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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_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number)[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, repository)[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_for_repository_in_tool_shed(user, repository)[source]¶
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)[source]¶
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)[source]¶
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)[source]¶
- galaxy.util.tool_shed.common_util.get_protocol_from_tool_shed_url(tool_shed_url)[source]¶
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)[source]¶
- galaxy.util.tool_shed.common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed)[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, tool_shed, owner, name)[source]¶
- galaxy.util.tool_shed.common_util.get_user_by_username(app, username)[source]¶
Get a user from the database by username.
- galaxy.util.tool_shed.common_util.handle_tool_shed_url_protocol(app, shed_url)[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)[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)[source]¶
Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists.