Tools split into new modules, core and utils are compileable now

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp

-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 <%@ var summary: Summary %>
 <%@ var rootPath: String %>

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp

-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 <%@ var summary: Summary %>
 <%@ var sampleId: Option[String] %>

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp

-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(java.io.File)
 <%@ var summary: Summary %>

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp

 #import(nl.lumc.sasc.biopet.utils.IoUtils)
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(org.apache.commons.io.FileUtils)
 #import(java.io.File)

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp

 #import(nl.lumc.sasc.biopet.utils.IoUtils)
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(org.apache.commons.io.FileUtils)
 #import(java.io.File)

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp

-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp

-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)

public/biopet-core/pom.xml

@@ -42,6 +42,11 @@
             <artifactId>gatk-queue</artifactId>
             <version>3.4</version>
         </dependency>
+        <dependency>
+            <groupId>org.broadinstitute.gatk</groupId>
+            <artifactId>gatk-queue-extensions-public</artifactId>
+            <version>3.4</version>
+        </dependency>
         <dependency>
             <groupId>org.scalatra.scalate</groupId>
             <artifactId>scalate-core_2.10</artifactId>

public/biopet-core/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
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+log4j.appender.A1.Target=System.err
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file

public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt

+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.
\ No newline at end of file

public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var pipeline: String = summary.getValue("meta", "pipeline_name").getOrElse("").toString %>
+#{
+    val executables = summary.getValue(sampleId, libId, pipeline, "executables").getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
+}#
+
+<table class="table">
+    <thead>
+        <tr>
+            <th>Name</th>
+            <th>Version</th>
+        </tr>
+    </thead>
+    <tbody>
+        #for (name <- executables.keySet.toList.sorted)
+            <tr>
+                <td>${name}</td>
+                #{
+                val version = executables(name).get("version") match {
+                case Some(x) if x != None => x.toString
+                case _ => "N/A"
+                }
+                }#
+                <td>${version}</td>
+            </tr>
+        #end
+    </tbody>
+</table>
\ No newline at end of file

public/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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GradientType=0);background-repeat:repeat-x}.progress-bar-striped{background-image:-webkit-linear-gradient(45deg,rgba(255,255,255,.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,.15) 50%,rgba(255,255,255,.15) 75%,transparent 75%,transparent);background-image:-o-linear-gradient(45deg,rgba(255,255,255,.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,.15) 50%,rgba(255,255,255,.15) 75%,transparent 75%,transparent);background-image:linear-gradient(45deg,rgba(255,255,255,.15) 25%,transparent 25%,transparent 50%,rgba(255,255,255,.15) 50%,rgba(255,255,255,.15) 75%,transparent 75%,transparent)}.list-group{border-radius:4px;-webkit-box-shadow:0 1px 2px rgba(0,0,0,.075);box-shadow:0 1px 2px rgba(0,0,0,.075)}.list-group-item.active,.list-group-item.active:focus,.list-group-item.active:hover{text-shadow:0 -1px 0 #286090;background-image:-webkit-linear-gradient(top,#337ab7 0,#2b669a 100%);background-image:-o-linear-gradient(top,#337ab7 0,#2b669a 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#337ab7),to(#2b669a));background-image:linear-gradient(to bottom,#337ab7 0,#2b669a 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2b669a', GradientType=0);background-repeat:repeat-x;border-color:#2b669a}.list-group-item.active .badge,.list-group-item.active:focus .badge,.list-group-item.active:hover .badge{text-shadow:none}.panel{-webkit-box-shadow:0 1px 2px rgba(0,0,0,.05);box-shadow:0 1px 2px rgba(0,0,0,.05)}.panel-default>.panel-heading{background-image:-webkit-linear-gradient(top,#f5f5f5 0,#e8e8e8 100%);background-image:-o-linear-gradient(top,#f5f5f5 0,#e8e8e8 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#f5f5f5),to(#e8e8e8));background-image:linear-gradient(to bottom,#f5f5f5 0,#e8e8e8 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);background-repeat:repeat-x}.panel-primary>.panel-heading{background-image:-webkit-linear-gradient(top,#337ab7 0,#2e6da4 100%);background-image:-o-linear-gradient(top,#337ab7 0,#2e6da4 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#337ab7),to(#2e6da4));background-image:linear-gradient(to bottom,#337ab7 0,#2e6da4 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0);background-repeat:repeat-x}.panel-success>.panel-heading{background-image:-webkit-linear-gradient(top,#dff0d8 0,#d0e9c6 100%);background-image:-o-linear-gradient(top,#dff0d8 0,#d0e9c6 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#dff0d8),to(#d0e9c6));background-image:linear-gradient(to bottom,#dff0d8 0,#d0e9c6 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffd0e9c6', GradientType=0);background-repeat:repeat-x}.panel-info>.panel-heading{background-image:-webkit-linear-gradient(top,#d9edf7 0,#c4e3f3 100%);background-image:-o-linear-gradient(top,#d9edf7 0,#c4e3f3 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#d9edf7),to(#c4e3f3));background-image:linear-gradient(to bottom,#d9edf7 0,#c4e3f3 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffc4e3f3', GradientType=0);background-repeat:repeat-x}.panel-warning>.panel-heading{background-image:-webkit-linear-gradient(top,#fcf8e3 0,#faf2cc 100%);background-image:-o-linear-gradient(top,#fcf8e3 0,#faf2cc 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#fcf8e3),to(#faf2cc));background-image:linear-gradient(to bottom,#fcf8e3 0,#faf2cc 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fffaf2cc', 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3px rgba(0,0,0,.05),0 1px 0 rgba(255,255,255,.1);box-shadow:inset 0 1px 3px rgba(0,0,0,.05),0 1px 0 rgba(255,255,255,.1)}
\ No newline at end of file

