Run-data-managers¶

Run-data-managers is a tool for provisioning data on a galaxy instance.

Run-data-managers has the ability to run multiple data managers that are interdependent. When a reference genome is needed for bwa-mem for example, Run-data-managers can first run a data manager to fetch the fasta file and run another data manager that indexes the fasta file for bwa-mem. This functionality depends on the “watch_tool_data_dir” setting in galaxy.ini to be True. Also, if a new data manager is installed, galaxy needs to be restarted in order for it’s tool_data_dir to be watched.

Run-data-managers needs a yaml that specifies what data managers are run and with which settings. Example files can be found here, here, and here.

By default run-data-managers skips entries in the yaml file that have already been run. It checks it in the following way: * If the data manager has input variables “name” or “sequence_name” it will check if the “name” column in the data table already has this entry.

“name” will take precedence over “sequence_name”.

If the data manager has input variables “value”, “sequence_id” or ‘dbkey’ it will check if the “value” column in the data table already has this entry. Value takes precedence over sequence_id which takes precedence over dbkey.
If none of the above input variables are specified the data manager will always run.

Usage¶

Running Galaxy data managers in a defined order with defined parameters.’watch_tool_data_dir’ in galaxy config should be set to true.’

usage: run-data-managers [-h] [-v] [--log_file LOG_FILE] [-g GALAXY] [-u USER]
                         [-p PASSWORD] [-a API_KEY] --config CONFIG
                         [--overwrite] [--ignore_errors]

Named Arguments¶

`--config`	Path to the YAML config file with the list of data managers and data to install.
`--overwrite`	Disables checking whether the item already exists in the tool data table. Default: False
`--ignore_errors`
	Do not stop running when jobs have failed. Default: False

General options¶

-v, --verbose

Increase output verbosity.

Default: False

--log_file

Where the log file should be stored. Default is a file in your system’s temp folder

Galaxy connection¶

`-g, --galaxy`	Target Galaxy instance URL/IP address Default: “http://localhost:8080”
`-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)