pom.xml

<?xml version="1.0" encoding="ISO-8859-1"?>
<!--

    biojava-adam  Biojava and ADAM integration.
    Copyright (c) 2017-2022 held jointly by the individual authors.

    This library is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published
    by the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.

    This library is distributed in the hope that it will be useful, but WITHOUT
    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
    License for more details.

    You should have received a copy of the GNU Lesser General Public License
    along with this library;  if not, write to the Free Software Foundation,
    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.

    > http://www.fsf.org/licensing/licenses/lgpl.html
    > http://www.opensource.org/licenses/lgpl-license.php

-->
<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/maven-v4_0_0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <parent>
    <groupId>org.sonatype.oss</groupId>
    <artifactId>oss-parent</artifactId>
    <version>9</version>
  </parent>
  <groupId>org.biojava</groupId>
  <artifactId>biojava-adam</artifactId>
  <packaging>jar</packaging>
  <name>biojava-adam</name>
  <version>1.1-SNAPSHOT</version>
  <description>Biojava and ADAM integration.</description>
  <url>http://www.biojava.org</url>
  <inceptionYear>2017</inceptionYear>
  <scm>
    <connection>scm:git:git@github.com:biojava/biojava-adam.git</connection>
    <developerConnection>scm:git:git@github.com:biojava/biojava-adam.git</developerConnection>
    <url>git@github.com:biojava/biojava-adam.git</url>
    <tag>HEAD</tag>
  </scm>
  <developers>
    <developer>
      <id>heuermh</id>
      <name>Michael Heuer</name>
    </developer>
  </developers>
  <issueManagement>
    <system>GitHub</system>
    <url>https://github.com/biojava/biojava-adam/issues</url>
  </issueManagement>
  <licenses>
    <license>
      <name>GNU Lesser General Public License (LGPL)</name>
      <url>http://www.gnu.org/licenses/lgpl.html</url>
      <distribution>repo</distribution>
    </license>
  </licenses>
  <properties>
    <adam.version>1.0</adam.version>
    <bdg-convert.version>1.0</bdg-convert.version>
    <biojava.version>6.1.0</biojava.version>
    <guava.version>31.1-jre</guava.version>
    <jdk.version>1.8</jdk.version>
    <junit.version>4.13.2</junit.version>
    <maven.enforcer.jdk-version>[1.8,)</maven.enforcer.jdk-version>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <project.build.targetEncoding>UTF-8</project.build.targetEncoding>
    <scala-guice.version>5.1.0</scala-guice.version>
    <scala.version>2.12.15</scala.version>
    <scala.version.prefix>2.12</scala.version.prefix>
    <slf4j.version>1.7.30</slf4j.version>
    <spark.version>3.2.1</spark.version>
  </properties>
  <build>
    <pluginManagement>
      <plugins>
        <plugin>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>3.3.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-clean-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.8.1</version>
          <configuration>
            <source>${jdk.version}</source>
            <target>${jdk.version}</target>
          </configuration>
        </plugin>
        <plugin>
          <artifactId>maven-deploy-plugin</artifactId>
          <version>3.0.0-M1</version>
        </plugin>
        <plugin>
          <artifactId>maven-enforcer-plugin</artifactId>
          <version>3.0.0-M3</version>
        </plugin>
        <plugin>
          <artifactId>maven-gpg-plugin</artifactId>
          <version>1.6</version>
        </plugin>
        <plugin>
          <artifactId>maven-install-plugin</artifactId>
          <version>3.0.0-M1</version>
        </plugin>
        <plugin>
          <artifactId>maven-jar-plugin</artifactId>
          <version>3.2.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-javadoc-plugin</artifactId>
          <version>3.2.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-release-plugin</artifactId>
          <version>3.0.0-M1</version>
        </plugin>
        <plugin>
          <artifactId>maven-resources-plugin</artifactId>
          <version>3.2.0</version>
        </plugin>
        <plugin>
          <artifactId>maven-shade-plugin</artifactId>
          <version>3.2.4</version>
        </plugin>
        <plugin>
          <artifactId>maven-site-plugin</artifactId>
          <version>3.9.1</version>
        </plugin>
        <plugin>
          <artifactId>maven-source-plugin</artifactId>
