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">

  <parent>
    <groupId>org.hammerlab</groupId>
    <artifactId>scala-parent-pom</artifactId>
    <version>1.0.3</version>
    <relativePath />
  </parent>

  <modelVersion>4.0.0</modelVersion>
  <artifactId>guacamole</artifactId>
  <version>0.0.1-SNAPSHOT</version>
  <packaging>jar</packaging>
  <name>guacamole: variant caller</name>

  <properties>
    <github.repo>hammerlab/guacamole</github.repo>
    <scala.version>2.10.6</scala.version>
    <scala.version.prefix>2.10</scala.version.prefix>
    <hadoop.version>2.7.0</hadoop.version>
    <spark.version>1.6.1</spark.version>
    <spark.hadoop.scope>provided</spark.hadoop.scope>
  </properties>

  <build>
    <!--
      The Guacamole JAR output by maven-jar-plugin, at the path configured here, can't run on its own; it needs some
      dependency-classes shaded in, as configured elsewhere in this file. However, the shade plugin requires it to be
      present in order to work.

      As such, we write it to a non-default path here, and treat the minimum-viable Guacamole+shaded-deps JAR (built by
      the default "guac" profile below) as the primary deliverable.
     -->
    <finalName>guacamole-unshaded-${project.version}</finalName>
    <plugins>
      <plugin>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest-maven-plugin</artifactId>
        <configuration>
          <!-- Bump the memory used by scalatest. -->
          <argLine>-Xmx4g</argLine>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-shade-plugin</artifactId>
        <version>2.4.3</version>
        <configuration>
          <transformers>
            <!-- Set "main" class. -->
            <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
              <mainClass>org.hammerlab.guacamole.Main</mainClass>
            </transformer>
          </transformers>

          <filters>
            <!-- Exclude signature files that we don't validate. -->
            <filter>
              <artifact>*:*</artifact>
              <excludes>
                <exclude>META-INF/*.SF</exclude>
                <exclude>META-INF/*.DSA</exclude>
                <exclude>META-INF/*.RSA</exclude>
                <exclude>META-INF/LICENSE</exclude>
                <exclude>META-INF/license</exclude>
              </excludes>
            </filter>
          </filters>

          <relocations>
            <!--
              Spark (MLLib) depends on Breeze 0.11.2 and we depend on 0.12. By Spark 2.0.1 we should be able to
              remove this.
            -->
            <relocation>
              <pattern>breeze</pattern>
              <shadedPattern>org.hammerlab.breeze</shadedPattern>
              <includes>
                <include>breeze.**</include>
              </includes>
            </relocation>
          </relocations>
        </configuration>
      </plugin>
    </plugins>
  </build>

  <dependencies>
    <dependency>
      <groupId>com.esotericsoftware.kryo</groupId>
      <artifactId>kryo</artifactId>
      <version>2.21</version>
    </dependency>
    <dependency>
      <groupId>args4j</groupId>
      <artifactId>args4j</artifactId>
      <version>[2.0.29,)</version>
    </dependency>
    <dependency>
      <groupId>org.hammerlab.adam</groupId>
      <artifactId>adam-core_${scala.version.prefix}</artifactId>
      <version>0.20.3</version>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.bdg-formats</groupId>
      <artifactId>bdg-formats</artifactId>
      <version>0.10.0</version>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.quinine</groupId>
      <artifactId>quinine-core_${scala.version.prefix}</artifactId>
      <version>0.0.2</version>
      <exclusions>
        <exclusion>
          <groupId>org.bdgenomics.adam</groupId>
          <artifactId>adam-core_2.10</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.spire-math</groupId>
      <artifactId>spire_${scala.version.prefix}</artifactId>
      <version>0.11.0</version>
    </dependency>
    <dependency>
      <groupId>org.scalanlp</groupId>
      <artifactId>breeze_${scala.version.prefix}</artifactId>
      <version>0.12</version>
    </dependency>
    <dependency>
      <groupId>com.github.samtools</groupId>
      <artifactId>htsjdk</artifactId>
      <version>2.6.1</version>
      <exclusions>
        <!--
          htsjdk:2.6.1 brings in snappy-java:1.0.3-rc3, but running tests on OSX requires ≥ 1.0.5, per
          http://stackoverflow.com/a/31482848/544236.
        -->
        <exclusion>
          <groupId>org.xerial.snappy</groupId>
          <artifactId>snappy-java</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.seqdoop</groupId>
      <artifactId>hadoop-bam</artifactId>
      <version>7.6.0</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-math3</artifactId>
      <version>3.0</version>
    </dependency>
    <dependency>
      <groupId>org.hammerlab</groupId>
      <artifactId>args4s_${scala.version.prefix}</artifactId>
      <version>1.0.0</version>
    </dependency>
    <dependency>
      <groupId>org.hammerlab</groupId>
      <artifactId>magic-rdds_${scala.version.prefix}</artifactId>
      <version>1.3.0</version>
    </dependency>
    <dependency>
      <groupId>org.hammerlab</groupId>
      <artifactId>spark-commands_${scala.version.prefix}</artifactId>
      <version>1.0.0-SNAPSHOT</version>
    </dependency>
    <dependency>
      <groupId>org.clapper</groupId>
      <artifactId>grizzled-slf4j_${scala.version.prefix}</artifactId>
      <version>1.0.3</version>
    </dependency>

