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<?xml version="1.0" encoding="UTF-8"?>
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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

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    A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
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    license; For commercial users or users who do not want to follow the AGPL
    license, please contact us to obtain a separate license.

-->
<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">
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    <modelVersion>4.0.0</modelVersion>
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    <artifactId>Biopet</artifactId>
    <groupId>nl.lumc.sasc</groupId>
    <name>Biopet</name>
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    <packaging>pom</packaging>
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    <version>0.9.0-SNAPSHOT</version>
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    <modules>
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        <module>gatk</module>
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        <module>biopet-package</module>
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        <module>bam2wig</module>
        <module>bammetrics</module>
        <module>basty</module>
        <module>carp</module>
        <module>flexiprep</module>
        <module>gears</module>
        <module>generate-indexes</module>
        <module>gentrap</module>
        <module>kopisu</module>
        <module>mapping</module>
        <module>sage</module>
        <module>shiva</module>
        <module>tinycap</module>
        <module>toucan</module>
        <module>biopet-core</module>
        <module>biopet-utils</module>
        <module>biopet-tools</module>
        <module>biopet-tools-extensions</module>
        <module>biopet-extensions</module>
        <module>biopet-tools-package</module>
        <module>gwas-test</module>
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        <module>external-example</module>
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    </modules>
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    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
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        <scalaVersion>2.11.4</scalaVersion>
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        <scoverage.aggregate>true</scoverage.aggregate>
    </properties>
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    <dependencies>
        <dependency>
            <groupId>org.testng</groupId>
            <artifactId>testng</artifactId>
            <version>6.8</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-all</artifactId>
            <version>1.9.5</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.scalatest</groupId>
            <artifactId>scalatest_2.11</artifactId>
            <version>2.2.1</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.scalatra.scalate</groupId>
            <artifactId>scalate-core_2.11</artifactId>
            <version>1.7.0</version>
        </dependency>
    </dependencies>

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    <build>
        <sourceDirectory>${basedir}/src/main/scala</sourceDirectory>
        <testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory>
        <testResources>
            <testResource>
                <directory>${basedir}/src/test/resources</directory>
                <includes>
                    <include>**/*</include>
                </includes>
            </testResource>
        </testResources>
        <resources>
            <resource>
                <directory>${basedir}/src/main/resources</directory>
                <includes>
                    <include>**/*</include>
                </includes>
            </resource>
        </resources>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.18.1</version>
                <configuration>
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                    <reuseForks>false</reuseForks>
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                    <forkCount>1C</forkCount>
                    <argLine>-Xmx300m</argLine>
                    <workingDirectory>${project.build.directory}</workingDirectory>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>2.10</version>
                <executions>
                    <execution>
                        <id>copy-installed</id>
                        <phase>prepare-package</phase>
                        <goals>
                            <goal>list</goal>
                        </goals>
                        <configuration>
                            <outputFile>${project.build.outputDirectory}/dependency_list.txt</outputFile>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>net.alchim31.maven</groupId>
                <artifactId>scala-maven-plugin</artifactId>
                <version>3.2.0</version>
                <executions>
                    <execution>
                        <id>scala-compile</id>
                        <goals>
                            <goal>compile</goal>
                            <goal>testCompile</goal>
                        </goals>
                        <configuration>
                            <args>
                                <arg>-dependencyfile</arg>
                                <arg>${project.build.directory}/.scala_dependencies</arg>
                                <arg>-deprecation</arg>
                                <arg>-feature</arg>
                            </args>
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                            <scalaVersion>${scalaVersion}</scalaVersion>
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                        </configuration>
                    </execution>
                </executions>
                <!-- ... (see other usage or goals for details) ... -->
            </plugin>
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            <plugin>
                <groupId>org.scalatra.scalate</groupId>
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                <artifactId>maven-scalate-plugin_2.11</artifactId>
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                <version>1.7.0</version>
                <executions>
                    <execution>
                        <phase>compile</phase>
                        <goals>
                            <goal>precompile</goal>
                        </goals>
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                        <configuration>
                            <contextClass>org.fusesource.scalate.DefaultRenderContext</contextClass>
                        </configuration>
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                    </execution>
                </executions>
            </plugin>
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            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>2.5</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>test-jar</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <archive>
                        <manifest>
                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                        </manifest>
                    </archive>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.3.2</version>
                <configuration>
                    <showDeprecation>true</showDeprecation>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.scalariform</groupId>
                <artifactId>scalariform-maven-plugin</artifactId>
                <version>0.1.4</version>
                <executions>
                    <execution>
                        <phase>process-sources</phase>
                        <goals>
                            <goal>format</goal>
                        </goals>
                        <configuration>
                            <baseDir>${basedir}/src</baseDir>
                            <rewriteArrowSymbols>false</rewriteArrowSymbols>
                            <alignParameters>true</alignParameters>
                            <alignSingleLineCaseStatements_maxArrowIndent>40
                            </alignSingleLineCaseStatements_maxArrowIndent>
                            <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
                            <compactStringConcatenation>false</compactStringConcatenation>
                            <compactControlReadability>false</compactControlReadability>
                            <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
                            <formatXml>true</formatXml>
                            <indentLocalDefs>false</indentLocalDefs>
                            <indentPackageBlocks>true</indentPackageBlocks>
                            <indentSpaces>2</indentSpaces>
                            <placeScaladocAsterisksBeneathSecondAsterisk>false
                            </placeScaladocAsterisksBeneathSecondAsterisk>
                            <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
                            <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
                            <rewriteArrowSymbols>false</rewriteArrowSymbols>
                            <spaceBeforeColon>false</spaceBeforeColon>
                            <spaceInsideBrackets>false</spaceInsideBrackets>
                            <spaceInsideParentheses>false</spaceInsideParentheses>
                            <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>pl.project13.maven</groupId>
                <artifactId>git-commit-id-plugin</artifactId>
                <version>2.1.10</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>revision</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <prefix>git</prefix>
                    <dateFormat>dd.MM.yyyy '@' HH:mm:ss z</dateFormat>
                    <verbose>false</verbose>
                    <dotGitDirectory>${basedir}/../../.git</dotGitDirectory>
                    <useNativeGit>true</useNativeGit>
                    <skipPoms>false</skipPoms>
                    <generateGitPropertiesFile>true</generateGitPropertiesFile>
                    <generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
                    <failOnNoGitDirectory>false</failOnNoGitDirectory>
                    <abbrevLength>8</abbrevLength>
                    <skip>false</skip>
                    <gitDescribe>
                        <skip>false</skip>
                        <always>false</always>
                        <abbrev>8</abbrev>
                        <dirty>-dirty</dirty>
                        <forceLongFormat>false</forceLongFormat>
                    </gitDescribe>
                </configuration>
            </plugin>
          <plugin>
              <groupId>com.mycila</groupId>
              <artifactId>license-maven-plugin</artifactId>
              <version>2.6</version>
              <configuration>
                  <excludes>
                      <exclude>**/*git*</exclude>
                      <exclude>**/License*</exclude>
                      <exclude>**/*.bam</exclude>
                      <exclude>**/*.bai</exclude>
                      <exclude>**/*.gtf</exclude>
                      <exclude>**/*.fq</exclude>
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                      <exclude>**/*.vcf</exclude>
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                      <exclude>**/*.sam</exclude>
                      <exclude>**/*.bed</exclude>
                      <exclude>**/*.refFlat</exclude>
                      <exclude>**/*.R</exclude>
                      <exclude>**/*.rscript</exclude>
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                      <exclude>**/*.txt</exclude>
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                  </excludes>
              </configuration>
          </plugin>
          <plugin>
              <groupId>org.scoverage</groupId>
              <artifactId>scoverage-maven-plugin</artifactId>
              <version>${scoverage.plugin.version}</version>
              <configuration>
                  <scalaVersion>${scalaVersion}</scalaVersion>
                  <aggregate>true</aggregate>
                  <highlighting>true</highlighting>
                  <aggregate>true</aggregate>
                  <!-- other parameters -->
              </configuration>
          </plugin>
      </plugins>
    </build>
    <reporting>
        <plugins>
            <plugin>
                <groupId>org.scoverage</groupId>
                <artifactId>scoverage-maven-plugin</artifactId>
                <version>${scoverage.plugin.version}</version>
                <configuration>
                    <aggregate>true</aggregate> <!-- for aggregated report -->
                    <highlighting>true</highlighting>
                </configuration>
                <reportSets>
                    <reportSet>
                        <reports>
                            <report>report</report> <!-- select only one report from: report, integration-report and report-only reporters -->
                        </reports>
                    </reportSet>
                </reportSets>
            </plugin>
        </plugins>
    </reporting>
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</project>