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  1. webservice {
  2.   port = 8000
  3.   interface = 0.0.0.0
  4.   instance.name = "reference"
  5. }
  6.  
  7. akka {
  8.   loggers = ["akka.event.slf4j.Slf4jLogger"]
  9.   actor {
  10.     default-dispatcher {
  11.       fork-join-executor {
  12.         # Number of threads = min(parallelism-factor * cpus, parallelism-max)
  13.         # Below are the default values set by Akka, uncomment to tune these
  14.         #parallelism-factor = 3.0
  15.         #parallelism-max = 64
  16.       }
  17.     }
  18.   }
  19.  
  20.   dispatchers {
  21.     # A dispatcher for actors performing blocking io operations
  22.     # Prevents the whole system from being slowed down when waiting for responses from external resources for instance
  23.     io-dispatcher {
  24.       type = Dispatcher
  25.       executor = "fork-join-executor"
  26.       # Using the forkjoin defaults, this can be tuned if we wish
  27.     }
  28.  
  29.     # A dispatcher for actors handling API operations
  30.     # Keeps the API responsive regardless of the load of workflows being run
  31.     api-dispatcher {
  32.       type = Dispatcher
  33.       executor = "fork-join-executor"
  34.     }
  35.  
  36.     # A dispatcher for engine actors
  37.     # Because backends behaviour is unpredictable (potentially blocking, slow) the engine runs
  38.     # on its own dispatcher to prevent backends from affecting its performance.
  39.     engine-dispatcher {
  40.       type = Dispatcher
  41.       executor = "fork-join-executor"
  42.     }
  43.     # A dispatcher used by supported backend actors
  44.     backend-dispatcher {
  45.       type = Dispatcher
  46.       executor = "fork-join-executor"
  47.     }
  48.     # Note that without further configuration, all other actors run on the default dispatcher
  49.   }
  50. }
  51.  
  52. spray.can {
  53.   server {
  54.     request-timeout = 40s
  55.   }
  56.   client {
  57.     request-timeout = 40s
  58.     connecting-timeout = 40s
  59.   }
  60. }
  61.  
  62. system {
  63.   // If 'true', a SIGINT will trigger Cromwell to attempt to abort all currently running jobs before exiting
  64.   abort-jobs-on-terminate = false
  65.  
  66.   // Max number of retries per job that the engine will attempt in case of a retryable failure received from the backend
  67.   max-retries = 10
  68.  
  69.   // If 'true' then when Cromwell starts up, it tries to restart incomplete workflows
  70.   workflow-restart = true
  71.  
  72.   // Cromwell will cap the number of running workflows at N
  73.   max-concurrent-workflows = 5000
  74.  
  75.   // Cromwell will launch up to N submitted workflows at a time, regardless of how many open workflow slots exist
  76.   max-workflow-launch-count = 50
  77.  
  78.   // Number of seconds between workflow launches
  79.   new-workflow-poll-rate = 20
  80.  
  81.   // Since the WorkflowLogCopyRouter is initialized in code, this is the number of workers
  82.   number-of-workflow-log-copy-workers = 10
  83. }
  84.  
  85. workflow-options {
  86.   // These workflow options will be encrypted when stored in the database
  87.   encrypted-fields: []
  88.  
  89.   // AES-256 key to use to encrypt the values in `encrypted-fields`
  90.   base64-encryption-key: "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="
  91.  
  92.   // Directory where to write per workflow logs
  93.   workflow-log-dir: "cromwell-workflow-logs"
  94.  
  95.   // When true, per workflow logs will be deleted after copying
  96.   workflow-log-temporary: true
  97.  
  98.   // Workflow-failure-mode determines what happens to other calls when a call fails. Can be either ContinueWhilePossible or NoNewCalls.
  99.   // Can also be overridden in workflow options. Defaults to NoNewCalls. Uncomment to change:
  100.   //workflow-failure-mode: "ContinueWhilePossible"
  101. }
  102.  
  103. // Optional call-caching configuration.
