diff --git a/biopet-framework/BiopetFramework.iml b/biopet-framework/BiopetFramework.iml
index 576d75a0e85692d1617394c0fee61366299e856c..3dcb6528e61ce918ca8776e785bec31720f9b2aa 100644
--- a/biopet-framework/BiopetFramework.iml
+++ b/biopet-framework/BiopetFramework.iml
@@ -5,7 +5,8 @@
<configuration>
<option name="compilerLibraryLevel" value="Project" />
<option name="compilerLibraryName" value="Maven: org.scala-lang:scala-compiler-bundle:2.11.2" />
- <option name="compilerOptions" value="-dependencyfile $MODULE_DIR$/target/.scala_dependencies" />
+ <option name="compilerOptions" value="-dependencyfile $MODULE_DIR$/target/.scala_dependencies -feature" />
+ <option name="deprecationWarnings" value="true" />
<option name="languageLevel" value="Scala 2.11" />
<option name="vmOptions" value="" />
</configuration>
@@ -29,15 +30,15 @@
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="library" name="com.twitter:algebird-core_2.10:0.8.1" level="project" />
<orderEntry type="library" name="gatk-protected" level="project" />
- <orderEntry type="library" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: junit:junit:4.10" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" />
<orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" />
- <orderEntry type="library" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
<orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
<orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
<orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.3" level="project" />
@@ -49,6 +50,5 @@
<orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
<orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
<orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
- <orderEntry type="library" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
</component>
-</module>
+</module>
\ No newline at end of file
diff --git a/biopet-framework/nb-configuration.xml b/biopet-framework/nb-configuration.xml
index c2f0518e2a30c8af3fb854bd8e16e70f23679e5f..d1da94c53d08d4b3d1ab9b48ebfd64d331cdf41c 100644
--- a/biopet-framework/nb-configuration.xml
+++ b/biopet-framework/nb-configuration.xml
@@ -25,6 +25,5 @@ Any value defined here will override the pom.xml file value but is only applicab
<com-junichi11-netbeans-changelf.use-global>false</com-junichi11-netbeans-changelf.use-global>
<com-junichi11-netbeans-changelf.show-dialog>true</com-junichi11-netbeans-changelf.show-dialog>
<org-netbeans-modules-javascript2-requirejs.enabled>true</org-netbeans-modules-javascript2-requirejs.enabled>
- <netbeans.hint.jdkPlatform>JDK_1.8</netbeans.hint.jdkPlatform>
</properties>
</project-shared-configuration>
diff --git a/biopet-framework/pom.xml b/biopet-framework/pom.xml
index ac2879e75dea217e25cc42adf3e9b0aae80cd277..d06905d40c8554edb08208518c9d6231d04767ba 100644
--- a/biopet-framework/pom.xml
+++ b/biopet-framework/pom.xml
@@ -31,10 +31,17 @@
<version>6.8</version>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.9.5</version>
+ <scope>test</scope>
+ </dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.11</artifactId>
<version>2.2.1</version>
+ <scope>test</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
@@ -71,11 +78,6 @@
<artifactId>scopt_2.10</artifactId>
<version>3.2.0</version>
</dependency>
- <dependency>
- <groupId>org.mockito</groupId>
- <artifactId>mockito-all</artifactId>
- <version>1.9.5</version>
- </dependency>
</dependencies>
<build>
<resources>
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
new file mode 100644
index 0000000000000000000000000000000000000000..a92926381614fc998a7a7afe367f1cb9457b79fc
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -0,0 +1,71 @@
+package nl.lumc.sasc.biopet.extensions
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import java.io.File
+
+class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
+
+ override val defaultThreads = 4
+ override def versionCommand = executable + " -v"
+ override val versionRegex = """.*version \w* .*""".r
+
+ @Input(doc = "Input phy/fasta file", required = true)
+ var input: File = _
+
+ @Argument(doc = "Model", required = true)
+ var m: String = _
+
+ @Argument(doc = "Parsimony seed", required = false)
+ var p: Option[Int] = config("p")
+
+ @Argument(doc = "Bootstrapping seed", required = false)
+ var b: Option[Int] = config("b")
+
+ @Argument(doc = "Number of runs", required = false)
+ var N: Option[Int] = config("N")
+
+ @Argument(doc = "Name of output files", required = true)
+ var n: String = _
+
+ @Argument(doc = "Name of output files", required = true)
+ var f: String = "d"
+
+ @Argument(doc = "Output directory", required = false)
+ var w: String = jobLocalDir.getAbsolutePath
+
+ @Input(required = false)
+ var t: File = _
+
+ @Input(required = false)
+ var z: File = _
+
+ @Output(doc = "Output files", required = false)
+ private var out: List[File] = Nil
+
+ executable = config("exe", default = "raxmlHPC")
+
+ override def afterGraph {
+ super.afterGraph
+ f match {
+ case "d" if b.isEmpty => out +:= getBestTree
+ case "d" if b.isDefined => out +:= getBootstrap
+ }
+ }
+
+ def getBestTree: File = new File(w + File.separator + "RAxML_bestTree." + n)
+ def getBootstrap: File = new File(w + File.separator + "RAxML_bootstrap." + n)
+
+ def cmdLine = required(executable) +
+ required("-m", m) +
+ required("-s", input) +
+ optional("-p", p) +
+ optional("-b", b) +
+ optional("-N", N) +
+ optional("-w", w) +
+ optional("-f", f) +
+ optional("-t", t) +
+ optional("-z", z) +
+ (if (threads > 1) required("-T", threads) else "")
+}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
new file mode 100644
index 0000000000000000000000000000000000000000..79877180170b8cb4ec1b4d10ebb9b8f74bc9f253
--- /dev/null
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
@@ -0,0 +1,37 @@
+package nl.lumc.sasc.biopet.extensions.gatk
+
+import java.io.File
+import nl.lumc.sasc.biopet.core.config.Configurable
+
+class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
+ override def afterGraph {
+ super.afterGraph
+ }
+}
+
+object VariantEval {
+ def apply(root: Configurable, sample: File, compareWith: File,
+ output: File): VariantEval = {
+ val vareval = new VariantEval(root)
+ vareval.eval = Seq(sample)
+ vareval.comp = Seq(compareWith)
+ vareval.out = output
+ vareval.afterGraph
+ return vareval
+ }
+
+ def apply(root: Configurable, sample: File, compareWith: File,
+ output: File, ST: Seq[String], EV: Seq[String]): VariantEval = {
+ val vareval = new VariantEval(root)
+ vareval.eval = Seq(sample)
+ vareval.comp = Seq(compareWith)
+ vareval.out = output
+ vareval.noST = true
+ vareval.ST = ST
+ vareval.noEV = true
+ vareval.EV = EV
+ vareval.afterGraph
+ return vareval
+ }
+
+}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
index 2ed691bb0d52b94a07b8ccef7c84909cbf3ff372..067012e443ee81958910e07fa0eb8c8361293bd8 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
@@ -5,8 +5,8 @@ import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.gatk.SelectVariants
+import nl.lumc.sasc.biopet.extensions.gatk.VariantEval
import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.extensions.gatk.{ CommandLineGATK, VariantEval }
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQScript {
@@ -28,12 +28,6 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
var sampleVcfs: Map[String, File] = Map()
def generalSampleDir = outputDir + "samples/"
- trait gatkArguments extends CommandLineGATK {
- this.reference_sequence = reference
- this.memoryLimit = 2
- this.jobResourceRequests :+= "h_vmem=4G"
- }
-
def init() {
if (reference == null) reference = config("reference")
if (config.contains("target_bed"))
@@ -70,14 +64,13 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
for ((sample, sampleVcf) <- sampleVcfs) {
val sampleDir = generalSampleDir + sample + File.separator
for ((compareSample, compareSampleVcf) <- sampleVcfs) {
- val variantEval = new VariantEval with gatkArguments
- variantEval.eval = Seq(sampleVcf)
- variantEval.comp = Seq(compareSampleVcf)
- variantEval.out = new File(sampleDir + sample + "-" + compareSample + ".eval.txt")
- variantEval.noST = true
- variantEval.ST = Seq("VariantType", "CompRod")
- variantEval.noEV = true
- variantEval.EV = Seq("CompOverlap")
+ val variantEval = VariantEval(this,
+ sampleVcf,
+ compareSampleVcf,
+ new File(sampleDir + sample + "-" + compareSample + ".eval.txt"),
+ Seq("VariantType", "CompRod"),
+ Seq("CompOverlap")
+ )
if (targetBed != null) variantEval.L = targetBed
add(variantEval)
sampleCompareMetrics.deps ::= variantEval.out