80 lines
4.2 KiB
Scala
80 lines
4.2 KiB
Scala
/*
|
|
* Copyright (c) 2012, The Broad Institute
|
|
*
|
|
* Permission is hereby granted, free of charge, to any person
|
|
* obtaining a copy of this software and associated documentation
|
|
* files (the "Software"), to deal in the Software without
|
|
* restriction, including without limitation the rights to use,
|
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
* copies of the Software, and to permit persons to whom the
|
|
* Software is furnished to do so, subject to the following
|
|
* conditions:
|
|
*
|
|
* The above copyright notice and this permission notice shall be
|
|
* included in all copies or substantial portions of the Software.
|
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
* OTHER DEALINGS IN THE SOFTWARE.
|
|
*/
|
|
|
|
package org.broadinstitute.sting.queue
|
|
|
|
import java.io.File
|
|
import org.broadinstitute.sting.commandline.Argument
|
|
|
|
/**
|
|
* Default settings settable on the command line and passed to CommandLineFunctions.
|
|
*/
|
|
class QSettings {
|
|
@Argument(fullName="run_name", shortName="runName", doc="A name for this run used for various status messages.", required=false)
|
|
var runName: String = _
|
|
|
|
@Argument(fullName="job_project", shortName="jobProject", doc="Default project for compute farm jobs.", required=false)
|
|
var jobProject: String = _
|
|
|
|
@Argument(fullName="job_queue", shortName="jobQueue", doc="Default queue for compute farm jobs.", required=false)
|
|
var jobQueue: String = _
|
|
|
|
@Argument(fullName="job_priority", shortName="jobPriority", doc="Default priority for jobs. Min = 0, Max = 100", required=false)
|
|
var jobPriority: Option[Int] = None
|
|
|
|
@Argument(fullName="job_native_arg", shortName="jobNative", doc="Native arguments to pass to the job runner.", required=false)
|
|
var jobNativeArgs: Seq[String] = Nil
|
|
|
|
@Argument(fullName="job_resource_request", shortName="jobResReq", doc="Resource requests to pass to the job runner.", required=false)
|
|
var jobResourceRequests: Seq[String] = Nil
|
|
|
|
@Argument(fullName="job_environment_name", shortName="jobEnv", doc="Environment names for the job runner.", required=false)
|
|
var jobEnvironmentNames: Seq[String] = Nil
|
|
|
|
@Argument(fullName="memory_limit", shortName="memLimit", doc="Default memory limit for jobs, in gigabytes.", required=false)
|
|
var memoryLimit: Option[Double] = None
|
|
|
|
@Argument(fullName="resident_memory_limit", shortName="resMemLimit", doc="Default resident memory limit for jobs, in gigabytes.", required=false)
|
|
var residentLimit: Option[Double] = None
|
|
|
|
@Argument(fullName="resident_memory_request", shortName="resMemReq", doc="Default resident memory request for jobs, in gigabytes.", required=false)
|
|
var residentRequest: Option[Double] = None
|
|
|
|
/** The name of the parallel environment (required for SGE, for example) */
|
|
@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)
|
|
var parallelEnvironmentName: String = "smp_pe" // Broad default
|
|
|
|
@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)
|
|
var dontRequestMultipleCores: Boolean = false
|
|
|
|
@Argument(fullName="run_directory", shortName="runDir", doc="Root directory to run functions from.", required=false)
|
|
var runDirectory = new File(".")
|
|
|
|
@Argument(fullName="temp_directory", shortName="tempDir", doc="Temp directory to pass to functions.", required=false)
|
|
var tempDirectory = new File(System.getProperty("java.io.tmpdir"))
|
|
|
|
@Argument(fullName="job_scatter_gather_directory", shortName="jobSGDir", doc="Default directory to place scatter gather output for compute farm jobs.", required=false)
|
|
var jobScatterGatherDirectory: File = _
|
|
}
|