Merge branch 'develop' of git.lumc.nl:biopet/biopet into fix-rename-extentsionsfolder

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -14,8 +14,8 @@ class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk
 
   override val defaultThreads = 3
 
-  override def beforeGraph() {
-    super.beforeGraph()
+  override def freezeFieldValues() {
+    super.freezeFieldValues()
 
     nt = Option(getThreads)
     memoryLimit = Option(nt.getOrElse(1) * 2)

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -20,7 +20,6 @@ object BaseRecalibrator {
     val br = new BaseRecalibrator(root)
     br.input_file :+= input
     br.out = output
-    br.beforeGraph()
     br
   }
 }
\ No newline at end of file

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -5,17 +5,19 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ CommandLineResources, Reference, BiopetJavaCommandLineFunction }
 import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
-trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
+trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference {
   memoryLimit = Option(3)
 
   override def subPath = "gatk" :: super.subPath
 
   jarFile = config("gatk_jar")
 
+  reference_sequence = referenceFasta()
+
   override def defaultCoreMemory = 4.0
   override def faiRequired = true
 
@@ -33,14 +35,9 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree")
 
-  override def versionRegex = """(.*)""".r
-  override def versionExitcode = List(0, 1)
-  override def versionCommand = executable + " -jar " + jarFile + " -version"
-
-  override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
+  //override def versionRegex = """(.*)""".r
+  //override def versionExitcode = List(0, 1)
+  //override def versionCommand = executable + " -jar " + jarFile + " -version"
 
-  override def beforeGraph(): Unit = {
-    super.beforeGraph()
-    if (reference_sequence == null) reference_sequence = referenceFasta()
-  }
+  //override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
 }

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -38,11 +38,11 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
     stand_emit_conf = config("stand_emit_conf", default = 0)
   }
 
-  override def beforeGraph() {
-    super.beforeGraph()
+  override def freezeFieldValues() {
+    super.freezeFieldValues()
     if (bamOutput != null && nct.getOrElse(1) > 1) {
-      threads = 1
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
+      nCoresRequest = Some(1)
     }
     nct = Some(getThreads)
     memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -28,8 +28,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
 
   override val defaultThreads = 1
 
-  override def beforeGraph() {
-    super.beforeGraph()
+  override def freezeFieldValues() {
+    super.freezeFieldValues()
 
     genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
     nct = Some(getThreads)

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -10,9 +10,6 @@ import java.io.File
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
-  override def beforeGraph() {
-    super.beforeGraph()
-  }
 }
 
 object VariantEval {
@@ -22,7 +19,6 @@ object VariantEval {
     vareval.eval = Seq(sample)
     vareval.comp = Seq(compareWith)
     vareval.out = output
-    vareval.beforeGraph()
     vareval
   }
 
@@ -36,7 +32,6 @@ object VariantEval {
     vareval.ST = ST
     vareval.noEV = true
     vareval.EV = EV
-    vareval.beforeGraph()
     vareval
   }
 

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

@@ -74,8 +74,6 @@ class ShivaTest extends TestNGSuite with Matchers {
       val numberLibs = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 2 else 0)
       val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0) + (if (sample3) 1 else 0)
 
-      pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
-      pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
       pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberLibs + (if (sample3) 1 else 0))
 
       // Gatk preprocess

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

@@ -137,7 +137,6 @@ trait BastyTrait extends MultiSampleQScript {
       val numBoot = config("boot_runs", default = 100, submodule = "raxml").asInt
       val bootList = for (t <- 0 until numBoot) yield {
         val raxmlBoot = new Raxml(this)
-        raxmlBoot.threads = 1
         raxmlBoot.input = variants
         raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
         raxmlBoot.p = Some(seed)

