Cromwell execution directory

• 

  Jason Cerrato

  • October 05, 2020 13:40

  Hi Stephen,

  Great question! Let me check on this and get back to you.

  Kind regards,

  Jason

  0
• 

  Jason Cerrato

  • October 05, 2020 15:16

  Hi Stephen,

  There isn't an environment variable for this, but you could strip the path out from a file that is localized to understand the path. I hope this helps!

   

  Kind regards,

  Jason
  0
• 

  Stephen Fleming

  • Edited October 05, 2020 23:46

  Thanks Jason!

   

  With a suggestion from Luca D'Alessio, I have attempted this, which seems to work:

  BUCKET=$(cat gcs_delocalization.sh | grep -o '"gs:\/\/.*/call' | sed 's/\/call/"/' | head -n 1)

   

  Full WDL example:

  task run_task {
    # Docker image
    String? docker_image = "ubuntu:16.04"
  
    # Hardware-related inputs
    String? hardware_zones = "us-east1-d us-east1-c us-central1-a us-central1-c us-west1-b"
    Int? hardware_disk_size_GB = 50
    Int? hardware_preemptible_tries = 0
    Int? hardware_num_cpu = 4
    Int? hardware_boot_disk_size_GB = 15
    Int? hardware_memory_GB = 15
  
    command {
      BUCKET=$(cat gcs_delocalization.sh | grep -o '"gs:\/\/.*/call' | sed 's/\/call/"/' | head -n 1)
      echo "Variable BUCKET contains" >> out.log
      echo "$BUCKET" >> out.log
    }
  
    output {
      File log = "out.log"
    }
  
    runtime {
      docker: "${docker_image}"
      bootDiskSizeGb: hardware_boot_disk_size_GB
      disks: "local-disk ${hardware_disk_size_GB} HDD"
      memory: "${hardware_memory_GB}G"
      cpu: hardware_num_cpu
      zones: "${hardware_zones}"
      preemptible: hardware_preemptible_tries
      maxRetries: 0
    }
  }
  
  workflow test {
    call run_task
    output {
      File log = run_task.log
    }
  }

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• 

  Jason Cerrato

  • October 06, 2020 13:08

  Hi Stephen,

  That makes sense! I'm glad to see you've found a solution that works for you. Thank you for sharing this, as it will be helpful to other users.

  If we can help with anything else, please let us know.

  Kind regards,

  Jason

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