstallRepositoryManager.update_tool_shed_repository_status()
RepositoriesInstalledException
- galaxy.tool_shed.galaxy_install.installed_repository_manager module
InstalledRepositoryManager
InstalledRepositoryManager.__init__()
InstalledRepositoryManager.app
InstalledRepositoryManager.installed_repository_dicts
InstalledRepositoryManager.repository_dependencies_of_installed_repositories
InstalledRepositoryManager.installed_repository_dependencies_of_installed_repositories
InstalledRepositoryManager.installed_dependent_repositories_of_installed_repositories
InstalledRepositoryManager.tool_paths
InstalledRepositoryManager.activate_repository()
InstalledRepositoryManager.add_entry_to_installed_repository_dependencies_of_installed_repositories()
InstalledRepositoryManager.add_entry_to_repository_dependencies_of_installed_repositories()
InstalledRepositoryManager.get_containing_repository_for_tool_dependency()
InstalledRepositoryManager.get_dependencies_for_repository()
InstalledRepositoryManager.get_installed_and_missing_repository_dependencies()
InstalledRepositoryManager.get_installed_and_missing_repository_dependencies_for_new_or_updated_install()
InstalledRepositoryManager.get_installed_and_missing_tool_dependencies_for_repository()
InstalledRepositoryManager.get_repository_dependency_tups_for_installed_repository()
InstalledRepositoryManager.get_repository_tuple_for_installed_repository_manager()
InstalledRepositoryManager.get_repository_install_dir()
InstalledRepositoryManager.handle_existing_tool_dependencies_that_changed_in_update()
InstalledRepositoryManager.uninstall_repository()
InstalledRepositoryManager.remove_entry_from_installed_repository_dependencies_of_installed_repositories()
InstalledRepositoryManager.remove_entry_from_repository_dependencies_of_installed_repositories()
InstalledRepositoryManager.repository_dependency_needed_only_for_compiling_tool_dependency()
InstalledRepositoryManager.set_only_if_compiling_contained_td()
InstalledRepositoryManager.set_prior_installation_required()
- galaxy.tool_shed.galaxy_install.update_repository_manager module
- galaxy.tool_shed.metadata package
- Submodules
- galaxy.tool_shed.metadata.metadata_generator module
MetadataGenerator
MetadataGenerator.__init__()
MetadataGenerator.generate_environment_dependency_metadata()
MetadataGenerator.generate_guid_for_object()
MetadataGenerator.generate_metadata_for_changeset_revision()
MetadataGenerator.generate_package_dependency_metadata()
MetadataGenerator.generate_repository_dependency_metadata()
MetadataGenerator.generate_tool_metadata()
MetadataGenerator.generate_tool_dependency_metadata()
MetadataGenerator.get_invalid_file_tups()
MetadataGenerator.get_metadata_dict()
MetadataGenerator.get_relative_path_to_repository_file()
MetadataGenerator.get_sample_files_from_disk()
MetadataGenerator.handle_repository_elem()
MetadataGenerator.set_changeset_revision()
MetadataGenerator.set_relative_install_dir()
MetadataGenerator.set_repository()
MetadataGenerator.set_repository_clone_url()
MetadataGenerator.set_repository_files_dir()
MetadataGenerator.update_repository_dependencies_metadata()
- galaxy.tool_shed.tools package
- Submodules
- galaxy.tool_shed.tools.data_table_manager module
ToolDataTableManager
ShedToolDataTableManager
ShedToolDataTableManager.__init__()
ShedToolDataTableManager.generate_repository_info_elem()
ShedToolDataTableManager.generate_repository_info_elem_from_repository()
ShedToolDataTableManager.get_tool_index_sample_files()
ShedToolDataTableManager.handle_missing_data_table_entry()
ShedToolDataTableManager.handle_sample_tool_data_table_conf_file()
ShedToolDataTableManager.get_target_install_dir()
ShedToolDataTableManager.install_tool_data_tables()
ShedToolDataTableManager.reset_tool_data_tables()
- galaxy.tool_shed.tools.tool_validator module
- galaxy.tool_shed.util package
- Submodules
- galaxy.tool_shed.util.basic_util module
- galaxy.tool_shed.util.container_util module
- galaxy.tool_shed.util.hg_util module
- galaxy.tool_shed.util.metadata_util module
- galaxy.tool_shed.util.repository_util module
check_for_updates()
create_or_update_tool_shed_repository()
extract_components_from_tuple()
generate_tool_shed_repository_install_dir()
get_absolute_path_to_file_in_repository()
get_ids_of_tool_shed_repositories_being_installed()
get_installed_repository()
get_installed_tool_shed_repository()
get_prior_import_or_install_required_dict()
get_repo_info_tuple_contents()
get_repository_admin_role_name()
get_repository_and_repository_dependencies_from_repo_info_dict()
get_repository_by_id()
get_repository_by_name()
get_repository_by_name_and_owner()
get_repository_dependency_types()
get_repository_for_dependency_relationship()
get_repository_ids_requiring_prior_import_or_install()
get_repository_owner()
get_repository_owner_from_clone_url()
get_repository_query()
get_role_by_id()
get_tool_shed_from_clone_url()
get_tool_shed_repository_by_id()
get_tool_shed_status_for_installed_repository()
is_tool_shed_client()
repository_was_previously_installed()
set_repository_attributes()
- galaxy.tool_shed.util.shed_util_common module
- galaxy.tool_shed.util.tool_dependency_util module
- galaxy.tool_shed.util.tool_util module