          <version>3.2.1</version>
        </plugin>
        <plugin>
          <artifactId>maven-surefire-plugin</artifactId>
          <version>3.0.0-M5</version>
        </plugin>
        <plugin>
          <groupId>net.alchim31.maven</groupId>
          <artifactId>scala-maven-plugin</artifactId>
          <version>4.5.6</version>
        </plugin>
        <plugin>
          <groupId>org.codehaus.mojo</groupId>
          <artifactId>templating-maven-plugin</artifactId>
          <version>1.0.0</version>
        </plugin>
        <plugin>
          <groupId>pl.project13.maven</groupId>
          <artifactId>git-commit-id-plugin</artifactId>
          <version>2.2.2</version>
        </plugin>
      </plugins>
    </pluginManagement>
    <plugins>
      <plugin>
        <artifactId>maven-enforcer-plugin</artifactId>
        <executions>
          <execution>
            <id>enforce-java</id>
            <goals>
              <goal>enforce</goal>
            </goals>
            <configuration>
              <rules>
                <requireJavaVersion>
                  <version>${maven.enforcer.jdk-version}</version>
                </requireJavaVersion>
              </rules>    
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <artifactId>maven-shade-plugin</artifactId>
        <configuration>
          <createDependencyReducedPom>false</createDependencyReducedPom>
          <filters>
            <filter>
              <artifact>*:*</artifact>
              <excludes>
                <exclude>META-INF/*.SF</exclude>
                <exclude>META-INF/*.DSA</exclude>
                <exclude>META-INF/*.RSA</exclude>
              </excludes>
            </filter>
          </filters>
          <relocations>
            <relocation>
              <pattern>com.google.common</pattern>
              <shadedPattern>org.biojava.nbio.adam.shaded.com.google.common</shadedPattern>
            </relocation>
          </relocations>
        </configuration>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>shade</goal>
            </goals>
            <configuration>
              <transformers>
                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
              </transformers>
            </configuration>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>net.alchim31.maven</groupId>
        <artifactId>scala-maven-plugin</artifactId>
        <executions>
          <execution>
            <id>scala-compile-first</id>
            <phase>process-resources</phase>
            <goals>
              <goal>compile</goal>
            </goals>
            <configuration>
              <args>
                <arg>-g:vars</arg>
              </args>
            </configuration>
          </execution>
          <execution>
            <id>scala-test-compile-first</id>
            <phase>process-test-resources</phase>
            <goals>
              <goal>testCompile</goal>
            </goals>
          </execution>
          <execution>
            <id>attach-scaladocs</id>
            <phase>verify</phase>
            <goals>
              <goal>doc-jar</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <scalaVersion>${scala.version}</scalaVersion>
          <useZincServer>true</useZincServer>
          <args>
            <arg>-unchecked</arg>
            <arg>-deprecation</arg>
          </args>
          <jvmArgs>
            <jvmArg>-Xms64m</jvmArg>
            <jvmArg>-Xms1024m</jvmArg>
            <jvmArg>-Xmx1024m</jvmArg>
          </jvmArgs>
          <javacArgs>
            <javacArg>-source</javacArg>
            <javacArg>${jdk.version}</javacArg>
            <javacArg>-target</javacArg>
            <javacArg>${jdk.version}</javacArg>
          </javacArgs>
        </configuration>
      </plugin>
    </plugins>
    <resources>
      <resource>
        <directory>${basedir}/src/main/resources</directory>
        <filtering>false</filtering>
      </resource>
      <resource>
        <targetPath>META-INF</targetPath>
        <filtering>false</filtering>
        <directory>${basedir}</directory>
        <includes>
          <include>COPYING</include>
          <include>COPYING.LESSER</include>
        </includes>
      </resource>
    </resources>
  </build>
  <dependencyManagement>
    <dependencies>
      <dependency>
        <groupId>junit</groupId>
        <artifactId>junit</artifactId>
        <version>${junit.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.spark</groupId>
        <artifactId>spark-core_${scala.version.prefix}</artifactId>
