Arvados

In a GATK Queue Job, runtime_constraints should just be sufficient to run the Queue process itself. It should find runtime constraints for individual tools in the Job's script_parameters like:

"script_parameters": {
  "runtime_constraints": {
    "value": {
      "RealignerTargetCreator": { "min_cores_per_node": 4, … },
      "IndelRealigner":         { "min_cores_per_node": 1, … },
      …
    }
  },
  …
}

Implementation:

1. In ArvadosJobRunner.scala, capture the tool name explicitly (the tool is already matched from the command line using the regxes on lines 213-217)
2. Use the tool name as a key into job.script_parameters.runtime_contraints.
3. Update the top level runtime constraints with any keys supplied the tool-specific runtime constraints.
4. Use the updated runtime constraints to submit the job using that tool.