Update licenses

protected/biopet-gatk-extensions/src/test/resources/log4j.properties

 #
-# 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.
+# Due to the license issue with GATK, this part of Biopet can only be used inside the
+# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+# on how to use this protected part of biopet or contact us at sasc@lumc.nl
 #
 
 # Set root logger level to DEBUG and its only appender to A1.

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

+/**
+ * Due to the license issue with GATK, this part of Biopet can only be used inside the
+ * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+ * on how to use this protected part of biopet or contact us at sasc@lumc.nl
+ */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.PipelineCommand

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

+/**
+ * Due to the license issue with GATK, this part of Biopet can only be used inside the
+ * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+ * on how to use this protected part of biopet or contact us at sasc@lumc.nl
+ */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.PipelineCommand

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

+/**
+ * Due to the license issue with GATK, this part of Biopet can only be used inside the
+ * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+ * on how to use this protected part of biopet or contact us at sasc@lumc.nl
+ */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.PipelineCommand

protected/biopet-gatk-pipelines/src/test/resources/log4j.properties

 #
-# 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.
+# Due to the license issue with GATK, this part of Biopet can only be used inside the
+# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+# on how to use this protected part of biopet or contact us at sasc@lumc.nl
 #
 
 # Set root logger level to DEBUG and its only appender to A1.

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

+/**
+ * Due to the license issue with GATK, this part of Biopet can only be used inside the
+ * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+ * on how to use this protected part of biopet or contact us at sasc@lumc.nl
+ */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
 import com.google.common.io.Files

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

+/**
+ * Due to the license issue with GATK, this part of Biopet can only be used inside the
+ * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+ * on how to use this protected part of biopet or contact us at sasc@lumc.nl
+ */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
 import java.io.File

protected/biopet-protected-package/src/test/resources/log4j.properties

 #
-# 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.
+# Due to the license issue with GATK, this part of Biopet can only be used inside the
+# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+# on how to use this protected part of biopet or contact us at sasc@lumc.nl
 #
 
 # Set root logger level to DEBUG and its only appender to A1.

protected/log4j.properties

 #
-# 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.
+# Due to the license issue with GATK, this part of Biopet can only be used inside the
+# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+# on how to use this protected part of biopet or contact us at sasc@lumc.nl
 #
 
 # Set root logger level to DEBUG and its only appender to A1.

protected/src/src/test/resources/log4j.properties

 #
-# 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.
+# Due to the license issue with GATK, this part of Biopet can only be used inside the
+# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+# on how to use this protected part of biopet or contact us at sasc@lumc.nl
 #
 
 # Set root logger level to DEBUG and its only appender to A1.

public/bam2wig/pom.xml

 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    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.
+
+-->
 <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">

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.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.pipelines.bamtobigwig
 
 import java.io.File

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.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.pipelines.bamtobigwig
 
 import java.io.{ PrintWriter, File }

public/basty/pom.xml

+<!--
+
+    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.
+
+-->
 <!--
 
     Due to the license issue with GATK, this part of Biopet can only be used inside the

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

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.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.
+ */
 /**
  * Due to the license issue with GATK, this part of Biopet can only be used inside the
  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.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 nl.lumc.sasc.biopet.core.config.Configurable

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.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.summary
 
 import java.io.File

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.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.summary
 
 import java.io.File

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.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.summary
 
 import java.io.{ FileInputStream, PrintWriter, File }