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Run tools

This document describes how to run tools on the Deep Origin platform.

Running packaged tools

In general, tools are best run by calling functions in the tools.run module. For example, to run Autodock Vina, use:

from deeporigin.tools import run
run.autodock_vina(...)

Running any tool

Any tool in the Deep Origin tool registry can be run using a generic tool run function. 

from deeporigin.tools.utils import run_tool
run_tool(data)

where data is a dictionary representing the DTO (Data Transfer Object) for the tool.

The DTO requires the following keys:

toolId

The toolId is used to identify the tool in the Deep Origin tool registry. For AutoDock Vina, this is deeporigin/autodock-vina.

inputs

The inputs key is a dictionary of input parameters for the tool.

outputs

The outputs key is a dictionary of output parameters for the tool.

clusterId (Optional)

The clusterId (optional) key is the id of the cluster to run the tool on. If this is not provided, it will be run on the default (us-west-2) cluster.