  104. call-caching {
  105.   enabled = false
  106. }
  107.  
  108. engine {
  109.   // This instructs the engine which filesystems are at its disposal to perform any IO operation that it might need.
  110.   // For instance, WDL variables declared at the Workflow level will be evaluated using the filesystems declared here.
  111.   // If you intend to be able to run workflows with this kind of declarations:
  112.   // workflow {
  113.   //    String str = read_string("gs://bucket/my-file.txt")
  114.   // }
  115.   // You will need to provide the engine with a gcs filesystem
  116.   // Note that the default filesystem (local) is always available.
  117.   //filesystems {
  118.   //  gcs {
  119.   //    auth = "application-default"
  120.   //  }
  121.   //}
  122. }
  123.  
  124. backend {
  125.   default = "LSF"
  126.   providers {
  127.     Local {
  128.       actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
  129.       config {
  130.         run-in-background = true
  131.         runtime-attributes = "String? docker"
  132.         submit = "/bin/bash ${script}"
  133.         submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"
  134.  
  135.         // Root directory where Cromwell writes job results.  This directory must be
  136.         // visible and writeable by the Cromwell process as well as the jobs that Cromwell
  137.         // launches.
  138.         root: "cromwell-executions"
  139.         filesystems {
  140.           local {
  141.             // Cromwell makes a link to your input files within <root>/<workflow UUID>/workflow-inputs
  142.             // The following are strategies used to make those links.  They are ordered.  If one fails
  143.             // The next one is tried:
  144.             //
  145.             // hard-link: attempt to create a hard-link to the file
  146.             // copy: copy the file
  147.             // soft-link: create a symbolic link to the file
  148.             //
  149.             // NOTE: soft-link will be skipped for Docker jobs
  150.             localization: [
  151.               "hard-link", "soft-link", "copy"
  152.             ]
  153.           }
  154.         }
  155.       }
  156.     }
  157.  
  158.     LSF {
  159.       actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
  160.       config {
  161.         runtime-attributes = """
  162.         Int cpu = 1
  163.         String? memory_gb
  164.         String? queue
  165.         String? project
  166.         String? docker_image
  167.         String? resource
  168.         String? job_group
  169.         """
  170.         submit = """
  171.         bsub \
  172.         -J ${job_name} \
  173.         -cwd ${cwd} \
  174.         -o ${out} \
  175.         -e ${err} \
  176.         ${"-a \"docker(" + docker_image + ")\""} \
  177.         ${"-P " + project} \
  178.         ${"-q " + queue} \
  179.         ${"-M " + memory_gb} \
  180.         ${"-n " + cpu} \
  181.         ${"-R \"" + resource + "\""} \
  182.         ${"-g \"" + job_group + "\""} \
  183.         /bin/bash ${script}
  184.         """
  185.  
  186.         kill = "bkill ${job_id}"
  187.         check-alive = "bjobs -noheader -o \"stat\" ${job_id} | /bin/grep 'PEND\\|RUN'"
  188.         job-id-regex = "Job <(\\d+)>.*"
  189.  
  190.       }
  191.     }
  192.   }
  193. }
  194.  
  195. services {
  196.   KeyValue {
  197.     class = "cromwell.services.keyvalue.impl.SqlKeyValueServiceActor"
  198.   }
  199.  
  200.   MetadataService {
  201.     class = "cromwell.services.metadata.impl.MetadataServiceActor"
  202.   }
  203. }
  204.  
  205. database {
  206.   // This specifies which database to use
  207.   config = main.mysql
  208.  
  209.   main {
  210.     mysql {
  211.       driver = "slick.driver.MySQLDriver$"
  212.       db {
  213.         driver = "com.mysql.jdbc.Driver"
  214.         url = "jdbc:mysql://localhost:3306/cromwell?socket=/tmp/mysqld.sock"
  215.         user = "cromwell"
  216.         password = "test4cromwell"
  217.         connectionTimeout = 5000
  218.       }
  219.     }
  220.   }
  221. }
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