galaxy_install Package¶

`galaxy_install` Package¶

class tool_shed.galaxy_install.install_manager.InstallRepositoryManager(app, tpm=None)[source]¶

Bases: object

get_repository_components_for_installation(encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys)[source]¶: The received encoded_tsr_ids, repo_info_dicts, and tool_panel_section_keys are 3 lists that contain associated elements at each location in the list. This method will return the elements from repo_info_dicts and tool_panel_section_keys associated with the received encoded_tsr_id by determining its location in the received encoded_tsr_ids list.

install(tool_shed_url, name, owner, changeset_revision, install_options)[source]¶

install_tool_shed_repository(tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path, install_tool_dependencies, reinstalling=False)[source]¶

order_components_for_installation(tsr_ids, repo_info_dicts, tool_panel_section_keys)[source]¶: Some repositories may have repository dependencies that are required to be installed before the dependent repository. This method will inspect the list of repositories about to be installed and make sure to order them appropriately. For each repository about to be installed, if required repositories are not contained in the list of repositories about to be installed, then they are not considered. Repository dependency definitions that contain circular dependencies should not result in an infinite loop, but obviously prior installation will not be handled for one or more of the repositories that require prior installation.

update_tool_shed_repository_status(tool_shed_repository, status, error_message=None)[source]¶: Update the status of a tool shed repository in the process of being installed into Galaxy.

class tool_shed.galaxy_install.install_manager.InstallToolDependencyManager(app)[source]¶

Bases: object

install_and_build_package(tool_shed_repository, tool_dependency, actions_dict)[source]¶: Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.

install_and_build_package_via_fabric(tool_shed_repository, tool_dependency, actions_dict)[source]¶

install_package(elem, tool_shed_repository, tool_dependencies=None, from_tool_migration_manager=False)[source]¶: Install a tool dependency package defined by the XML element elem. The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository.

install_specified_tool_dependencies(tool_shed_repository, tool_dependencies_config, tool_dependencies, from_tool_migration_manager=False)[source]¶: Follow the recipe in the received tool_dependencies_config to install specified packages for repository tools. The received list of tool_dependencies are the database records for those dependencies defined in the tool_dependencies_config that are to be installed. This list may be a subset of the set of dependencies defined in the tool_dependencies_config. This allows for filtering out dependencies that have not been checked for installation on the ‘Manage tool dependencies’ page for an installed Tool Shed repository.

install_via_fabric(tool_shed_repository, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None, actions_elem=None, action_elem=None, **kwd)[source]¶: Parse a tool_dependency.xml file’s <actions> tag set to gather information for installation using self.install_and_build_package(). The use of fabric is being eliminated, so some of these functions may need to be renamed at some point.

exception tool_shed.galaxy_install.install_manager.RepositoriesInstalledException[source]¶: Bases: galaxy.exceptions.RequestParameterInvalidException

tool_shed.galaxy_install.install_manager.fetch_tool_versions(app, tool_shed_repository)[source]¶: Fetch a data structure describing tool shed versions from the tool shed corresponding to a tool_shed_repository object.