BiopetJavaCommandLineFunction.scala 823 Bytes
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package nl.lumc.sasc.biopet.core

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import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
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trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
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  executable = "java"
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  javaGCThreads = config("java_gc_threads")
  javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
  javaGCTimeLimit = config("java_gc_timelimit")

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  override def javaOpts = super.javaOpts + optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)

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  override def afterGraph {
    memoryLimit = config("memory_limit")
  }
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  override def commandLine: String = {
    preCmdInternal
    val cmd = super.commandLine
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    val finalCmd = executable + cmd.substring(cmd.indexOf(" "))
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    //    addJobReportBinding("command", cmd)
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    return cmd
  }
}