Also a class for JavaCommandLineTools

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

 package nl.lumc.sasc.biopet.core
 
-import java.io.File
-import org.broadinstitute.sting.queue.QException
-import org.broadinstitute.sting.queue.function.CommandLineFunction
 import org.broadinstitute.sting.commandline._
 import scala.sys.process._
-import scala.util.matching.Regex
 import nl.lumc.sasc.biopet.core.config._
 
-abstract class BiopetCommandLineFunction extends CommandLineFunction with Configurable {
-  analysisName = getClass.getSimpleName
-  
-  @Input(doc="deps", required=false)
-  var deps: List[File] = Nil
-  
-  @Argument(doc="Threads", required=false)
-  var threads = 0
-  val defaultThreads = 1
-  
-  @Argument(doc="Vmem", required=false)
-  var vmem: String = _
-  val defaultVmem: String = ""
-  
-  @Argument(doc="Executeble")
-  var executeble: String = _
-  
-  protected def beforeCmd {
-  }
-  
-  protected def afterGraph {
-  }
-  
-  override def freezeFieldValues() {
-    checkExecuteble
-    afterGraph
-    jobOutputFile = new File(firstOutput.getParent + "/."  + firstOutput.getName + "." + analysisName + ".out")
-    
-    super.freezeFieldValues()
-  }
-  
-  protected def checkExecuteble {
-    try if (executeble != null) {
-      val buffer = new StringBuffer()
-      val cmd = Seq("which", executeble)
-      val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
-      if (process.exitValue == 0) {
-        executeble = buffer.toString
-        val file = new File(executeble)
-        executeble = file.getCanonicalPath
-      } else {
-        logger.error("executeble: '" + executeble + "' not found, please check config")
-        throw new QException("executeble: '" + executeble + "' not found, please check config")
-      }
-    } catch {
-      case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executeble skipped: " + ioe)
-    }
-  }
-  
-  final protected def preCmdInternal {
-    checkExecuteble
-    //for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
-    //logger.debug("Config for " + analysisName + ": " + localConfig)
-    
-    beforeCmd
-    
-    addJobReportBinding("version", getVersion)
-    
-    if (threads == 0) threads = getThreads(defaultThreads)
-    if (threads > 1) nCoresRequest = Option(threads)
-    addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
-    
-    if (vmem == null) {
-      if (configContains("vmem")) vmem = config("vmem")
-      else if (!defaultVmem.isEmpty) vmem = defaultVmem
-    }
-    if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
-    jobName = this.analysisName + ":" + firstOutput.getName
-  }
-  
+abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {  
   protected def cmdLine: String
   final def commandLine: String = {
     preCmdInternal
     val cmd = cmdLine
     addJobReportBinding("command", cmd)
-    cmd
-  }
-  
-  protected var versionCommand: String = _
-  protected val versionRegex: Regex = null
-  def getVersion : String = {
-    if (versionCommand == null || versionRegex == null) return "N/A"
-    val buffer = new StringBuffer()
-    val process = Process(versionCommand).run(ProcessLogger(buffer append _))
-    if (process.exitValue != 0) {
-      logger.warn("Version command: '" + versionCommand + "' give exit code " + process.exitValue + ", version not found")
-      return "N/A"
-    }
-    val lines = versionCommand lines_! ProcessLogger(buffer append _)
-    for (line <- lines) {
-      line match { 
-        case versionRegex(m) => return m
-        case _ =>
-      }
-    }
-    logger.warn("Version command: '" + versionCommand + "' give a exit code 0 but no version was found, executeble oke?")
-    return "N/A"
-  }
-  
-  def getThreads(default:Int) : Int = {
-    val maxThreads: Int = config("maxthreads", 8)
-    val threads: Int = config("threads", default)
-    if (maxThreads > threads) return threads
-    else return maxThreads
-  }
-  
-  def getThreads(default:Int, module:String) : Int = {
-    val maxThreads: Int = config("maxthreads", 8, module)
-    val threads: Int = config("threads", default, module)
-    if (maxThreads > threads) return threads
-    else return maxThreads
+    return cmd
   }
 }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config._
