51 lines
1.3 KiB
Scala
51 lines
1.3 KiB
Scala
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package org.broadinstitute.sting.queue
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import engine.Pipeline
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import tools.nsc.MainGenericRunner
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import org.broadinstitute.sting.queue.util.ClasspathUtils
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import org.apache.log4j._
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import collection.mutable.ListBuffer
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import org.broadinstitute.sting.queue.util.Logging
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object QCommandLine extends Application with Logging {
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var usage = """usage: java -jar Queue.jar [ -P name=value ] [ -P file.properties ] [ -I input.file ] [ -I input_files.list ] [ -bsub ] [ -dry ] [ -debug ] -S pipeline.scala"""
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override def main(args: Array[String]) = {
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try {
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QArguments.parseArgs(args.clone)
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} catch {
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case e: Exception => {
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println(usage)
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System.exit(-1)
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}
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}
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var newArgs = new ListBuffer[String]
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newArgs.appendAll(args)
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QArguments.strip(newArgs, "-S")
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logger.debug("starting")
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if (QArguments.scripts.size == 0) {
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println("Error: Missing script")
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println(usage)
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System.exit(-1)
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}
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if (Pipeline.inputPaths.size == 0) {
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println("Error: No inputs specified")
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println(usage)
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System.exit(-1)
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}
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for (script <- QArguments.scripts) {
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var clone = newArgs.clone
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clone.prepend("-nocompdaemon", "-classpath", ClasspathUtils.manifestAwareClassPath, script)
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MainGenericRunner.main(clone.toArray)
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}
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logger.debug("exiting")
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}
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}
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