public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css

+/*
+ * Base structure
+ */
+
+/* Move down content because we have a fixed navbar that is 50px tall */
+body {
+    padding-top: 50px;
+}
+
+/*
+ * Global add-ons
+ */
+
+.sub-header {
+    padding-bottom: 10px;
+    border-bottom: 1px solid #eee;
+}
+
+/*
+ * Top navigation
+ * Hide default border to remove 1px line.
+ */
+.navbar-fixed-top {
+    border: 0;
+}
+
+/*
+ * Sidebar
+ */
+
+/* Hide for mobile, show later */
+.sidebar {
+    display: none;
+}
+
+@media (min-width: 768px) {
+    .sidebar {
+        position: fixed;
+        top: 51px;
+        bottom: 0;
+        left: 0;
+        z-index: 1000;
+        display: block;
+        padding: 20px;
+        overflow-x: hidden;
+        overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
+        background-color: #f5f5f5;
+        border-right: 1px solid #eee;
+    }
+}
+
+/* Sidebar navigation */
+.nav-sidebar {
+    margin-right: -21px; /* 20px padding + 1px border */
+    margin-bottom: 20px;
+    margin-left: -20px;
+}
+
+.nav-sidebar > li > a {
+    padding-right: 20px;
+    padding-left: 20px;
+}
+
+.nav-sidebar > .active > a,
+.nav-sidebar > .active > a:hover,
+.nav-sidebar > .active > a:focus {
+    color: #fff;
+    background-color: #428bca;
+}
+
+/*
+ * Main content
+ */
+
+.main {
+    padding: 20px;
+}
+
+@media (min-width: 768px) {
+    .main {
+        padding-right: 40px;
+        padding-left: 40px;
+    }
+}
+
+.main .page-header {
+    margin-top: 0;
+}
+
+/*
+ * Placeholder dashboard ideas
+ */
+
+.placeholders {
+    margin-bottom: 30px;
+    text-align: center;
+}
+
+.placeholders h4 {
+    margin-bottom: 0;
+}
+
+.placeholder {
+    margin-bottom: 20px;
+}
+
+.placeholder img {
+    display: inline-block;
+    border-radius: 50%;
+}
+
+/*
+ * dropdown menu
+ */
+
+ .dropdown-submenu{
+     position:relative;
+ }
+ .dropdown-submenu > .dropdown-menu
+ {
+     top:0;
+     left:100%;
+     margin-top:-6px;
+     margin-left:-1px;
+     -webkit-border-radius:0 6px 6px 6px;
+     -moz-border-radius:0 6px 6px 6px;
+     border-radius:0 6px 6px 6px;
+ }
+ .dropdown-submenu:hover > .dropdown-menu{
+     display:block;
+ }
+
+ .dropdown-submenu > a:after{
+     display:block;
+     content:" ";
+     float:right;
+     width:0;
+     height:0;
+     border-color:transparent;
+     border-style:solid;
+     border-width:5px 0 5px 5px;
+     border-left-color:#cccccc;
+     margin-top:5px;
+     margin-right:-10px;
+ }
+
+ .dropdown-submenu:hover > a:after{
+     border-left-color:#ffffff;
+ }
+
+ .dropdown-submenu .pull-left{
+     float:none;
+ }
+
+ .dropdown-submenu.pull-left > .dropdown-menu{
+     left:-100%;
+     margin-left:10px;
+     -webkit-border-radius:6px 0 6px 6px;
+     -moz-border-radius:6px 0 6px 6px;
+     border-radius:6px 0 6px 6px;
+ }
+
+ .root:hover > .dropdown-menu{
+     display: block;
+ }
\ No newline at end of file

