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)

galaxy.util.tool_shed.common_util.check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number)

galaxy.util.tool_shed.common_util.check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict)

galaxy.util.tool_shed.common_util.generate_clone_url_for_installed_repository(app, repository)

Generate the URL for cloning a repository that has been installed into a Galaxy instance.

galaxy.util.tool_shed.common_util.generate_clone_url_for_repository_in_tool_shed(user, repository)

Generate the URL for cloning a repository that is in the tool shed.

galaxy.util.tool_shed.common_util.generate_clone_url_from_repo_info_tup(app, repo_info_tup)

Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision.

galaxy.util.tool_shed.common_util.get_non_shed_tool_panel_configs(app)

Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml.

galaxy.util.tool_shed.common_util.get_repository_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision)

galaxy.util.tool_shed.common_util.get_protocol_from_tool_shed_url(tool_shed_url)

Return the protocol from the received tool_shed_url if it exists.

galaxy.util.tool_shed.common_util.get_tool_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision)

galaxy.util.tool_shed.common_util.get_tool_shed_repository_ids(as_string=False, **kwd)

galaxy.util.tool_shed.common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed)

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, tool_shed, owner, name)

galaxy.util.tool_shed.common_util.get_user_by_username(app, username)

Get a user from the database by username.

galaxy.util.tool_shed.common_util.handle_galaxy_url(trans, **kwd)

galaxy.util.tool_shed.common_util.handle_tool_shed_url_protocol(app, shed_url)

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)

galaxy.util.tool_shed.common_util.remove_port_from_tool_shed_url(tool_shed_url)

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)

Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists.

galaxy.util.tool_shed.common_util.remove_protocol_and_user_from_clone_url(repository_clone_url)

Return a URL that can be used to clone a repository, eliminating the protocol and user if either exists.

galaxy.util.tool_shed.common_util.remove_protocol_from_tool_shed_url(tool_shed_url)

Return a partial Tool Shed URL, eliminating the protocol if it exists.

galaxy.util.tool_shed.encoding_util module

galaxy.util.tool_shed.encoding_util.tool_shed_decode(value)

galaxy.util.tool_shed.encoding_util.tool_shed_encode(val)

galaxy.util.tool_shed.xml_util module

galaxy.util.tool_shed.xml_util.create_and_write_tmp_file(elem)

galaxy.util.tool_shed.xml_util.create_element(tag, attributes=None, sub_elements=None)

Create a new element whose tag is the value of the received tag, and whose attributes are all key / value pairs in the received attributes and sub_elements.

galaxy.util.tool_shed.xml_util.parse_xml(file_name, check_exists=True)

Returns a parsed xml tree with comments intact.