change ALL licenses across all files.

bam2wig/pom.xml

@@ -10,8 +10,7 @@
 
     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
+    A dual licensing mode is applied. The source code within this project 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.
 

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

bam2wig/src/test/resources/log4j.properties

@@ -8,8 +8,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.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 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

bammetrics/pom.xml

@@ -9,8 +9,7 @@
 
     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
+    A dual licensing mode is applied. The source code within this project 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.
 

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py

@@ -9,8 +9,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

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

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

bammetrics/src/test/resources/log4j.properties

@@ -8,8 +8,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

basty/pom.xml

@@ -9,8 +9,7 @@
 
     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
+    A dual licensing mode is applied. The source code within this project 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.
 

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

@@ -8,8 +8,7 @@
  *
  * 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
+ * A dual licensing mode is applied. The source code within this project 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.
  */

basty/src/test/resources/log4j.properties

@@ -8,8 +8,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

biopet-aggregate/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 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">

biopet-core/pom.xml

@@ -10,8 +10,7 @@
 
     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
+    A dual licensing mode is applied. The source code within this project 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.
 

biopet-core/src/main/resources/log4j.properties

@@ -8,8 +8,7 @@
 #
 # 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
+# A dual licensing mode is applied. The source code within this project 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.
 #

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css

-/*!
- * Bootstrap v3.3.4 (http://getbootstrap.com)
- * Copyright 2011-2015 Twitter, Inc.
- * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  */.btn-danger,.btn-default,.btn-info,.btn-primary,.btn-success,.btn-warning{text-shadow:0 -1px 0 rgba(0,0,0,.2);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075)}.btn-danger.active,.btn-danger:active,.btn-default.active,.btn-default:active,.btn-info.active,.btn-info:active,.btn-primary.active,.btn-primary:active,.btn-success.active,.btn-success:active,.btn-warning.active,.btn-warning:active{-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,.125);box-shadow:inset 0 3px 5px rgba(0,0,0,.125)}.btn-danger .badge,.btn-default .badge,.btn-info .badge,.btn-primary .badge,.btn-success .badge,.btn-warning .badge{text-shadow:none}.btn.active,.btn:active{background-image:none}.btn-default{text-shadow:0 1px 0 #fff;background-image:-webkit-linear-gradient(top,#fff 0,#e0e0e0 100%);background-image:-o-linear-gradient(top,#fff 0,#e0e0e0 100%);background-image:-webkit-gradient(linear,left top,left 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