+import org.broadinstitute.sting.queue.QException
+import org.broadinstitute.sting.queue.function.CommandLineFunction
+import org.broadinstitute.sting.commandline._
+import scala.sys.process._
+import scala.util.matching.Regex
+
+trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
+  analysisName = getClass.getSimpleName
+  
+  @Input(doc="deps", required=false)
+  var deps: List[File] = Nil
+  
+  @Argument(doc="Threads", required=false)
+  var threads = 0
+  val defaultThreads = 1
+  
+  @Argument(doc="Vmem", required=false)
+  var vmem: String = _
+  val defaultVmem: String = ""
+  
+  @Argument(doc="Executeble")
+  var executeble: String = _
+  
+  protected def beforeCmd {
+  }
+  
+  protected def afterGraph {
+  }
+  
+  override def freezeFieldValues() {
+    checkExecuteble
+    afterGraph
+    jobOutputFile = new File(firstOutput.getParent + "/."  + firstOutput.getName + "." + analysisName + ".out")
+    
+    super.freezeFieldValues()
+  }
+  
+  protected def checkExecuteble {
+    try if (executeble != null) {
+      val buffer = new StringBuffer()
+      val cmd = Seq("which", executeble)
+      val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
+      if (process.exitValue == 0) {
+        executeble = buffer.toString
+        val file = new File(executeble)
+        executeble = file.getCanonicalPath
+      } else {
+        logger.error("executeble: '" + executeble + "' not found, please check config")
+        throw new QException("executeble: '" + executeble + "' not found, please check config")
+      }
+    } catch {
+      case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executeble skipped: " + ioe)
+    }
+  }
+  
+  final protected def preCmdInternal {
+    checkExecuteble
+    //for (input <- this.inputs) if (!input.exists) throw new IllegalStateException("Input: " + input + " for " + analysisName + " is missing")
+    //logger.debug("Config for " + analysisName + ": " + localConfig)
+    
+    beforeCmd
+    
+    addJobReportBinding("version", getVersion)
+    
+    if (threads == 0) threads = getThreads(defaultThreads)
+    if (threads > 1) nCoresRequest = Option(threads)
+    addJobReportBinding("cores", if (nCoresRequest.get.toInt > 0) nCoresRequest.get.toInt else 1)
+    
+    if (vmem == null) {
+      if (configContains("vmem")) vmem = config("vmem")
+      else if (!defaultVmem.isEmpty) vmem = defaultVmem
+    }
+    if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
+    jobName = this.analysisName + ":" + firstOutput.getName
+  }
+  
+  protected var versionCommand: String = _
+  protected val versionRegex: Regex = null
+  def getVersion : String = {
+    if (versionCommand == null || versionRegex == null) return "N/A"
+    val buffer = new StringBuffer()
+    val process = Process(versionCommand).run(ProcessLogger(buffer append _))
+    if (process.exitValue != 0) {
+      logger.warn("Version command: '" + versionCommand + "' give exit code " + process.exitValue + ", version not found")
+      return "N/A"
+    }
+    val lines = versionCommand lines_! ProcessLogger(buffer append _)
+    for (line <- lines) {
+      line match { 
+        case versionRegex(m) => return m
+        case _ =>
+      }
+    }
+    logger.warn("Version command: '" + versionCommand + "' give a exit code 0 but no version was found, executeble oke?")
+    return "N/A"
+  }
+  
+  def getThreads(default:Int) : Int = {
+    val maxThreads: Int = config("maxthreads", 8)
+    val threads: Int = config("threads", default)
+    if (maxThreads > threads) return threads
+    else return maxThreads
+  }
+  
+  def getThreads(default:Int, module:String) : Int = {
+    val maxThreads: Int = config("maxthreads", 8, module)
+    val threads: Int = config("threads", default, module)
+    if (maxThreads > threads) return threads
+    else return maxThreads
+  }
+}

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

+package nl.lumc.sasc.biopet.core
+
+import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
+
+abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
+  executeble = "java"
+  
+  override def commandLine: String = {
+    preCmdInternal
+    val cmd = super.commandLine
+    val finalCmd = executeble + cmd.substring(cmd.indexOf(" "))
+    addJobReportBinding("command", cmd)
+    return cmd
+  }
+}