pom.xml 6.08 KB
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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.

-->
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<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>

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    <artifactId>BiopetPackage</artifactId>
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    <packaging>jar</packaging>
    
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    <parent>
        <groupId>nl.lumc.sasc</groupId>
        <artifactId>Biopet</artifactId>
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        <version>0.7.0</version>
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        <relativePath>../</relativePath>
    </parent>
    
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    <inceptionYear>2014</inceptionYear>
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    <name>BiopetPackage</name>
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    <url>http://maven.apache.org</url>

    <properties>
        <sting.shade.phase>package</sting.shade.phase>
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        <app.main.class>nl.lumc.sasc.biopet.BiopetExecutableMain</app.main.class>
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    </properties>

    <dependencies>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
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            <artifactId>BiopetCore</artifactId>
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            <version>${project.version}</version>
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        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>GenerateIndexes</artifactId>
            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Flexiprep</artifactId>
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            <version>${project.version}</version>
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        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Mapping</artifactId>
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            <version>${project.version}</version>
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        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>BamMetrics</artifactId>
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            <version>${project.version}</version>
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        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Gentrap</artifactId>
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            <version>${project.version}</version>
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        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>TinyCap</artifactId>
            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Sage</artifactId>
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            <version>${project.version}</version>
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        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
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            <artifactId>Kopisu</artifactId>
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            <version>${project.version}</version>
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        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
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            <artifactId>GwasTest</artifactId>
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            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Gears</artifactId>
            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
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            <artifactId>Bam2Wig</artifactId>
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            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Carp</artifactId>
            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Toucan</artifactId>
            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Shiva</artifactId>
            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Basty</artifactId>
            <version>${project.version}</version>
        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>BiopetToolsPackage</artifactId>
            <version>${project.version}</version>
        </dependency>
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    </dependencies>
    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
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                <version>2.4.1</version>
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                <configuration>
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                    <!--suppress MavenModelInspection -->
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                    <finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                            <manifestEntries>
                                <Main-Class>${app.main.class}</Main-Class>
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                                <!--suppress MavenModelInspection -->
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                                <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
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                                <!--suppress MavenModelInspection -->
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                                <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
                            </manifestEntries>
                        </transformer>
                    </transformers>
                    <filters>
                    </filters>
                </configuration>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
</project>