99 lines
5.3 KiB
Scala
99 lines
5.3 KiB
Scala
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.queue
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import java.io.File
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import org.broadinstitute.sting.commandline.{ClassType, Argument}
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/**
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* Default settings settable on the command line and passed to CommandLineFunctions.
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*/
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class QSettings {
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@Argument(fullName="run_name", shortName="runName", doc="A name for this run used for various status messages.", required=false)
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var runName: String = _
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@Argument(fullName="job_project", shortName="jobProject", doc="Default project for compute farm jobs.", required=false)
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var jobProject: String = _
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@Argument(fullName="job_queue", shortName="jobQueue", doc="Default queue for compute farm jobs.", required=false)
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var jobQueue: String = _
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@Argument(fullName="job_priority", shortName="jobPriority", doc="Default priority for jobs. Min = 0, Max = 100", required=false)
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@ClassType(classOf[Int])
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var jobPriority: Option[Int] = None
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@Argument(fullName="job_native_arg", shortName="jobNative", doc="Native arguments to pass to the job runner.", required=false)
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var jobNativeArgs: Seq[String] = Nil
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@Argument(fullName="job_resource_request", shortName="jobResReq", doc="Resource requests to pass to the job runner.", required=false)
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var jobResourceRequests: Seq[String] = Nil
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@Argument(fullName="job_environment_name", shortName="jobEnv", doc="Environment names for the job runner.", required=false)
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var jobEnvironmentNames: Seq[String] = Nil
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@Argument(fullName="memory_limit", shortName="memLimit", doc="Default memory limit for jobs, in gigabytes. If not set defaults to 2GB.", required=false)
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@ClassType(classOf[Double])
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var memoryLimit: Option[Double] = Some(2)
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@Argument(fullName="memory_limit_threshold", shortName="memLimitThresh", doc="After passing this threshold stop increasing memory limit for jobs, in gigabytes.", required=false)
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@ClassType(classOf[Double])
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var memoryLimitThreshold: Option[Double] = None
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@Argument(fullName="resident_memory_limit", shortName="resMemLimit", doc="Default resident memory limit for jobs, in gigabytes.", required=false)
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@ClassType(classOf[Double])
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var residentLimit: Option[Double] = None
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@Argument(fullName="resident_memory_request", shortName="resMemReq", doc="Default resident memory request for jobs, in gigabytes.", required=false)
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@ClassType(classOf[Double])
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var residentRequest: Option[Double] = None
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@Argument(fullName="resident_memory_request_parameter", shortName="resMemReqParam", doc="Parameter for resident memory requests. By default not requested.", required=false)
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var residentRequestParameter: String = _
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@Argument(fullName="job_walltime", shortName="wallTime", doc="Setting the required DRMAA walltime or LSF run limit.", required=false)
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@ClassType(classOf[Long])
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var jobWalltime: Option[Long] = None
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/** The name of the parallel environment (required for SGE, for example) */
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@Argument(fullName="job_parallel_env", shortName="jobParaEnv", doc="An SGE style parallel environment to use for jobs requesting more than 1 core. Equivalent to submitting jobs with -pe ARG nt for jobs with nt > 1", required=false)
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var parallelEnvironmentName: String = "smp_pe" // Broad default
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@Argument(fullName="dontRequestMultipleCores", shortName="multiCoreJerk", doc="If provided, Queue will not request multiple processors for jobs using multiple processors. Sometimes you eat the bear, sometimes the bear eats you.", required=false)
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var dontRequestMultipleCores: Boolean = false
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@Argument(fullName="disableDefaultJavaGCOptimizations", shortName="noGCOpt", doc="If provided, Queue will not ensure that java GC threads are limited and that the a minimum amount of time is spent in GC.")
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var disableDefaultJavaGCOptimizations = false
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@Argument(fullName="run_directory", shortName="runDir", doc="Root directory to run functions from.", required=false)
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var runDirectory = new File(".")
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@Argument(fullName="temp_directory", shortName="tempDir", doc="Temp directory to pass to functions.", required=false)
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var tempDirectory = new File(System.getProperty("java.io.tmpdir"))
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@Argument(fullName="job_scatter_gather_directory", shortName="jobSGDir", doc="Default directory to place scatter gather output for compute farm jobs.", required=false)
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var jobScatterGatherDirectory: File = _
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}
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