    <dependency>
      <groupId>org.apache.hadoop</groupId>
      <artifactId>hadoop-client</artifactId>
      <version>${hadoop.version}</version>
      <scope>${spark.hadoop.scope}</scope>
      <exclusions>
        <!--
          hadoop-client's javax.servlet:servlet-api dependency includes classes that conflict with spark-core's
          org.eclipse.jetty.orbit:javax.servlet dependency; excluding the former resolves this, cf.
          https://issues.apache.org/jira/browse/SPARK-1693.
        -->
        <exclusion>
          <groupId>javax.servlet</groupId>
          <artifactId>*</artifactId>
        </exclusion>
      </exclusions>
    </dependency>
    <dependency>
      <groupId>org.apache.spark</groupId>
      <artifactId>spark-core_${scala.version.prefix}</artifactId>
      <version>${spark.version}</version>
      <scope>${spark.hadoop.scope}</scope>
    </dependency>
    <dependency>
      <groupId>org.apache.spark</groupId>
      <artifactId>spark-mllib_${scala.version.prefix}</artifactId>
      <version>${spark.version}</version>
      <scope>${spark.hadoop.scope}</scope>
    </dependency>
    <dependency>
      <groupId>org.hammerlab</groupId>
      <artifactId>spark-util_${scala.version.prefix}</artifactId>
      <version>1.1.0</version>
    </dependency>
    <dependency>
      <groupId>org.hammerlab</groupId>
      <artifactId>genomic-loci_${scala.version.prefix}</artifactId>
      <version>1.4.1</version>
    </dependency>

    <!-- Test deps -->
    <dependency>
      <groupId>com.holdenkarau</groupId>
      <artifactId>spark-testing-base_${scala.version.prefix}</artifactId>
      <version>${spark.version}_0.4.4</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.bdgenomics.bdg-utils</groupId>
      <artifactId>bdg-utils-misc</artifactId>
      <version>0.1.1</version>
      <type>test-jar</type>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.hammerlab</groupId>
      <artifactId>spark-tests_${scala.version.prefix}</artifactId>
      <version>1.1.0</version>
    </dependency>
  </dependencies>

  <profiles>
    <profile>
      <!--
        Default profile: build a Guacamole jar with shaded Breeze, and write transitive-dependency-JAR paths
        to target/dependencies (comma-delimited to serve the common case of passing the values to Spark's "jars" flag).
      -->
      <id>guac</id>
      <activation>
        <activeByDefault>true</activeByDefault>
      </activation>
      <build>
        <!--
          `mvn install` will look for a JAR with this name, which is taken to be the main deliverable JAR of this
          project.

