45 lines
2.2 KiB
Scala
45 lines
2.2 KiB
Scala
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package org.broadinstitute.sting.queue.engine
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import java.io.File
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import org.broadinstitute.sting.queue.QSettings
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import org.broadinstitute.sting.commandline.{ArgumentCollection, Argument}
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import org.broadinstitute.sting.queue.util.SystemUtils
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/**
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* Command line options for a QGraph.
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*/
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class QGraphSettings {
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@ArgumentCollection
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val qSettings = new QSettings
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@Argument(fullName="bsub_all_jobs", shortName="bsub", doc="Use bsub to submit jobs", required=false)
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var bsubAllJobs = false
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@Argument(fullName="run_scripts", shortName="run", doc="Run QScripts. Without this flag set only performs a dry run.", required=false)
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var run = false
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@Argument(fullName="dot_graph", shortName="dot", doc="Outputs the queue graph to a .dot file. See: http://en.wikipedia.org/wiki/DOT_language", required=false)
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var dotFile: File = _
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@Argument(fullName="expanded_dot_graph", shortName="expandedDot", doc="Outputs the queue graph of scatter gather to a .dot file. Otherwise overwrites the dot_graph", required=false)
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var expandedDotFile: File = _
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@Argument(fullName="start_from_scratch", shortName="startFromScratch", doc="Runs all command line functions even if the outputs were previously output successfully.", required=false)
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var startFromScratch = false
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@Argument(fullName="status",shortName="status",doc="Get status of jobs for the qscript",required=false)
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var getStatus = false
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@Argument(fullName="status_email_from", shortName="statusFrom", doc="Email address to send emails from upon completion or on error.", required=false)
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var statusEmailFrom: String = System.getProperty("user.name") + "@" + SystemUtils.domainName
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@Argument(fullName="status_email_to", shortName="statusTo", doc="Email address to send emails to upon completion or on error.", required=false)
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var statusEmailTo: List[String] = Nil
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@Argument(fullName="delete_intermediate_outputs", shortName="deleteIntermediates", doc="After a successful run delete the outputs of any Function marked as intermediate.", required=false)
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var deleteIntermediates = false
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@Argument(fullName="retry_failed", shortName="retry", doc="Retry the specified number of times after a command fails. Defaults to no retries.", required=false)
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var retries = 0
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}
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