Commit 49517b11 authored by Peter van 't Hof's avatar Peter van 't Hof

Move public to root

parent d61516a5
......@@ -10,7 +10,5 @@ git.properties
.idea/*
*.iml
target/
public/target/
protected/target/
site/
*.sc
\ No newline at end of file
......@@ -98,6 +98,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a stackbar plot for alignment stats
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......@@ -161,6 +162,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for insertsize
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......@@ -249,6 +251,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for wgs coverage
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......@@ -339,6 +342,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for rna coverage
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
......
<?xml version="1.0" encoding="UTF-8"?>
<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>
<artifactId>BiopetAggregate</artifactId>
<packaging>pom</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../public</relativePath>
</parent>
<modules>
<module>../public/biopet-core</module>
<module>../public/biopet-public-package</module>
<module>../public/bammetrics</module>
<module>../public/flexiprep</module>
<module>../public/gentrap</module>
<module>../public/mapping</module>
<module>../public/sage</module>
<module>../public/kopisu</module>
<module>../public/gears</module>
<module>../public/bam2wig</module>
<module>../public/carp</module>
<module>../public/toucan</module>
<module>../public/gwas-test</module>
<module>../public/shiva</module>
<module>../public/basty</module>
<module>../public/tinycap</module>
<module>../public/biopet-utils</module>
<module>../public/biopet-tools</module>
<module>../public/biopet-tools-extensions</module>
<module>../public/biopet-extensions</module>
<module>../public/biopet-tools-package</module>
</modules>
</project>
\ No newline at end of file
......@@ -125,7 +125,7 @@ trait ReportBuilder extends ToolCommand {
"fonts/glyphicons-halflings-regular.woff",
"fonts/glyphicons-halflings-regular.ttf",
"fonts/glyphicons-halflings-regular.woff2"
).map(x => ExtFile("/nl/lumc/sasc/biopet/core/report/ext/" + x, x))
).map(x => ExtFile("/nl/lumc/sasc/biopet/core/report/ext" + x, x))
/** Main function to for building the report */
def main(args: Array[String]): Unit = {
......@@ -189,6 +189,7 @@ trait ReportBuilder extends ToolCommand {
/**
* This method will render the page and the subpages recursivly
*
* @param summary The summary object
* @param page Page to render
* @param outputDir Root output dir of the report
......@@ -204,7 +205,7 @@ trait ReportBuilder extends ToolCommand {
val pageOutputDir = new File(outputDir, path.mkString(File.separator))
pageOutputDir.mkdirs()
val rootPath = "./" + Array.fill(path.size)("../").mkString("")
val rootPath = "./" + Array.fill(path.size)("src/main").mkString("")
val pageArgs = args ++ page.args ++
Map("page" -> page,
"path" -> path,
......