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)