43 lines
1.8 KiB
Scala
43 lines
1.8 KiB
Scala
package org.broadinstitute.sting.queue
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import java.io.File
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import org.broadinstitute.sting.commandline.{ArgumentCollection, Argument}
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import org.broadinstitute.sting.queue.util.{SystemUtils, EmailSettings}
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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="job_name_prefix", shortName="jobPrefix", doc="Default name prefix for compute farm jobs.", required=false)
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var jobNamePrefix: String = QSettings.processNamePrefix
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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_project", shortName="jobProject", doc="Default project for compute farm jobs.", required=false)
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var jobProject: String = "Queue"
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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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@Argument(fullName="default_memory_limit", shortName="memLimit", doc="Default memory limit for jobs, in gigabytes.", required=false)
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var memoryLimit: Option[Int] = None
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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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@ArgumentCollection
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val emailSettings = new EmailSettings
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}
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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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object QSettings {
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/** A semi-unique job prefix using the host name and the process id. */
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private val processNamePrefix = "Q-" + SystemUtils.pidAtHost.split('.')(0)
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}
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