Added License to header of all files

protected/basty/pom.xml

+<!--
+
+    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
+
+-->
 <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>

protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/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.basty
 
 import java.io.File

protected/biopet-gatk-extensions/pom.xml

+<!--
+
+    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
+
+-->
 <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>

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.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.extensions.gatk
 
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.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.extensions.gatk
 
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.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.extensions.gatk
 
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.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.extensions.gatk
 
 import java.io.File

protected/biopet-gatk-pipelines/pom.xml

+<!--
+
+    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
+
+-->
 <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>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.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.{ BiopetQScript, PipelineCommand }

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.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.{ BiopetQScript, PipelineCommand }

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

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

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.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.{ BiopetQScript, PipelineCommand }

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.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.{ BiopetQScript, PipelineCommand }

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/SampleCompareMetrics.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/pom.xml

+<!--
+
+    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
+
+-->
 <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>

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.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.core
 
 object BiopetExecutableProtected extends BiopetExecutable {

protected/pom.xml

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

public/bammetrics/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.
+
+-->
 <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>

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.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.bammetrics
 
 import nl.lumc.sasc.biopet.scripts.CoverageStats

public/biopet-framework/nb-configuration.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-shared-configuration>
     <!--
 This file contains additional configuration written by modules in the NetBeans IDE.

public/biopet-framework/nbactions-yamsvp.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.
+
+-->
 <actions>
         <action>
             <actionName>run</actionName>

public/biopet-framework/nbactions.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.
+
+-->
 <actions>
         <action>
             <actionName>run</actionName>

public/biopet-framework/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.
+
+-->
 <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>

public/biopet-framework/src/main/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.
+#
+
 # Set root logger level to DEBUG and its only appender to A1.
 log4j.rootLogger=INFO, A1
 

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py

 #!/usr/bin/env python
+#
+# 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.
+#
+
 
 __copyright__ = """
 Copyright (C) 2013 - Tim te Beek

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/bam_rna.py

 #!/usr/bin/env python2.7
+#
+# 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.
+#
+
 
 # bam_rna.py
 #

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/gc_dist.py

 #!/usr/bin/env python
+#
+# 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.
+#
+
 #
 # gc_dist.py
 #

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/insert_dist.py

 #!/usr/bin/env python
+#
+# 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.
+#
+
 #
 # insert_dist.py
 #

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/parse_cuffcmp.py

 #!/usr/bin/env python
+#
+# 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.
+#
+
 #
 # oarse_cuffcmp.py
 #

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py

 #!/usr/bin/env python
+#
+# 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.
+#
+
 
 # pdf_report.py
 

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/rna_metrics.py

 #!/usr/bin/env python2
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running