serve.rst

serve command

This section is auto-generated from the help text for the planemo command serve. This help message can be generated with planemo serve --help.

Usage:

planemo serve [OPTIONS] TOOL_PATH

Help

Launch a Galaxy instance with the specified tool in the tool panel.

The Galaxy tool panel will include just the referenced tool or tools (by default all the tools in the current working directory) and the upload tool.

planemo will search parent directories to see if any is a Galaxy instance - but one can pick the Galaxy instance to use with the --galaxy_root option or force planemo to download a disposable instance with the --install_galaxy flag.

planemo uses temporarily generated config files and environment variables to attempt to shield this execution of Galaxy from manually launched runs against that same Galaxy root - but this may not be bullet proof yet so please careful and do not try this against production Galaxy instances.

Options:

--galaxy_root DIRECTORY         Root of development galaxy directory to
                                execute command with.
--install_galaxy                Download and configure a disposable copy of
                                Galaxy from github.
--no_cleanup                    Do not cleanup temp files created for and by
                                Galaxy.
--test_data DIRECTORY           test-data directory to for specified
                                tool(s).
--dependency_resolvers_config_file PATH
                                Dependency resolver configuration for Galaxy
                                to target.
--job_config_file PATH          Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
                                Tool dependency dir for Galaxy to target.
--brew_dependency_resolution    Configure Galaxy to use plain brew
                                dependency resolution.
--help                          Show this message and exit.