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]
[--data-manager-mode {bundle,populate,dry_run}]
[--history-name HISTORY_NAME]
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, --ignore_errors
Do not stop running when jobs have failed.
Default: False
- --data-manager-mode, --data_manager_mode
Possible choices: bundle, populate, dry_run
Default: “populate”
- --history-name
General options¶
- -v, --verbose
Increase output verbosity.
Default: False
- --log-file, --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 email address
- -p, --password
Password for the Galaxy user
- -a, --api-key, --api_key
Galaxy admin user API key (required if not defined in the tools list file)