gatk-3.8/public/c++/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.sting</groupId>
        <artifactId>sting-root</artifactId>
        <version>2.8-SNAPSHOT</version>
        <relativePath>../../public/sting-root</relativePath>
    </parent>

    <artifactId>pairhmm-native</artifactId>
    <packaging>pom</packaging>
    <name>PairHMM Native Libraries</name>

    <description>Builds a platform dependent version of pairhmm. During install, copies it into sting-utils.</description>

    <properties>
        <sourceEncoding>UTF-8</sourceEncoding>
        <project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
        <project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
        <sting.basedir>${project.basedir}/../..</sting.basedir>
        <sting-utils.basedir>${sting.basedir}/public/sting-utils</sting-utils.basedir>
        <!-- Where to place the library in sting-utils -->
        <pairhmm.resources.directory>${sting-utils.basedir}/src/main/resources/org/broadinstitute/sting/utils/pairhmm</pairhmm.resources.directory>

        <!-- Per architecture properties, overriden in profiles below -->
        <!--
        NOTE: cxxflags is for currently only for -fPIC on linux.
        For other architectures still have to pass something, until possibly
        switching to command line arguments with exec-maven-plugin 1.3
        http://jira.codehaus.org/browse/MEXEC-104
        -->
        <pairhmm.build.architecture>x86_64</pairhmm.build.architecture>
        <pairhmm.build.extension>so</pairhmm.build.extension>
        <pairhmm.build.cxxflags>-Wall</pairhmm.build.cxxflags>
        <pairhmm.build.ldflags>-dynamiclib</pairhmm.build.ldflags>
    </properties>
    <build>
        <plugins>
            <!-- Print out the current architecture, to know which profile is being activated. -->
            <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>VectorPairHMM</workingDirectory>
                            <environmentVariables>
                                <ARCHITECTURE>${pairhmm.build.architecture}</ARCHITECTURE>
                                <LIB_EXT>${pairhmm.build.extension}</LIB_EXT>
                                <CXXFLAGS>${pairhmm.build.cxxflags}</CXXFLAGS>
                                <LDFLAGS>${pairhmm.build.ldflags}</LDFLAGS>
                                <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 sting-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 sting-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>

    <profiles>

        <profile>
            <id>mac_x86_64</id>
            <activation>
                <os>
                    <family>mac</family>
                    <arch>x86_64</arch>
                </os>
            </activation>
            <properties>
                <pairhmm.build.architecture>mac_x86_64</pairhmm.build.architecture>
                <pairhmm.build.extension>jnilib</pairhmm.build.extension>
                <pairhmm.build.ldflags>-dynamiclib</pairhmm.build.ldflags>
            </properties>
        </profile>

        <profile>
            <id>linux_x86_64</id>
            <activation>
                <os>
                    <name>linux</name>
                    <arch>amd64</arch>
                </os>
            </activation>
            <properties>
                <pairhmm.build.architecture>linux_x86_64</pairhmm.build.architecture>
                <pairhmm.build.extension>jnilib</pairhmm.build.extension>
                <pairhmm.build.cxxflags>-fPIC</pairhmm.build.cxxflags>
                <pairhmm.build.ldflags>-shared</pairhmm.build.ldflags>
            </properties>
        </profile>

    </profiles>
</project>