IGVTools.scala 1.17 KB
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/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
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 * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
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 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
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package nl.lumc.sasc.biopet.extensions.igvtools

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import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
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/**
 * General igvtools extension
 *
 * Created by wyleung on 5-1-15
 */
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abstract class IGVTools extends BiopetCommandLineFunction with Version {
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  executable = config("exe", default = "igvtools", namespace = "igvtools", freeVar = false)
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  def versionCommand = executable + " version"
  def versionRegex = """IGV Version:? ([\w\.]*) .*""".r
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  override def versionExitcode = List(0)
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}