          We name it here in a manner that matches what we tell the shade-plugin to output below.
        -->
        <finalName>guacamole-${project.version}</finalName>
        <plugins>
          <plugin>
            <artifactId>maven-shade-plugin</artifactId>
            <executions>
              <execution>
                <id>guac</id>
                <goals>
                  <goal>shade</goal>
                </goals>
                <configuration>
                  <finalName>guacamole-${project.version}</finalName>
                  <!--
                    Don't "attach" this shaded JAR to the project (in addition to the default unshaded JAR that would be
                    produced by the jar-plugin; this JAR *is* the deliverable of the project.
                  -->
                  <shadedArtifactAttached>false</shadedArtifactAttached>
                  <artifactSet>
                    <includes>
                      <include>org.hammerlab.guacamole:*</include>
                      <include>org.scalanlp:breeze_${scala.version.prefix}</include>
                    </includes>
                  </artifactSet>
                </configuration>
              </execution>
            </executions>
          </plugin>

          <!-- Write a file with paths to all transitive-dependencies to target/dependencies. -->
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-dependency-plugin</artifactId>
            <version>2.10</version>
            <executions>
              <execution>
                <goals>
                  <goal>build-classpath</goal>
                </goals>
                <configuration>
                  <outputFile>${target.dir}/dependencies</outputFile>

                  <!-- Use commas for ease of passing to spark-{submit,shell}'s "jars" flag. -->
                  <pathSeparator>,</pathSeparator>

                  <!-- Leave Breeze out, as they are included in the Guacamole JAR defined above. -->
                  <excludeArtifactIds>
                    breeze_${scala.version.prefix}
                  </excludeArtifactIds>
                </configuration>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>

    <!--
      "uber" profile: build a JAR with Guacamole and all transitive dependencies shaded, and Breeze relocated.
    -->
    <profile>
      <id>uber</id>
      <build>
        <plugins>
          <plugin>
            <artifactId>maven-shade-plugin</artifactId>
            <executions>
              <execution>
                <id>assembly</id>
                <goals>
                  <goal>shade</goal>
                </goals>
                <configuration>
                  <finalName>guacamole-assembly-${project.version}</finalName>
                </configuration>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>

    <profile>
      <!--
        "deps" profile: build a JAR with just Guacamole's transitive dependencies, excluding those that are shaded into
        the Guacamole JAR itself.
      -->
      <id>deps</id>
      <build>
        <plugins>
          <plugin>
            <artifactId>maven-shade-plugin</artifactId>
            <executions>
              <execution>
                <id>deps</id>
                <goals>
                  <goal>shade</goal>
                </goals>
                <configuration>
                  <finalName>guacamole-deps-${project.version}</finalName>
                  <transformers combine.children="append">
                    <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer" />
                  </transformers>
                  <filters combine.children="append">
                    <!-- Leave all Guacamole classes out of this JAR. -->
                    <filter>
                      <artifact>*:guacamole</artifact>
                      <excludes>
                        <exclude>org/hammerlab/guacamole/**</exclude>
                      </excludes>
                    </filter>
                  </filters>
                  <artifactSet>
                    <excludes>
                      <!-- These are shaded into the "guac"-profile JAR. -->
                      <exclude>org.scalanlp:breeze_${scala.version.prefix}</exclude>
                    </excludes>
                  </artifactSet>
                </configuration>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>

    <profile>
      <!--
        "local" profile puts Spark and Hadoop into "compile" scope (rather than "provided"); generally not desirable,
        unless intending to run Guacamole directly from the command-line using the `java` executable, instead of
        spark-{submit,shell}.
      -->
      <id>local</id>
      <properties>
        <spark.hadoop.scope>compile</spark.hadoop.scope>
      </properties>
      <build>
        <plugins>
          <plugin>
            <artifactId>maven-shade-plugin</artifactId>
            <configuration>
              <transformers combine.children="append">
                <!-- Akka (which Spark depends on) needs this reference.conf munging in order to work correctly in -->
                <!-- shaded JARs, cf. http://stackoverflow.com/questions/31011243/#31011315 -->
                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                  <resource>reference.conf</resource>
                </transformer>

                <!-- Necessary for Hadoop to load local files correctly, cf. http://stackoverflow.com/a/27532248/544236 -->
                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
              </transformers>
            </configuration>
          </plugin>
        </plugins>
      </build>
    </profile>

    <profile>
      <id>test</id>
      <build>
        <plugins>
          <plugin>
            <artifactId>maven-jar-plugin</artifactId>
            <executions>
              <execution>
                <id>test-jar</id>
                <phase>package</phase>
                <goals>
                  <goal>test-jar</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>

  </profiles>
</project>