gatk-3.8/public/VectorPairHMM/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/maven-v4_0_0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <parent>
        <groupId>org.broadinstitute.gatk</groupId>
        <artifactId>gatk-root</artifactId>
        <version>3.7-SNAPSHOT</version>
        <relativePath>../../public/gatk-root</relativePath>
    </parent>

    <artifactId>VectorPairHMM</artifactId>
    <packaging>pom</packaging>
    <name>Vectorized PairHMM native libraries</name>

    <description>Builds a GNU/Linux x86_64 library of VectorPairHMM using icc (Intel C++ compiler). During install, copies it into gatk-utils. Neither tested nor expected to work on any other platform.</description>

    <properties>
        <sourceEncoding>UTF-8</sourceEncoding>
        <project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
        <project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
        <gatk.basedir>${project.basedir}/../..</gatk.basedir>
        <gatk-utils.basedir>${gatk.basedir}/public/gatk-utils</gatk-utils.basedir>
        <!-- Where to place the library in gatk-utils -->
        <pairhmm.resources.directory>${gatk-utils.basedir}/src/main/resources/org/broadinstitute/gatk/utils/pairhmm</pairhmm.resources.directory>
    </properties>
    <build>
        <plugins>
            <!-- Print out the architecture - works only on GNU/Linux x86_64 systems -->
            <!-- Neither tested nor expected to work on any other platform. -->
            <!-- Requires icc (Intel C++ compiler) to be in your PATH. -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-enforcer-plugin</artifactId>
                <executions>
                    <execution>
                        <goals>
                            <goal>display-info</goal>
                        </goals>
                        <phase>validate</phase>
                    </execution>
                </executions>
            </plugin>

            <!-- Run make -->
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>exec-maven-plugin</artifactId>
                <executions>
                    <execution>
                        <goals>
                            <goal>exec</goal>
                        </goals>
                        <phase>compile</phase>
                        <configuration>
                            <executable>make</executable>
                            <workingDirectory>src/main/c++</workingDirectory>
                            <environmentVariables>
                                <JRE_HOME>${java.home}</JRE_HOME>
                                <!--<USE_GCC>1</USE_GCC>-->
                                <!--<C_COMPILER>/opt/gcc-4.8.2/bin/gcc</C_COMPILER>-->
                                <!--<CPP_COMPILER>/opt/gcc-4.8.2/bin/g++</CPP_COMPILER>-->
                                <OUTPUT_DIR>${project.build.directory}</OUTPUT_DIR>
                            </environmentVariables>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Don't actually install this artifact into the user's repo -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-install-plugin</artifactId>
                <configuration>
                    <skip>true</skip>
                </configuration>
            </plugin>

            <!-- Copy the built library into gatk-utils -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-resources-plugin</artifactId>
                <executions>
                    <execution>
                        <id>default-install</id>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <phase>install</phase>
                        <configuration>
                            <outputDirectory>${pairhmm.resources.directory}</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>${project.build.directory}</directory>
                                    <includes>
                                        <include>**/*</include>
                                    </includes>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- pom.xml cleanup, always sort according to the definitions in gatk-root -->
            <plugin>
                <groupId>com.google.code.sortpom</groupId>
                <artifactId>maven-sortpom-plugin</artifactId>
                <configuration>
                    <createBackupFile>false</createBackupFile>
                    <predefinedSortOrder>custom_1</predefinedSortOrder>
                    <lineSeparator>\n</lineSeparator>
                    <encoding>${sourceEncoding}</encoding>
                    <keepBlankLines>true</keepBlankLines>
                    <sortDependencies>scope</sortDependencies>
                    <nrOfIndentSpace>4</nrOfIndentSpace>
                    <expandEmptyElements>false</expandEmptyElements>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>