Configuration

Configuration for Oliver is stored in the config file as JSON. By default, the dotfile is location at ~/.oliver_config. One of the benefits of using Oliver is the "set and forget" nature of configuration. For instance, a common configuration option that you might want to set rather than providing on the command line is the URL to your Cromwell server.

Basics

Before using Oliver, you should run the configuration quickstart wizard:

oliver configure

If you just want to accept the defaults, or if you are using Oliver in a non interactive environment like CI, you can just start with the default configuration.

oliver configure --defaults

Similarly, you can use the oliver config subcommand to display current config values, get specific key-value pairs, or set new values for configuration options.

# list all config values
oliver config list

# get a particular key
oliver config get cromwell_server

# set a particular key's value
oliver config set cromwell_server http://foo:8000

Commonly Used Options

The following key values pairs are commonly used to configure Oliver. Note that any key in the argparse parser can be specified in the configuration — if you would like to set any of these options and don't mind looking through Python code, you can do so (we do not exhaustively list all possible config options here).

Key	Description	Type	Default
cromwell_server	HTTP/HTTPS root URL for the Cromwell server to use by default.	String	http://localhost:8000
cromwell_api_version	Cromwell API version to use by default.	String	v1
batch_interval_mins	When inferring batches, how many minutes should separate two batches?	Int	2
output_prefix	Prefix to append to file locations.	String	None

Cromwell on Azure Specific

Key	Description	Type	Default
azure_resource_group	If using Cromwell on Azure, resource group associated with your Cromwell instance.	String
cosmos_account_name	If using Cromwell on Azure, name of CosmosDB associated with your Cromwell instance.	String