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

@@ -15,25 +15,276 @@
  */
 package nl.lumc.sasc.biopet.core
 
-/**
- * This class is for commandline programs where the executable is a non JVM based program
- */
-abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {
+import java.io.{ PrintWriter, File, FileInputStream }
+import java.security.MessageDigest
+
+import nl.lumc.sasc.biopet.utils.Logging
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import org.broadinstitute.gatk.utils.runtime.ProcessSettings
+import org.ggf.drmaa.JobTemplate
+
+import scala.collection.mutable
+import scala.io.Source
+import scala.sys.process.{ Process, ProcessLogger }
+import scala.util.matching.Regex
+import scala.collection.JavaConversions._
+
+/** Biopet command line trait to auto check executable and cluster values */
+trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
+  analysisName = configName
+
+  @Input(doc = "deps", required = false)
+  var deps: List[File] = Nil
+
+  @Output
+  var outputFiles: List[File] = Nil
+
+  var executable: String = _
+
+  /** This is the default shell for drmaa jobs */
+  def defaultRemoteCommand = "bash"
+  private val remoteCommand: String = config("remote_command", default = defaultRemoteCommand)
+
+  private def changeScript(file: File): Unit = {
+    val lines = Source.fromFile(file).getLines().toList
+    val writer = new PrintWriter(file)
+    writer.println("set -eubf")
+    writer.println("set -o pipefail")
+    lines.foreach(writer.println(_))
+    writer.close()
+  }
+
+  // This overrides the default "sh" from queue. For Biopet the default is "bash"
+  updateJobRun = {
+    case jt: JobTemplate => {
+      changeScript(new File(jt.getArgs.head.toString))
+      jt.setRemoteCommand(remoteCommand)
+    }
+    case ps: ProcessSettings => {
+      changeScript(new File(ps.getCommand.tail.head))
+      ps.setCommand(Array(remoteCommand) ++ ps.getCommand.tail)
+    }
+  }
+
+  /**
+   * Can override this method. This is executed just before the job is ready to run.
+   * Can check on run time files from pipeline here
+   */
+  def beforeCmd() {}
+
+  /** Can override this method. This is executed after the script is done en queue starts to generate the graph */
+  def beforeGraph() {}
+
+  override def freezeFieldValues() {
+    preProcessExecutable()
+    beforeGraph()
+    internalBeforeGraph()
+
+    super.freezeFieldValues()
+  }
+
+  /** Set default output file, threads and vmem for current job */
+  final def internalBeforeGraph(): Unit = {
+
+    pipesJobs.foreach(_.beforeGraph())
+    pipesJobs.foreach(_.internalBeforeGraph())
+
+  }
+
+  /** can override this value is executable may not be converted to CanonicalPath */
+  val executableToCanonicalPath = true
+
+  /**
+   * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
+   */
+  protected[core] def preProcessExecutable() {
+    if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
+      if (executable != null) {
+        if (!BiopetCommandLineFunction.executableCache.contains(executable)) {
+          try {
+            val oldExecutable = executable
+            val buffer = new StringBuffer()
+            val cmd = Seq("which", executable)
+            val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
+            if (process.exitValue == 0) {
+              executable = buffer.toString
+              val file = new File(executable)
+              if (executableToCanonicalPath) executable = file.getCanonicalPath
+              else executable = file.getAbsolutePath
+            } else Logging.addError("executable: '" + executable + "' not found, please check config")
+            BiopetCommandLineFunction.executableCache += oldExecutable -> executable
+            BiopetCommandLineFunction.executableCache += executable -> executable
+          } catch {
+            case ioe: java.io.IOException =>
+              logger.warn(s"Could not use 'which' on '$executable', check on executable skipped: " + ioe)
+          }
+        } else executable = BiopetCommandLineFunction.executableCache(executable)
+
+        if (!BiopetCommandLineFunction.executableMd5Cache.contains(executable)) {
+          if (new File(executable).exists()) {
+            val is = new FileInputStream(executable)
+            val cnt = is.available
+            val bytes = Array.ofDim[Byte](cnt)
+            is.read(bytes)
+            is.close()
+            val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
+            BiopetCommandLineFunction.executableMd5Cache += executable -> temp
