pom.xml

<?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>edu.sdsc.benchmark</groupId>
  <artifactId>mmtf-benchmark</artifactId>
  <version>1.0-SNAPSHOT</version>

  <name>mmtf-benchmark</name>
  <url>https://mmtf.rcsb.org</url>

  <properties>
        <maven.compiler.release>11</maven.compiler.release>
  </properties>

  <dependencies>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.11</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>biojava-core</artifactId>
      <version>6.1.0</version>
    </dependency>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>biojava-structure</artifactId>
      <version>6.1.0</version>
    </dependency>
      <!-- other biojava jars as needed -->
  </dependencies>

  <build>
    <pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
      <plugins>
        <!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
        <plugin>
          <artifactId>maven-clean-plugin</artifactId>
          <version>3.2.0</version>
        </plugin>
        <!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
        <plugin>
          <artifactId>maven-resources-plugin</artifactId>
          <version>3.3.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.10.1</version>
        </plugin>
        <plugin>
          <artifactId>maven-surefire-plugin</artifactId>
          <version>3.0.0-M8</version>
        </plugin>
        <plugin>
          <artifactId>maven-jar-plugin</artifactId>
          <version>3.3.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-install-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-deploy-plugin</artifactId>
          <version>3.0.0</version>
        </plugin>
        <!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
        <plugin>
          <artifactId>maven-site-plugin</artifactId>
          <version>4.0.0-M4</version>
        </plugin>
        <plugin>
          <artifactId>maven-project-info-reports-plugin</artifactId>
          <version>3.4.2</version>
        </plugin>
        <plugin>
          <artifactId>maven-shade-plugin</artifactId>
          <version>3.4.1</version>
        </plugin>
      </plugins>
    </pluginManagement>
    <plugins>
      <plugin>
        <artifactId>maven-shade-plugin</artifactId>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <transformers>
            <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
              <mainClass>edu.sdsc.benchmark.Test</mainClass>
            </transformer>
          </transformers>
        </configuration>
      </plugin>
    </plugins>
  </build>
</project>