        <version>${spark.version}</version>
        <exclusions>
          <exclusion>
            <groupId>com.google.code.findbugs</groupId>
            <artifactId>jsr305</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.apache.avro</groupId>
            <artifactId>avro</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.apache.hadoop</groupId>
            <artifactId>hadoop-client</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.apache.hadoop</groupId>
            <artifactId>hadoop-mapreduce</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.xerial.snappy</groupId>
            <artifactId>snappy-java</artifactId>
          </exclusion>
        </exclusions>
      </dependency>
      <dependency>
        <groupId>org.apache.spark</groupId>
        <artifactId>spark-sql_${scala.version.prefix}</artifactId>
        <version>${spark.version}</version>
        <exclusions>
          <exclusion>
            <groupId>com.google.code.findbugs</groupId>
            <artifactId>jsr305</artifactId>
          </exclusion>
        </exclusions>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-assembly-spark3_${scala.version.prefix}</artifactId>
        <version>${adam.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.convert</groupId>
        <artifactId>convert</artifactId>
        <version>${bdg-convert.version}</version>
        <exclusions>
          <exclusion>
            <groupId>com.google.code.findbugs</groupId>
            <artifactId>jsr305</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.apache.avro</groupId>
            <artifactId>avro</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
          </exclusion>
        </exclusions>
      </dependency>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-core</artifactId>
        <exclusions>
          <exclusion>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
          </exclusion>
        </exclusions>
        <version>${biojava.version}</version>
      </dependency>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-genome</artifactId>
        <exclusions>
          <exclusion>
            <groupId>com.google.guava</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.apache.logging.log4j</groupId>
            <artifactId>*</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
          </exclusion>
        </exclusions>
        <version>${biojava.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>slf4j-log4j12</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.guava</groupId>
        <artifactId>guava</artifactId>
        <version>${guava.version}</version>
      </dependency>
    </dependencies>
  </dependencyManagement>
  <dependencies>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.apache.spark</groupId>
      <artifactId>spark-core_${scala.version.prefix}</artifactId>
      <scope>provided</scope>
    </dependency>
    <dependency>
      <groupId>org.apache.spark</groupId>
      <artifactId>spark-sql_${scala.version.prefix}</artifactId>
      <scope>provided</scope>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.adam</groupId>
      <artifactId>adam-assembly-spark3_${scala.version.prefix}</artifactId>
      <scope>provided</scope>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.convert</groupId>
      <artifactId>convert</artifactId>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>biojava-core</artifactId>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>biojava-genome</artifactId>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-log4j12</artifactId>
      <scope>test</scope>
    </dependency>
  </dependencies>
  <profiles>
    <profile>
      <!-- Override maven plugin versions in release profile -->
      <id>sonatype-oss-release</id>
      <build>
        <plugins>
          <plugin>
            <artifactId>maven-enforcer-plugin</artifactId>
            <version>3.0.0-M3</version>
          </plugin>
          <plugin>
            <artifactId>maven-gpg-plugin</artifactId>
            <version>1.6</version>
          </plugin>
          <plugin>
            <artifactId>maven-jar-plugin</artifactId>
            <version>3.2.0</version>
          </plugin>
          <plugin>
            <artifactId>maven-javadoc-plugin</artifactId>
            <version>3.2.0</version>
          </plugin>
          <plugin>
            <artifactId>maven-source-plugin</artifactId>
            <version>3.2.1</version>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>
</project>