Run-data-managers¶
Run-data-managers is a tool for provisioning data on a galaxy instance.
Run-data-managers has the ability to reload the datatables after a data manager has finished. It is therefore able 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, reload the data table and run another data manager that indexes the fasta file for bwa-mem.
Run-data-managers needs a yaml that specifies what data managers are run and with which settings. An example file can be found 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.
usage: run-data-managers [-h] [-v] [-g GALAXY] [-u USER] [-p PASSWORD]
[-a API_KEY] --config CONFIG [--overwrite]
- Optional Arguments
--config Path to the YAML config file with the list of data managers and data to install. --overwrite=False Disables checking whether the item already exists in the tool data table. - 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)