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

+/* line 2, ../sass/_sortable.sass */
+table[data-sortable] {
+    border-collapse: collapse;
+    border-spacing: 0;
+}
+/* line 6, ../sass/_sortable.sass */
+table[data-sortable] th {
+    vertical-align: bottom;
+    font-weight: bold;
+}
+/* line 10, ../sass/_sortable.sass */
+table[data-sortable] th, table[data-sortable] td {
+    text-align: left;
+    padding: 10px;
+}
+/* line 14, ../sass/_sortable.sass */
+table[data-sortable] th:not([data-sortable="false"]) {
+    -webkit-user-select: none;
+    -moz-user-select: none;
+    -ms-user-select: none;
+    -o-user-select: none;
+    user-select: none;
+    -webkit-tap-highlight-color: rgba(0, 0, 0, 0);
+    -webkit-touch-callout: none;
+    cursor: pointer;
+}
+/* line 26, ../sass/_sortable.sass */
+table[data-sortable] th:after {
+    content: "";
+    visibility: hidden;
+    display: inline-block;
+    vertical-align: inherit;
+    height: 0;
+    width: 0;
+    border-width: 5px;
+    border-style: solid;
+    border-color: transparent;
+    margin-right: 1px;
+    margin-left: 10px;
+    float: right;
+}
+/* line 40, ../sass/_sortable.sass */
+table[data-sortable] th[data-sorted="true"]:after {
+    visibility: visible;
+}
+/* line 43, ../sass/_sortable.sass */
+table[data-sortable] th[data-sorted-direction="descending"]:after {
+    border-top-color: inherit;
+    margin-top: 8px;
+}
+/* line 47, ../sass/_sortable.sass */
+table[data-sortable] th[data-sorted-direction="ascending"]:after {
+    border-bottom-color: inherit;
+    margin-top: 3px;
+}
+
+/* line 5, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap {
+    font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
+    font-size: 14px;
+    line-height: 20px;
+    color: #333333;
+    background: white;
+}
+/* line 12, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap thead th {
+    border-bottom: 2px solid #e0e0e0;
+}
+/* line 15, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap tbody td {
+    border-top: 1px solid #e0e0e0;
+}
+/* line 18, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"] {
+    color: #3a87ad;
+    background: #d9edf7;
+    border-bottom-color: #bce8f1;
+}
+/* line 23, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"][data-sorted-direction="descending"]:after {
+    border-top-color: #3a87ad;
+}
+/* line 26, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"][data-sorted-direction="ascending"]:after {
+    border-bottom-color: #3a87ad;
+}
+/* line 31, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap.sortable-theme-bootstrap-striped tbody > tr:nth-child(odd) > td {
+    background-color: #f9f9f9;
+}
\ No newline at end of file