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galaxy.tool_shed package

Subpackages

• galaxy.tool_shed.galaxy_install package
  • Subpackages
    • galaxy.tool_shed.galaxy_install.datatypes package
      • Submodules
      • galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager module
    • galaxy.tool_shed.galaxy_install.metadata package
      • Submodules
      • galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager module
    • galaxy.tool_shed.galaxy_install.repository_dependencies package
      • Submodules
      • galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager module
    • galaxy.tool_shed.galaxy_install.tools package
      • Submodules
      • galaxy.tool_shed.galaxy_install.tools.data_manager module
      • galaxy.tool_shed.galaxy_install.tools.tool_panel_manager module
  • 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
      • RepositoriesInstalledException.__init__()
  • 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
    • UpdateToChangeset
      • UpdateToChangeset.changeset_revision
      • UpdateToChangeset.ctx_rev
    • UpdateRepositoryManager
      • UpdateRepositoryManager.__init__()
      • UpdateRepositoryManager.get_update_to_changeset_revision_and_ctx_rev()
      • UpdateRepositoryManager.shutdown()
      • UpdateRepositoryManager.update_repository_record()
• galaxy.tool_shed.metadata package
  • Submodules
  • galaxy.tool_shed.metadata.metadata_generator module
    • RepositoryMetadataToolDict
      • RepositoryMetadataToolDict.id
      • RepositoryMetadataToolDict.guid
      • RepositoryMetadataToolDict.name
      • RepositoryMetadataToolDict.version
      • RepositoryMetadataToolDict.profile
      • RepositoryMetadataToolDict.description
      • RepositoryMetadataToolDict.version_string_cmd
      • RepositoryMetadataToolDict.tool_config
      • RepositoryMetadataToolDict.tool_type
      • RepositoryMetadataToolDict.requirements
      • RepositoryMetadataToolDict.tests
      • RepositoryMetadataToolDict.add_to_tool_panel
    • RepositoryProtocol
      • RepositoryProtocol.name
      • RepositoryProtocol.id
      • RepositoryProtocol.repo_path()
      • RepositoryProtocol.__init__()
    • 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
      • GalaxyMetadataGenerator.__init__()
      • GalaxyMetadataGenerator.app
      • GalaxyMetadataGenerator.repository
      • GalaxyMetadataGenerator.initial_metadata_dict()
      • GalaxyMetadataGenerator.set_repository()
      • GalaxyMetadataGenerator.handle_repository_elem()
• 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
    • ToolValidator
      • ToolValidator.__init__()
      • ToolValidator.check_tool_input_params()
      • ToolValidator.load_tool_from_config()
• galaxy.tool_shed.util package
  • Submodules
  • galaxy.tool_shed.util.basic_util module
    • get_file_type_str()
    • move_file()
    • remove_dir()
    • size_string()
    • stringify()
    • strip_path()
    • to_html_string()
  • galaxy.tool_shed.util.container_util module
    • generate_repository_dependencies_key_for_repository()
    • get_components_from_key()
  • galaxy.tool_shed.util.hg_util module
    • clone_repository()
    • copy_file_from_manifest()
    • get_changectx_for_changeset()
    • get_config_from_disk()
    • get_ctx_file_path_from_manifest()
    • get_file_context_from_ctx()
    • pull_repository()
    • reversed_lower_upper_bounded_changelog()
    • reversed_upper_bounded_changelog()
    • update_repository()
  • galaxy.tool_shed.util.metadata_util module
    • get_updated_changeset_revisions_from_tool_shed()
  • 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
    • can_eliminate_repository_dependency()
    • clean_dependency_relationships()
    • generate_tool_guid()
    • get_ctx_rev()
    • get_next_prior_import_or_install_required_dict_entry()
    • get_tool_panel_config_tool_path_install_dir()
    • get_user()
    • have_shed_tool_conf_for_install()
    • set_image_paths()
  • galaxy.tool_shed.util.tool_dependency_util module
    • get_tool_dependency()
    • get_tool_dependency_by_name_type_repository()
    • get_tool_dependency_by_name_version_type()
    • get_tool_dependency_by_name_version_type_repository()
    • get_tool_dependency_ids()
    • parse_package_elem()
    • remove_tool_dependency()
    • remove_tool_dependency_installation_directory()
  • galaxy.tool_shed.util.tool_util module
    • build_shed_tool_conf_select_field()
    • build_tool_panel_section_select_field()
    • copy_sample_file()
    • copy_sample_files()
    • generate_message_for_invalid_tools()
    • handle_missing_index_file()
    • panel_entry_per_tool()

Submodules

galaxy.tool_shed.repository_type module

galaxy.tool_shed.tool_shed_registry module