Switched Basty to Shiva

protected/biopet-gatk-pipelines/pom.xml

@@ -39,6 +39,11 @@
             <artifactId>Mapping</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Basty</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Shiva</artifactId>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala

+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 3/4/15.
+ */
+class Basty(val root: Configurable) extends QScript with BastyTrait {
+  qscript =>
+  def this() = this(null)
+
+  override def variantcallers = List("unifiedgenotyper")
+
+  override lazy val shiva = new Shiva(qscript)
+}
+
+object Basty extends PipelineCommand
\ No newline at end of file

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala

@@ -11,7 +11,7 @@ object BiopetExecutableProtected extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
     nl.lumc.sasc.biopet.pipelines.gatk.Shiva,
     nl.lumc.sasc.biopet.pipelines.gatk.ShivaVariantcalling,
-    nl.lumc.sasc.biopet.pipelines.basty.Basty)
+    nl.lumc.sasc.biopet.pipelines.gatk.Basty)
 
   def tools = BiopetExecutablePublic.tools
 }
\ No newline at end of file

protected/pom.xml

@@ -20,7 +20,6 @@
     <modules>
         <module>biopet-gatk-extensions</module>
         <module>biopet-gatk-pipelines</module>
-        <module>basty</module>
         <module>biopet-protected-package</module>
     </modules>
 </project>
\ No newline at end of file

protected/basty/pom.xml → public/basty/pom.xml

@@ -31,7 +31,7 @@
         </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetGatkPipelines</artifactId>
+            <artifactId>Shiva</artifactId>
             <version>${project.version}</version>
         </dependency>
         <dependency>

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

+package nl.lumc.sasc.biopet.pipelines.basty
+
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 3/4/15.
+ */
+class Basty(val root: Configurable) extends QScript with BastyTrait {
+  def this() = this(null)
+}
+
+object Basty extends PipelineCommand
\ No newline at end of file

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

@@ -8,17 +8,13 @@ package nl.lumc.sasc.biopet.pipelines.basty
 import java.io.File
 import nl.lumc.sasc.biopet.core.MultiSampleQScript
 import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.{ RunGubbins, Cat, Raxml }
-import nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
-import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
+import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, Shiva }
 import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QScript
 
-class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
+trait BastyTrait extends MultiSampleQScript {
   qscript =>
-  def this() = this(null)
 
   case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
 
@@ -26,10 +22,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
 
   override def defaults = ConfigUtils.mergeMaps(Map(
     "ploidy" -> 1,
-    "variantscallers" -> variantcallers
+    "variantcallers" -> variantcallers
   ), super.defaults)
 
-  val shiva = new Shiva(qscript)
+  lazy val shiva: ShivaTrait = new Shiva(qscript)
 
   def summaryFile: File = new File(outputDir, "Sage.summary.json")
 
@@ -114,7 +110,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
       val raxmlMl = new Raxml(this)
       raxmlMl.input = variants
       raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
-      raxmlMl.p = seed
+      raxmlMl.p = Some(seed)
       raxmlMl.n = outputName + "_ml"
       raxmlMl.w = dirSufixRaxml
       raxmlMl.N = config("ml_runs", default = 20, submodule = "raxml")
@@ -127,10 +123,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
         raxmlBoot.threads = 1
         raxmlBoot.input = variants
         raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
-        raxmlBoot.p = seed
-        raxmlBoot.b = math.abs(r.nextInt)
+        raxmlBoot.p = Some(seed)
+        raxmlBoot.b = Some(math.abs(r.nextInt))
         raxmlBoot.w = dirSufixRaxml
-        raxmlBoot.N = 1
+        raxmlBoot.N = Some(1)
         raxmlBoot.n = outputName + "_boot_" + t
         add(raxmlBoot)
         raxmlBoot.getBootstrapFile
@@ -144,7 +140,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
       raxmlBi.t = raxmlMl.getBestTreeFile
       raxmlBi.z = cat.output
       raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
-      raxmlBi.p = seed
+      raxmlBi.p = Some(seed)
       raxmlBi.f = "b"
       raxmlBi.n = outputName + "_bi"
       raxmlBi.w = dirSufixRaxml
@@ -181,5 +177,3 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     return FastaOutput(bastyGenerateFasta.outputVariants, bastyGenerateFasta.outputConsensus, bastyGenerateFasta.outputConsensusVariants)
   }
 }
-
-object Basty extends PipelineCommand

public/biopet-public-package/pom.xml

@@ -100,6 +100,11 @@
             <artifactId>Shiva</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Basty</artifactId>
+            <version>${project.version}</version>
+        </dependency>
     </dependencies>
     <build>
         <plugins>

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

@@ -31,7 +31,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
 
   def pipelines: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
-    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
+    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
+    nl.lumc.sasc.biopet.pipelines.basty.Basty
   ) ::: protectedPipelines
 
   def tools: List[MainCommand] = List(

public/pom.xml

@@ -38,6 +38,7 @@
         <module>carp</module>
 	    <module>toucan</module>
         <module>shiva</module>
+        <module>basty</module>
     </modules>
     
     <properties>