Conifer.scala 1.36 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
 *
 * A dual licensing mode is applied. The source code within this project that are
 * not part of GATK Queue is freely available for non-commercial use under an AGPL
 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
package nl.lumc.sasc.biopet.extensions.conifer

import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
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import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
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abstract class Conifer extends PythonCommandLineFunction {
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  override def subPath = "conifer" :: super.subPath
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  //  executable = config("exe", default = "conifer")
  setPythonScript(config("script", default = "conifer"))
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  override val versionRegex = """(.*)""".r
  override val versionExitcode = List(0)
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  override def versionCommand = executable + " " + python_script + " --version"

  override val defaultVmem = "8G"
  override val defaultThreads = 1

  def cmdLine = getPythonCommand

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}