Commit eb97957f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

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

parent f4b5230c
#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)
......
#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 %>
......
#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] %>
......
#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 %>
......
#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)
......
#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)
......
#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)
......
#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)
......
......@@ -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>
......
#
# 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
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
#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
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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', GradientType=0);background-repeat:repeat-x}.panel-danger>.panel-heading{background-image:-webkit-linear-gradient(top,#f2dede 0,#ebcccc 100%);background-image:-o-linear-gradient(top,#f2dede 0,#ebcccc 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#f2dede),to(#ebcccc));background-image:linear-gradient(to bottom,#f2dede 0,#ebcccc 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffebcccc', GradientType=0);background-repeat:repeat-x}.well{background-image:-webkit-linear-gradient(top,#e8e8e8 0,#f5f5f5 100%);background-image:-o-linear-gradient(top,#e8e8e8 0,#f5f5f5 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#e8e8e8),to(#f5f5f5));background-image:linear-gradient(to bottom,#e8e8e8 0,#f5f5f5 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffe8e8e8', endColorstr='#fff5f5f5', GradientType=0);background-repeat:repeat-x;border-color:#dcdcdc;-webkit-box-shadow:inset 0 1px 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
/*
* 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
/* 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
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