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.util.tool_shed package
Submodules
galaxy.util.tool_shed.common_util module
- galaxy.util.tool_shed.common_util.accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies)[source]
- galaxy.util.tool_shed.common_util.check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict)[source]
- galaxy.util.tool_shed.common_util.generate_clone_url_for_installed_repository(app: HasToolShedRegistry, repository) str[source]
Generate the URL for cloning a repository that has been installed into a Galaxy instance.
- galaxy.util.tool_shed.common_util.generate_clone_url_from_repo_info_tup(app: HasToolShedRegistry, repo_info_tup) str[source]
Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision.
- galaxy.util.tool_shed.common_util.get_repository_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision)[source]
- galaxy.util.tool_shed.common_util.get_protocol_from_tool_shed_url(tool_shed_url: str) str[source]
Return the protocol from the received tool_shed_url if it exists.
- galaxy.util.tool_shed.common_util.get_tool_shed_url_from_tool_shed_registry(app: HasToolShedRegistry, tool_shed: str) str | None[source]
The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is something like: http://toolshed.g2.bx.psu.edu/
- galaxy.util.tool_shed.common_util.get_tool_shed_repository_url(app: HasToolShedRegistry, tool_shed: str, owner: str, name: str)[source]
- galaxy.util.tool_shed.common_util.handle_tool_shed_url_protocol(app: HasToolShedRegistry, shed_url: str) str[source]
Handle secure and insecure HTTP protocol since they may change over time.
- galaxy.util.tool_shed.common_util.parse_repository_dependency_tuple(repository_dependency_tuple, contains_error=False)[source]
- galaxy.util.tool_shed.common_util.remove_port_from_tool_shed_url(tool_shed_url: str) str[source]
Return a partial Tool Shed URL, eliminating the port if it exists.
- galaxy.util.tool_shed.common_util.remove_protocol_and_port_from_tool_shed_url(tool_shed_url: str) str[source]
Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists.