Commit 26ea8a50 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Init framework for BamToBigWig

parent c2fb1f5b
......@@ -95,6 +95,7 @@
<orderEntry type="module" module-name="Gentrap" />
<orderEntry type="module" module-name="Sage" />
<orderEntry type="module" module-name="Yamsvp" />
<orderEntry type="module" module-name="bamtobigwig" />
<orderEntry type="module" module-name="BiopetGatkPipelines" />
<orderEntry type="module" module-name="BiopetGatkExtensions" />
<orderEntry type="module" module-name="Basty" />
......
<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" inherit-compiler-output="false">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
<sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
<sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
<excludeFolder url="file://$MODULE_DIR$/target" />
</content>
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<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="module" module-name="BiopetFramework" />
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<root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
</CLASSES>
<JAVADOC />
<SOURCES />
</library>
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<JAVADOC />
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</component>
</module>
\ No newline at end of file
<?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>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BamToBigWig</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.3.0-DEV</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>BamToBigWig</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
package nl.lumc.sasc.biopet.pipelines.bamtobigwig
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 1/29/15.
*/
class BamToBigWig(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
def init(): Unit = {
}
def biopetScript(): Unit = {
}
}
object BamToBigWig extends PipelineCommand
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
<component name="FacetManager">
<facet type="Python" name="Python">
<configuration sdkName="" />
</facet>
</component>
<component name="NewModuleRootManager" inherit-compiler-output="false">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
......
......@@ -94,5 +94,6 @@
<orderEntry type="module" module-name="Gentrap" />
<orderEntry type="module" module-name="Sage" />
<orderEntry type="module" module-name="Yamsvp" />
<orderEntry type="module" module-name="bamtobigwig" />
</component>
</module>
\ No newline at end of file
......@@ -75,6 +75,11 @@
<artifactId>Yamsvp</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BamToBigWig</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
......
......@@ -22,7 +22,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
nl.lumc.sasc.biopet.pipelines.sage.Sage
nl.lumc.sasc.biopet.pipelines.sage.Sage,
nl.lumc.sasc.biopet.pipelines.bamtobigwig.BamToBigWig
)
def tools: List[MainCommand] = List(
......
......@@ -33,6 +33,7 @@
<module>mapping</module>
<module>sage</module>
<module>yamsvp</module>
<module>bamtobigwig</module>
</modules>
<properties>
......
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