+          } else BiopetCommandLineFunction.executableMd5Cache += executable -> "file_does_not_exist"
+        }
+      }
+    }
+    val md5 = BiopetCommandLineFunction.executableMd5Cache.get(executable)
+    addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
+  }
+
+  /** executes checkExecutable method and fill job report */
+  final protected def preCmdInternal() {
+    preProcessExecutable()
+    beforeCmd()
+
+    addJobReportBinding("cores", nCoresRequest match {
+      case Some(n) if n > 0 => n
+      case _                => 1
+    })
+    addJobReportBinding("version", getVersion)
+  }
+
+  /** Command to get version of executable */
+  protected[core] def versionCommand: String = null
+
+  /** Regex to get version from version command output */
+  protected[core] def versionRegex: Regex = null
+
+  /** Allowed exit codes for the version command */
+  protected[core] def versionExitcode = List(0)
+
+  /** Executes the version command */
+  private[core] def getVersionInternal: Option[String] = {
+    if (versionCommand == null || versionRegex == null) None
+    else getVersionInternal(versionCommand, versionRegex)
+  }
+
+  /** Executes the version command */
+  private[core] def getVersionInternal(versionCommand: String, versionRegex: Regex): Option[String] = {
+    if (versionCommand == null || versionRegex == null) return None
+    val exe = new File(versionCommand.trim.split(" ")(0))
+    if (!exe.exists()) return None
+    val stdout = new StringBuffer()
+    val stderr = new StringBuffer()
+    def outputLog = "Version command: \n" + versionCommand +
+      "\n output log: \n stdout: \n" + stdout.toString +
+      "\n stderr: \n" + stderr.toString
+    val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
+    if (!versionExitcode.contains(process.exitValue())) {
+      logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
+      return None
+    }
+    for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
+      line match {
+        case versionRegex(m) => return Some(m)
+        case _               =>
+      }
+    }
+    logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
+    None
+  }
+
+  /** Get version from cache otherwise execute the version command  */
+  def getVersion: Option[String] = {
+    if (!BiopetCommandLineFunction.executableCache.contains(executable))
+      preProcessExecutable()
+    if (!BiopetCommandLineFunction.versionCache.contains(versionCommand))
+      getVersionInternal match {
+        case Some(version) => BiopetCommandLineFunction.versionCache += versionCommand -> version
+        case _             =>
+      }
+    BiopetCommandLineFunction.versionCache.get(versionCommand)
+  }
+
+  private[core] var _inputAsStdin = false
+  def inputAsStdin = _inputAsStdin
+  private[core] var _outputAsStdout = false
+  def outputAsStsout = _outputAsStdout
+
+  /**
+   * This operator sends stdout to `that` and combine this into 1 command line function
+   * @param that Function that will read from stdin
+   * @return BiopetPipe function
+   */
+  def |(that: BiopetCommandLineFunction): BiopetCommandLineFunction = {
+    this._outputAsStdout = true
+    that._inputAsStdin = true
+    this.beforeGraph()
+    this.internalBeforeGraph()
+    that.beforeGraph()
+    that.internalBeforeGraph()
+    this match {
+      case p: BiopetPipe => {
+        p.commands.last._outputAsStdout = true
+        new BiopetPipe(p.commands ::: that :: Nil)
+      }
+      case _ => new BiopetPipe(List(this, that))
+    }
+  }
+
+  /**
+   * This operator can be used to give a program a file as stdin
+   * @param file File that will become stdin for this program
+   * @return It's own class
+   */
+  def :<:(file: File): BiopetCommandLineFunction = {
+    this._inputAsStdin = true
+    this.stdinFile = Some(file)
+    this
+  }
+
+  /**
+   * This operator can be used to give a program a file write it's atdout
+   * @param file File that will become stdout for this program
+   * @return It's own class
+   */
+  def >(file: File): BiopetCommandLineFunction = {
+    this._outputAsStdout = true
+    this.stdoutFile = Some(file)
+    this
+  }
+
+  @Output(required = false)
+  private[core] var stdoutFile: Option[File] = None
+
+  @Input(required = false)
+  private[core] var stdinFile: Option[File] = None
+
   /**
    * This function needs to be implemented to define the command that is executed
    * @return Command to run
    */
-  protected def cmdLine: String
+  protected[core] def cmdLine: String
 
