Arvados

Story #8662

Updated by Brett Smith almost 9 years ago

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: 

 <pre> 
 "script_parameters": { 
   "runtime_constraints": { 
     "value": { 
       "RealignerTargetCreator": { "min_cores_per_node": 4, … }, 
       } 
     "IndelRealigner":           { "min_cores_per_node": 1, … }, 
       } 
     … 
     
   } 
   }, 
   … 
 } 
 </pre> 

 Implementation: 

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

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