toolshed

This section is auto-generated from the help text for the arrow command toolshed.

get_repositories command

Usage:

parsec toolshed get_repositories [OPTIONS]

Help

Get the list of all installed Tool Shed repositories on this Galaxy instance.

Options:

-h, --help  Show this message and exit.

install_repository_revision command

Usage:

parsec toolshed install_repository_revision [OPTIONS] TOOL_SHED_URL NAME

Help

Install a specified repository revision from a specified Tool Shed into this Galaxy instance. This example demonstrates installation of a repository that contains valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section. You can choose if tool dependencies or repository dependencies should be installed through the Tool Shed, (use install_tool_dependencies or install_repository_dependencies) or through a resolver that supports installing dependencies (use install_resolver_dependencies). Note that any combination of the three dependency resolving variables is valid.

Options:

--install_tool_dependencies     Whether or not to automatically handle tool
                                dependencies (see
                                https://galaxyproject.org/toolshed/tool-
                                dependency-recipes/ for more details)
--install_repository_dependencies
                                Whether or not to automatically handle
                                repository dependencies (see
                                https://galaxyproject.org/toolshed/defining-
                                repository-dependencies/ for more details)
--install_resolver_dependencies
                                Whether or not to automatically install
                                resolver dependencies (e.g. conda). This
                                parameter is silently ignored in Galaxy
                                ``release_16.04`` and earlier.
--tool_panel_section_id TEXT    The ID of the Galaxy tool panel section where
                                the tool should be insterted under. Note that
                                you should specify either this parameter or
                                the ``new_tool_panel_section_label``. If both
                                are specified, this one will take precedence.
--new_tool_panel_section_label TEXT
                                The name of a Galaxy tool panel section that
                                should be created and the repository installed
                                into.
-h, --help                      Show this message and exit.

show_repository command

Usage:

parsec toolshed show_repository [OPTIONS] TOOLSHED_ID

Help

Get details of a given Tool Shed repository as it is installed on this Galaxy instance.

Options:

-h, --help  Show this message and exit.