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biopet.biopet
Commit eb97957f authored by Peter van 't Hof's avatar Peter van 't Hof
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Tools split into new modules, core and utils are compileable now

parent f4b5230c
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public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @ eb97957f
#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
View file @ eb97957f
#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
View file @ eb97957f
#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
View file @ eb97957f
#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
View file @ eb97957f
#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
View file @ eb97957f
#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
View file @ eb97957f
#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
View file @ eb97957f
#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
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......@@ -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 0 → 100644
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#
# 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 0 → 100644
View file @ eb97957f
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 0 → 100644
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#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.min.css 0 → 100644
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public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css 0 → 100644
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/*
* 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 0 → 100644
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/* 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
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js 0 → 100644
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/*! sortable.js 0.5.0 */
(function(){var a,b,c,d,e,f;a="table[data-sortable]",c=/^-?[£$¤]?[\d,.]+%?$/,f=/^\s+|\s+$/g,e="ontouchstart"in document.documentElement,b=e?"touchstart":"click",d={init:function(){var b,c,e,f,g;for(c=document.querySelectorAll(a),g=[],e=0,f=c.length;f>e;e++)b=c[e],g.push(d.initTable(b));return g},initTable:function(a){var b,c,e,f,g;if(1===a.tHead.rows.length&&"true"!==a.getAttribute("data-sortable-initialized")){for(a.setAttribute("data-sortable-initialized","true"),e=a.querySelectorAll("th"),b=f=0,g=e.length;g>f;b=++f)c=e[b],"false"!==c.getAttribute("data-sortable")&&d.setupClickableTH(a,c,b);return a}},setupClickableTH:function(a,c,e){var f;return f=d.getColumnType(a,e),c.addEventListener(b,function(){var b,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u;for(j="true"===this.getAttribute("data-sorted"),k=this.getAttribute("data-sorted-direction"),b=j?"ascending"===k?"descending":"ascending":f.defaultSortDirection,m=this.parentNode.querySelectorAll("th"),n=0,q=m.length;q>n;n++)c=m[n],c.setAttribute("data-sorted","false"),c.removeAttribute("data-sorted-direction");for(this.setAttribute("data-sorted","true"),this.setAttribute("data-sorted-direction",b),l=a.tBodies[0],h=[],t=l.rows,o=0,r=t.length;r>o;o++)g=t[o],h.push([d.getNodeValue(g.cells[e]),g]);for(j?h.reverse():h.sort(f.compare),u=[],p=0,s=h.length;s>p;p++)i=h[p],u.push(l.appendChild(i[1]));return u})},getColumnType:function(a,b){var e,f,g,h,i;for(i=a.tBodies[0].rows,g=0,h=i.length;h>g;g++)if(e=i[g],f=d.getNodeValue(e.cells[b]),""!==f&&f.match(c))return d.types.numeric;return d.types.alpha},getNodeValue:function(a){return a?null!==a.getAttribute("data-value")?a.getAttribute("data-value"):"undefined"!=typeof a.innerText?a.innerText.replace(f,""):a.textContent.replace(f,""):""},types:{numeric:{defaultSortDirection:"descending",compare:function(a,b){var c,d;return c=parseFloat(a[0].replace(/[^0-9.-]/g,"")),d=parseFloat(b[0].replace(/[^0-9.-]/g,"")),isNaN(c)&&(c=0),isNaN(d)&&(d=0),d-c}},alpha:{defaultSortDirection:"ascending",compare:function(a,b){var c,d;return c=a[0].toLowerCase(),d=b[0].toLowerCase(),c===d?0:d>c?-1:1}}}},setTimeout(d.init,0),window.Sortable=d}).call(this);
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp 0 → 100644
View file @ eb97957f
#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 %>
<table class="table">
<thead><tr><th>Libraries</th></tr></thead>
<tbody>
#for (lib <- summary.libraries(sampleId.get))
<tr><td><a href="${rootPath}Samples/${sampleId}/Libraries/${lib}/index.html">${lib}</a></td></tr>
#end
</tbody>
</table>
\ No newline at end of file
public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp 0 → 100644
View file @ eb97957f
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var indexPage: ReportPage %>
<%@ var reportName: String %>
<%@ var page: ReportPage %>
<%@ var path: List[String] %>
<%@ var args: Map[String, Any] %>
<%@ var rootPath: String %>
#{
def createMenu(page: ReportPage, path: List[String] = Nil, first: Boolean = true): String = {
val buffer: StringBuffer = new StringBuffer()
if (page.subPages.nonEmpty){
buffer.append("<ul class=\"dropdown-menu\">")
}
for (subPage <- page.subPages) {
val href: String = {
if (path.isEmpty) rootPath + subPage._1 + "/index.html"
else rootPath + path.mkString("","/","/") + subPage._1 + "/index.html"
}
buffer.append("<li")
if(subPage._2.subPages.nonEmpty) buffer.append(" class=\"dropdown-submenu\"")
buffer.append("><a href=\"" + href + "\"")
if (first) buffer.append(" tabindex=\"-1\"")
buffer.append(">" + subPage._1 + "</a>")
buffer.append(createMenu(subPage._2, path ::: subPage._1 :: Nil, first = false))
buffer.append("</li>")
}
if(page.subPages.nonEmpty) {
buffer.append("</ul>\n")
}
buffer.toString
}
def getSubPage(path:List[String]): ReportPage = {
path.foldLeft(indexPage)((c, p) => {
val foundPages = c.subPages.filter(_._1 == p)
require(foundPages.size == 1, "Name of page not found or duplicate is found, page:: " + p + " in path: " + path)
foundPages.head._2
})
}
}#
<!DOCTYPE html>
<html>
<head>
<title>${reportName}</title>
<!-- Bootstrap core JavaScript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="${rootPath}ext/js/jquery.min.js"></script>
<!-- Latest compiled and minified CSS -->
<link rel="stylesheet" href="${rootPath}ext/css/bootstrap.min.css">
<!-- Optional theme -->
<link rel="stylesheet" href="${rootPath}ext/css/bootstrap-theme.min.css">
<!-- Latest compiled and minified JavaScript -->
<script src="${rootPath}ext/js/bootstrap.min.js"></script>
<link rel="stylesheet" type="text/css" href="${rootPath}ext/css/bootstrap_dashboard.css">
<link rel="stylesheet" type="text/css" href="${rootPath}ext/css/sortable-theme-bootstrap.css">
<!-- sortable tables //-->
<script src="${rootPath}ext/js/sortable.min.js"></script>
<script language="JavaScript">
<!--
$(document).ready(function() {
Sortable.init()
$('body').scrollspy({
target: '.bs-sidebar',
});
});
//-->
</script>
</head>
<body>
<nav class="navbar navbar-inverse navbar-fixed-top">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-ex1-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<ul class="nav navbar-nav">
<li class="root #if (path.isEmpty) active #end">
<a class="navbar-brand" href="${rootPath}index.html">${reportName}
#if (indexPage.subPages.nonEmpty) <b class="caret"></b> #end