Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
galaxy.tool_shed package¶
Subpackages¶
- galaxy.tool_shed.galaxy_install package
- Subpackages
- Submodules
- galaxy.tool_shed.galaxy_install.install_manager module
get_install_info_from_tool_shed()
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
RepositoryProtocol
BaseMetadataGenerator
BaseMetadataGenerator.app
BaseMetadataGenerator.repository
BaseMetadataGenerator.invalid_file_tups
BaseMetadataGenerator.changeset_revision
BaseMetadataGenerator.repository_clone_url
BaseMetadataGenerator.shed_config_dict
BaseMetadataGenerator.metadata_dict
BaseMetadataGenerator.relative_install_dir
BaseMetadataGenerator.repository_files_dir
BaseMetadataGenerator.persist
BaseMetadataGenerator.initial_metadata_dict()
BaseMetadataGenerator.handle_repository_elem()
BaseMetadataGenerator.generate_environment_dependency_metadata()
BaseMetadataGenerator.generate_metadata_for_changeset_revision()
BaseMetadataGenerator.generate_package_dependency_metadata()
BaseMetadataGenerator.generate_repository_dependency_metadata()
BaseMetadataGenerator.generate_tool_metadata()
BaseMetadataGenerator.generate_tool_dependency_metadata()
BaseMetadataGenerator.get_invalid_file_tups()
BaseMetadataGenerator.get_metadata_dict()
BaseMetadataGenerator.get_relative_path_to_repository_file()
BaseMetadataGenerator.get_sample_files_from_disk()
BaseMetadataGenerator.set_changeset_revision()
BaseMetadataGenerator.set_relative_install_dir()
BaseMetadataGenerator.set_repository_files_dir()
GalaxyMetadataGenerator
- galaxy.tool_shed.tools package
- Submodules
- galaxy.tool_shed.tools.data_table_manager module
ToolDataTableManager
ShedToolDataTableManager
ShedToolDataTableManager.__init__()
ShedToolDataTableManager.app
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