43 lines
1.7 KiB
Scala
43 lines
1.7 KiB
Scala
package org.broadinstitute.sting.queue
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import org.broadinstitute.sting.commandline.Argument
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import java.io.File
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import java.lang.management.ManagementFactory
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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="runJobsIfPrecedingFail", shortName="runIfFail", doc="If this flag is set then ALL jobs will run even if the previous jobs fail.", required=false)
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var runJobsIfPrecedingFail = false
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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-" + {
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var prefix = ManagementFactory.getRuntimeMXBean.getName
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val index = prefix.indexOf(".")
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if (index >= 0)
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prefix = prefix.substring(0, index)
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prefix
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}
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}
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