pom.xml 5.62 KB
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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>

  <groupId>nl.lumc.sasc</groupId>
  <artifactId>Biopet-Framework</artifactId>
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  <version>0.1.3</version>
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  <packaging>jar</packaging>

  <name>Biopet-Framework</name>
  <url>http://maven.apache.org</url>

  <parent>
      <groupId>nl.lumc.sasc</groupId>
      <artifactId>Biopet</artifactId>
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      <version>0.1.3</version>
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      <relativePath>../</relativePath>
  </parent>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <sting.unpack.phase>prepare-package</sting.unpack.phase>
    <sting.shade.phase>package</sting.shade.phase>
    <sting.binary-dist.name>SASC-Pipelines</sting.binary-dist.name>
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    <app.main.class>org.broadinstitute.gatk.queue.QCommandLine</app.main.class>
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  </properties>
  
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    <dependencies>
<!--    <dependency>
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      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>3.8.1</version>
      <scope>test</scope>
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    </dependency>-->
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        <dependency>
            <groupId>org.scala-lang</groupId>
            <artifactId>scala-compiler</artifactId>
            <version>2.11.0</version>
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            <scope>compile</scope>
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        </dependency>
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        <dependency>
            <groupId>org.scala-lang</groupId>
            <artifactId>scala-library</artifactId>
            <version>2.11.0</version>
        </dependency>
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<!--        <dependency>
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            <groupId>org.scalatest</groupId>
            <artifactId>scalatest_2.9.2</artifactId>
            <version>2.0.M4</version>
            <scope>test</scope>
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        </dependency>-->
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        <dependency>
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            <groupId>org.broadinstitute.gatk</groupId>
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            <artifactId>gatk-queue-package-distribution</artifactId>
            <version>3.2</version>
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        </dependency>
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        <dependency>
            <groupId>io.argonaut</groupId>
            <artifactId>argonaut_2.11</artifactId>
            <version>6.1-M3</version>
        </dependency>
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    </dependencies>
    <build>
        <plugins>
            <plugin>
                <groupId>org.scala-tools</groupId>
                <artifactId>maven-scala-plugin</artifactId>
                <version>2.15.2</version>
                <executions>
                    <execution>
                        <id>scala-compile</id>
                        <goals>
                            <goal>compile</goal>
                            <goal>testCompile</goal>
                        </goals>
                        <configuration>
                            <args>
<!--                                <arg>-make:transitive</arg>-->
                                <arg>-dependencyfile</arg>
                                <arg>${project.build.directory}/.scala_dependencies</arg>
                            </args>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
<!--            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.7.2</version>
                <executions>
                    <execution>
                        <id>default-test</id>
                         Disable the default-test by putting it in phase none 
                        <phase>none</phase>
                    </execution>
                </executions>
            </plugin>-->
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            <plugin>
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            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-shade-plugin</artifactId>
            <version>2.3</version>
            <configuration>
              <transformers>
                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                  <manifestEntries>
                    <Main-Class>${app.main.class}</Main-Class>
                    <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
                    <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
                  </manifestEntries>
                </transformer>
              </transformers>
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              <artifactSet>
                <excludes>
                  <exclude>junit:junit</exclude>
<!--                  <exclude>org.scala-lang:scala-compiler</exclude>-->
<!--                  <exclude>org.scala-lang:scala-library</exclude>-->
                  <exclude>org.scala-lang:scala-reflect</exclude>
                  <exclude>org.scala-lang.modules:*</exclude>
                </excludes>
              </artifactSet>
              <filters>
                <filter>
                  <artifact>org.scala-lang:scala-compiler</artifact>
                  <includes>
                    <include>scala/tools/nsc/reporters/**</include>
                  </includes>
                </filter>
                <filter>
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                  <artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
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                  <excludes>
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<!--                      <exclude>scala/**</exclude>-->
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                  </excludes>
                  <includes>
                    <include>*/**</include>
                  </includes>
                </filter>
              </filters>
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            </configuration>
            <executions>
              <execution>
                <phase>package</phase>
                <goals>
                  <goal>shade</goal>
                </goals>
              </execution>
            </executions>
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          </plugin>
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        </plugins>
    </build>
</project>