   /**
    * implementing a final version of the commandLine from org.broadinstitute.gatk.queue.function.CommandLineFunction
    * User needs to implement cmdLine instead
    * @return Command to run
    */
-  final def commandLine: String = {
+  override final def commandLine: String = {
     preCmdInternal()
-    val cmd = cmdLine
+    val cmd = cmdLine +
+      stdinFile.map(file => " < " + required(file.getAbsoluteFile)).getOrElse("") +
+      stdoutFile.map(file => " > " + required(file.getAbsoluteFile)).getOrElse("")
     addJobReportBinding("command", cmd)
     cmd
   }
+
+  private[core] var pipesJobs: List[BiopetCommandLineFunction] = Nil
+  def addPipeJob(job: BiopetCommandLineFunction) {
+    pipesJobs :+= job
+    pipesJobs = pipesJobs.distinct
+  }
+}
+
+/** stores global caches */
+object BiopetCommandLineFunction {
+  private[core] val versionCache: mutable.Map[String, String] = mutable.Map()
+  private[core] val executableMd5Cache: mutable.Map[String, String] = mutable.Map()
+  private[core] val executableCache: mutable.Map[String, String] = mutable.Map()
 }

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

-/**
- * 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.core
-
-import java.io.{ File, FileInputStream }
-import java.security.MessageDigest
-
-import nl.lumc.sasc.biopet.utils.Logging
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.function.CommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.Input
-
-import scala.collection.mutable
-import scala.sys.process.{ Process, ProcessLogger }
-import scala.util.matching.Regex
-
-/** Biopet command line trait to auto check executable and cluster values */
-trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
-  analysisName = configName
-
-  @Input(doc = "deps", required = false)
-  var deps: List[File] = Nil
-
-  var threads = 0
-  def defaultThreads = 1
-
-  var vmem: Option[String] = config("vmem")
-  protected def defaultCoreMemory: Double = 1.0
-  protected def defaultVmemFactor: Double = 1.4
-  var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
-
-  var residentFactor: Double = config("resident_factor", default = 1.2)
-
-  private var coreMemory: Double = _
-
-  var executable: String = _
-
-  /**
-   * Can override this method. This is executed just before the job is ready to run.
-   * Can check on run time files from pipeline here
-   */
-  protected[core] def beforeCmd() {}
-
-  /** Can override this method. This is executed after the script is done en queue starts to generate the graph */
-  protected[core] def beforeGraph() {}
-
-  /** Set default output file, threads and vmem for current job */
-  override def freezeFieldValues() {
-    preProcessExecutable()
-    beforeGraph()
-    if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
-
-    if (threads == 0) threads = getThreads(defaultThreads)
-    if (threads > 1) nCoresRequest = Option(threads)
-
-    coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry)
-
-    if (config.contains("memory_limit")) memoryLimit = config("memory_limit")
-    else memoryLimit = Some(coreMemory * threads)
-
-    if (config.contains("resident_limit")) residentLimit = config("resident_limit")
-    else residentLimit = Some((coreMemory + (0.5 * retry)) * residentFactor)
-
-    if (!config.contains("vmem")) vmem = Some((coreMemory * (vmemFactor + (0.5 * retry))) + "G")
-    if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
-    jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
-
-    super.freezeFieldValues()
-  }
-
-  var retry = 0
-
-  override def setupRetry(): Unit = {
-    super.setupRetry()
-    if (vmem.isDefined) jobResourceRequests = jobResourceRequests.filterNot(_.contains("h_vmem="))
-    logger.info("Auto raise memory on retry")
-    retry += 1
-    this.freeze()
-  }
-
-  /** can override this value is executable may not be converted to CanonicalPath */
-  val executableToCanonicalPath = true
-
-  /**
-   * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
-   */
-  protected[core] def preProcessExecutable() {
-    if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
-      try if (executable != null) {
-        if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
-          val oldExecutable = executable
-          val buffer = new StringBuffer()
-          val cmd = Seq("which", executable)
-          val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
-          if (process.exitValue == 0) {
-            executable = buffer.toString
-            val file = new File(executable)
-            if (executableToCanonicalPath) executable = file.getCanonicalPath
-            else executable = file.getAbsolutePath
-          } else {
-            Logging.addError("executable: '" + executable + "' not found, please check config")
-          }
-          BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
-          BiopetCommandLineFunctionTrait.executableCache += executable -> executable
-        } else {
-          executable = BiopetCommandLineFunctionTrait.executableCache(executable)
-        }
-
-        if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
-          val is = new FileInputStream(executable)
-          val cnt = is.available
-          val bytes = Array.ofDim[Byte](cnt)
-          is.read(bytes)
-          is.close()
-          val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
-          BiopetCommandLineFunctionTrait.executableMd5Cache += executable -> temp
-        }
-      } catch {
-        case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
-      }
-    }
-    val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable