Init framework for BamToBigWig

protected/biopet-protected-package/BiopetProtectedPackage.iml

@@ -95,6 +95,7 @@
     <orderEntry type="module" module-name="Gentrap" />
     <orderEntry type="module" module-name="Sage" />
     <orderEntry type="module" module-name="Yamsvp" />
+    <orderEntry type="module" module-name="bamtobigwig" />
     <orderEntry type="module" module-name="BiopetGatkPipelines" />
     <orderEntry type="module" module-name="BiopetGatkExtensions" />
     <orderEntry type="module" module-name="Basty" />

public/bamtobigwig/bamtobigwig.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="false">
+    <output url="file://$MODULE_DIR$/target/classes" />
+    <output-test url="file://$MODULE_DIR$/target/test-classes" />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module" module-name="BiopetFramework" />
+    <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:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
+    <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
+    <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
+    <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
+    <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
+    <orderEntry type="module-library">
+      <library name="Maven: com.sun:tools:1.4.2">
+        <CLASSES>
+          <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
+    <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
+    <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
+    <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
+    <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
+    <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
+    <orderEntry type="module-library">
+      <library name="Maven: com.sun:tools.jar:1.5">
+        <CLASSES>
+          <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+    <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
+    <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
+    <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
+    <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
+    <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+    <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
+    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
+    <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
+    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
+    <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
+    <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
+    <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
+    <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
+    <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
+    <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
+    <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
+    <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
+    <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
+    <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" 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: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
+    <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" />
+  </component>
+</module>
\ No newline at end of file

public/bamtobigwig/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>nl.lumc.sasc</groupId>
+    <artifactId>BamToBigWig</artifactId>
+    <packaging>jar</packaging>
+
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.3.0-DEV</version>
+        <relativePath>../</relativePath>
+    </parent>
+
+    <inceptionYear>2014</inceptionYear>
+    <name>BamToBigWig</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+</project>
\ No newline at end of file

public/bamtobigwig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToBigWig.scala

+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 1/29/15.
+ */
+class BamToBigWig(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  def init(): Unit = {
+  }
+
+  def biopetScript(): Unit = {
+  }
+}
+
+object BamToBigWig extends PipelineCommand
\ No newline at end of file

public/biopet-framework/BiopetFramework.iml

 <?xml version="1.0" encoding="UTF-8"?>
 <module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="FacetManager">
+    <facet type="Python" name="Python">
+      <configuration sdkName="" />
+    </facet>
+  </component>
   <component name="NewModuleRootManager" inherit-compiler-output="false">
     <output url="file://$MODULE_DIR$/target/classes" />
     <output-test url="file://$MODULE_DIR$/target/test-classes" />

public/biopet-public-package/BiopetPublicPackage.iml

@@ -94,5 +94,6 @@
     <orderEntry type="module" module-name="Gentrap" />
     <orderEntry type="module" module-name="Sage" />
     <orderEntry type="module" module-name="Yamsvp" />
+    <orderEntry type="module" module-name="bamtobigwig" />
   </component>
 </module>
\ No newline at end of file

public/biopet-public-package/pom.xml

@@ -75,6 +75,11 @@
             <artifactId>Yamsvp</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BamToBigWig</artifactId>
+            <version>${project.version}</version>
+        </dependency>
     </dependencies>
     <build>
         <plugins>

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

@@ -22,7 +22,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
     nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
     nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
-    nl.lumc.sasc.biopet.pipelines.sage.Sage
+    nl.lumc.sasc.biopet.pipelines.sage.Sage,
+    nl.lumc.sasc.biopet.pipelines.bamtobigwig.BamToBigWig
   )
 
   def tools: List[MainCommand] = List(

public/pom.xml

@@ -33,6 +33,7 @@
         <module>mapping</module>
         <module>sage</module>
         <module>yamsvp</module>
+        <module>bamtobigwig</module>
     </modules>
     
     <properties>