<commit_before><?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>
  <parent>
    <groupId>net.fnothaft</groupId>
    <artifactId>gnocchi-parent</artifactId>
    <version>0.0.1-SNAPSHOT</version>
    <relativePath>../pom.xml</relativePath>
  </parent>

  <artifactId>gnocchi-cli</artifactId>
  <packaging>jar</packaging>
  <name>gnocchi-cli: Command line interface for managing and querying variant store</name>

  <build>
    <plugins>
      <plugin>
        <groupId>org.codehaus.mojo</groupId>
        <artifactId>appassembler-maven-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>net.alchim31.maven</groupId>
        <artifactId>scala-maven-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-gpg-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
      </plugin>
      <!-- enable scalatest -->
      <plugin>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest-maven-plugin</artifactId>
      </plugin>
<!--       <plugin>
    	  <artifactId>maven-clean-plugin</artifactId>
    	  <version>3.0.0</version>
    	  <executions>
          <execution>
            <id>auto-clean</id>
            <phase>initialize</phase>
            <goals>
              <goal>clean</goal>
            </goals>
            <configuration>
             <filesets>
                <fileset>
                  <directory>gnocchi-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0</directory>
                </fileset>
              </filesets>
            </configuration>
          </execution>
        </executions>
      </plugin> -->
    </plugins>
  </build>

  <dependencies>
    <dependency>
      <groupId>net.fnothaft</groupId>
      <artifactId>gnocchi-core</artifactId>
    </dependency>
    <dependency>
      <groupId>org.apache.parquet</groupId>
      <artifactId>parquet-avro</artifactId>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.utils</groupId>
      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
      <version>${utils.version}</version>
      <type>test-jar</type>
      <scope>test</scope>
      <exclusions>
        <exclusion>  <!-- declare the exclusion here -->
          <groupId>com.esotericsoftware.kryo</groupId>
          <artifactId>kryo</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>com.esotericsoftware.kryo</groupId>
      <artifactId>kryo</artifactId>
      <version>2.21.1</version>
    </dependency>
    <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-cli_2.10</artifactId>
        <version>0.19.0</version>
    </dependency>
    <dependency>
      <groupId>org.apache.directory.studio</groupId>
      <artifactId>org.apache.commons.io</artifactId>
      <version>2.4</version>
    </dependency>
    <dependency>
      <groupId>args4j</groupId>
      <artifactId>args4j</artifactId>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.utils</groupId>
      <artifactId>utils-cli_${scala.version.prefix}</artifactId>
    </dependency>
    <dependency>
      <groupId>org.apache.hadoop</groupId>
      <artifactId>hadoop-client</artifactId>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.adam</groupId>
      <artifactId>adam-core_${scala.version.prefix}</artifactId>
    </dependency>
    <dependency>
      <groupId>org.apache.spark</groupId>
      <artifactId>spark-core_${scala.version.prefix}</artifactId><commit_msg>downgrading kryo to 2.21<commit_after><?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>
  <parent>
    <groupId>net.fnothaft</groupId>
    <artifactId>gnocchi-parent</artifactId>
    <version>0.0.1-SNAPSHOT</version>
    <relativePath>../pom.xml</relativePath>
  </parent>

  <artifactId>gnocchi-cli</artifactId>
  <packaging>jar</packaging>
  <name>gnocchi-cli: Command line interface for managing and querying variant store</name>

  <build>
    <plugins>
      <plugin>
        <groupId>org.codehaus.mojo</groupId>
        <artifactId>appassembler-maven-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>net.alchim31.maven</groupId>
        <artifactId>scala-maven-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-gpg-plugin</artifactId>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
      </plugin>
      <!-- enable scalatest -->
      <plugin>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest-maven-plugin</artifactId>
      </plugin>
<!--       <plugin>
    	  <artifactId>maven-clean-plugin</artifactId>
    	  <version>3.0.0</version>
    	  <executions>
          <execution>
            <id>auto-clean</id>
            <phase>initialize</phase>
            <goals>
              <goal>clean</goal>
            </goals>
            <configuration>
             <filesets>
                <fileset>
                  <directory>gnocchi-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0</directory>
                </fileset>
              </filesets>
            </configuration>
          </execution>
        </executions>
      </plugin> -->
    </plugins>
  </build>

  <dependencies>
    <dependency>
      <groupId>net.fnothaft</groupId>
      <artifactId>gnocchi-core</artifactId>
    </dependency>
    <dependency>
      <groupId>org.apache.parquet</groupId>
      <artifactId>parquet-avro</artifactId>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.utils</groupId>
      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
      <version>${utils.version}</version>
      <type>test-jar</type>
      <scope>test</scope>
      <exclusions>
        <exclusion>  <!-- declare the exclusion here -->
          <groupId>com.esotericsoftware.kryo</groupId>
          <artifactId>kryo</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>com.esotericsoftware.kryo</groupId>
      <artifactId>kryo</artifactId>
      <version>2.21</version>
    </dependency>
    <dependency>
        <groupId>org.bdgenomics.adam</groupId>
        <artifactId>adam-cli_2.10</artifactId>
        <version>0.19.0</version>
    </dependency>
    <dependency>
      <groupId>org.apache.directory.studio</groupId>
      <artifactId>org.apache.commons.io</artifactId>
      <version>2.4</version>
    </dependency>
    <dependency>
      <groupId>args4j</groupId>
      <artifactId>args4j</artifactId>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.utils</groupId>
      <artifactId>utils-cli_${scala.version.prefix}</artifactId>
    </dependency>
    <dependency>
      <groupId>org.apache.hadoop</groupId>
      <artifactId>hadoop-client</artifactId>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.adam</groupId>
      <artifactId>adam-core_${scala.version.prefix}</artifactId>
    </dependency>
    <dependency>
      <groupId>org.apache.spark</groupId>
      <artifactId>spark-core_${scala.version.prefix}</artifactId>
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