Shed-install¶

NOTE: While shed-install can be used to run data managers, it is recommended to use run-data-managers instead.

A script to automate installation of tool repositories from a Galaxy Tool Shed into an instance of Galaxy. Galaxy instance details and the installed tools can be provided in one of three ways:

In the YAML format via dedicated files (a sample can be found here).
On the command line as dedicated script options (see the usage help).
As a single composite parameter to the script. The parameter must be a single, YAML-formatted string with the keys corresponding to the keys available for use in the YAML formatted file (for example: –yaml_tool “{‘owner’: ‘kellrott’, ‘tool_shed_url’: ‘https://testtoolshed.g2.bx.psu.edu’, ‘tool_panel_section_id’: ‘peak_calling’, ‘name’: ‘synapse_interface’}”).

Only one of the methods can be used with each invocation of the script but if more than one are provided are provided, precedence will correspond to order of the items in the list above. When installing tools, Galaxy expects any tool_panel_section_id provided when installing a tool to already exist in the configuration. If the section does not exist, the tool will be installed outside any section. See shed_tool_conf.xml.sample in this directory for a sample of such file. Before running this script to install the tools, make sure to place such file into Galaxy’s configuration directory and set Galaxy configuration option tool_config_file to include it.

Usage¶

usage: usage: python shed-install <options>

Optional Arguments

`-d, --dbkeysfile`
	Reference genome dbkeys to install (see dbkeys_list.yaml.sample)
`-t, --toolsfile`
	Tools file to use (see tool_list.yaml.sample)
`-y, --yaml_tool`
	Install tool represented by yaml string
`--name`	The name of the tool to install (only applicable if the tools file is not provided).
`--owner`	The owner of the tool to install (only applicable if the tools file is not provided).
`--section`	Galaxy tool panel section ID where the tool will be installed (the section must exist in Galaxy; only applicable if the tools file is not provided).
`--section_label`
	Galaxy tool panel section label where tool will be installed (if the section does not exist, it will be created; only applicable if the tools file is not provided).
`--toolshed`	The Tool Shed URL where to install the tool from. This is applicable only if the tool info is provided as an option vs. in the tools file.
`--skip_install_tool_dependencies=False`
	Skip the installation of tool dependencies using classic toolshed packages. Can be overwritten on a per-tool basis in the tools file.
`--install_resolver_dependencies=False`
	Install tool dependencies through resolver (e.g. conda). Will be ignored on galaxy releases older than 16.07. Can be overwritten on a per-tool basis in the tools file

Galaxy connection

`-v=False, --verbose=False`
	Increase output verbosity.
`-g="http://localhost:8080", --galaxy="http://localhost:8080"`
	Target Galaxy instance URL/IP address
`-u, --user`	Galaxy user name
`-p, --password`	Password for the Galaxy user
`-a, --api_key`	Galaxy admin user API key (required if not defined in the tools list file)