Commit 2916f72b authored by Peter van 't Hof's avatar Peter van 't Hof

Moved extensions to new module

parent eceac8c1
......@@ -40,6 +40,11 @@
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
......@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions
package nl.lumc.sasc.biopet.core.extensions
import java.io.File
......
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.extensions.Md5sum
import nl.lumc.sasc.biopet.core.extensions.Md5sum
import scala.collection.mutable
......
<?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">
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.5.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>BiopetExtensions</artifactId>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
\ 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.
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
# 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
......@@ -31,7 +31,7 @@ class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
val file = new File(Paths.get(getClass.getResource("/picard.alignmentMetrics").toURI).toString)
val file = new File(Paths.get(getClass.getResource("picard.alignmentMetrics").toURI).toString)
val job = new CollectAlignmentSummaryMetrics(null)
job.output = file
......
......@@ -31,7 +31,7 @@ class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
val file = new File(Paths.get(getClass.getResource("/picard.insertsizemetrics").toURI).toString)
val file = new File(Paths.get(getClass.getResource("picard.insertsizemetrics").toURI).toString)
val job = new CollectInsertSizeMetrics(null)
job.output = file
......
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