Commit 0a33b3d3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Update to Queue/GATK 3.2

parent 719894d1
......@@ -4,4 +4,6 @@
/pipeline-template/nbactions.xml
/gatk-variantcalling/nbactions.xml
/gatk-variantcalling/dependency-reduced-pom.xml
/bam-metrics/nbactions.xml
\ No newline at end of file
/bam-metrics/nbactions.xml
dependency-reduced-pom.xml
nbactions.xml
......@@ -55,7 +55,7 @@
<dependency>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>queue-package</artifactId>
<version>3.1</version>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......
package nl.lumc.sasc.biopet.pipelines.bammetrics
import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.gatk.queue.QScript
import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
import java.io.File
import nl.lumc.sasc.biopet.core.apps.{BedToInterval, BiopetFlagstat}
......
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
import org.broadinstitute.sting.commandline._
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
import java.io.File
class CoverageStats(val root:Configurable) extends PythonCommandLineFunction {
......
......@@ -52,7 +52,7 @@
<dependency>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>queue-package</artifactId>
<version>3.1</version>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......
package nl.lumc.sasc.biopet.core
import org.broadinstitute.sting.commandline._
import org.broadinstitute.gatk.utils.commandline._
import scala.sys.process._
import nl.lumc.sasc.biopet.core.config._
......
......@@ -2,9 +2,9 @@ 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 org.broadinstitute.gatk.queue.QException
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline._
import scala.sys.process._
import scala.util.matching.Regex
......
package nl.lumc.sasc.biopet.core
import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
abstract class BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
executeble = "java"
......
......@@ -27,21 +27,21 @@
package nl.lumc.sasc.biopet.core
import java.io.File
import org.broadinstitute.sting.commandline._
import org.broadinstitute.sting.queue.util._
import org.broadinstitute.sting.queue.QCommandPlugin
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.QScriptManager
import org.broadinstitute.sting.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
import org.broadinstitute.gatk.utils.commandline._
import org.broadinstitute.gatk.queue.util._
import org.broadinstitute.gatk.queue.QCommandPlugin
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.QScriptManager
import org.broadinstitute.gatk.queue.engine.{QStatusMessenger, QGraphSettings, QGraph}
import collection.JavaConversions._
import org.broadinstitute.sting.utils.classloader.PluginManager
import org.broadinstitute.sting.utils.exceptions.UserException
import org.broadinstitute.sting.utils.io.IOUtils
import org.broadinstitute.sting.utils.help.ApplicationDetails
import org.broadinstitute.gatk.utils.classloader.PluginManager
import org.broadinstitute.gatk.utils.exceptions.UserException
import org.broadinstitute.gatk.utils.io.IOUtils
import org.broadinstitute.gatk.utils.help.ApplicationDetails
import java.io.FileOutputStream
import java.net.URL
import java.util.{ResourceBundle, Arrays}
import org.broadinstitute.sting.utils.text.TextFormattingUtils
import org.broadinstitute.gatk.utils.text.TextFormattingUtils
import org.apache.commons.io.FilenameUtils
/**
......
......@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.sting.commandline._
import org.broadinstitute.sting.queue.QSettings
import org.broadinstitute.sting.queue.function.QFunction
import org.broadinstitute.gatk.utils.commandline._
import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
trait BiopetQScript extends Configurable {
@Argument(doc="Config Json file",shortName="config", required=false)
......
......@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.core
import java.io.FileOutputStream
//import org.broadinstitute.sting.queue.QCommandLine
import org.broadinstitute.sting.queue.util.Logging
import org.broadinstitute.gatk.queue.util.Logging
trait PipelineCommand extends Logging {
// val src = ""
......
package nl.lumc.sasc.biopet.core.apps
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMSequenceRecord
import java.io.File
import net.sf.samtools.SAMSequenceRecord
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.sting.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import java.io.PrintWriter
import net.sf.samtools.SAMFileReader
import scala.io.Source
class BedToInterval(val root:Configurable) extends BiopetJavaCommandLineFunction {
......
package nl.lumc.sasc.biopet.core.apps
import htsjdk.samtools.SAMFileReader
import htsjdk.samtools.SAMRecord
import java.io.{BufferedInputStream, File, FileInputStream, PrintWriter}
import net.sf.samtools.SAMFileReader
import net.sf.samtools.SAMRecord
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import scala.io.Source
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.sting.commandline.{Input, Output}
import org.broadinstitute.sting.queue.util.Logging
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.queue.util.Logging
import scala.collection.JavaConversions._
import scala.collection.mutable.Map
......
......@@ -5,7 +5,7 @@ import java.util.zip.GZIPInputStream
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import scala.io.Source
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.sting.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
class FastqSplitter(val root:Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
......
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.config
import nl.lumc.sasc.biopet.core._
import scala.util.parsing.json._
import java.io.File
import org.broadinstitute.sting.queue.util.Logging
import org.broadinstitute.gatk.queue.util.Logging
class Config(var map: Map[String,Any]) extends Logging {
logger.debug("Init phase of config")
......
package nl.lumc.sasc.biopet.core.config
import java.io.File
import org.broadinstitute.sting.queue.util.Logging
import org.broadinstitute.gatk.queue.util.Logging
trait Configurable extends Logging {
val root: Configurable
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.sting.commandline._
import org.broadinstitute.gatk.utils.commandline._
import java.io.File
class Cat(val root:Configurable) extends BiopetCommandLineFunction {
......
......@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import org.broadinstitute.sting.queue.function.InProcessFunction
import org.broadinstitute.sting.commandline._
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline._
import java.io.File
import scala.sys.process._
......
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
//import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import org.broadinstitute.gatk.utils.commandline._
import java.io.File
class Pbzip2(val root:Configurable) extends BiopetCommandLineFunction {
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.function
import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.commandline._
import org.broadinstitute.gatk.utils.commandline._
import java.io.File
import scala.collection.JavaConversions._
......
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