123 lines
5.6 KiB
XML
123 lines
5.6 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<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">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.broadinstitute.gatk</groupId>
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<artifactId>gatk-root</artifactId>
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<version>3.8-SNAPSHOT</version>
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<relativePath>../../public/gatk-root</relativePath>
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</parent>
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<artifactId>VectorPairHMM</artifactId>
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<packaging>pom</packaging>
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<name>Vectorized PairHMM native libraries</name>
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<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>
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<properties>
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<sourceEncoding>UTF-8</sourceEncoding>
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<project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
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<project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
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<gatk.basedir>${project.basedir}/../..</gatk.basedir>
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<gatk-utils.basedir>${gatk.basedir}/public/gatk-utils</gatk-utils.basedir>
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<!-- Where to place the library in gatk-utils -->
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<pairhmm.resources.directory>${gatk-utils.basedir}/src/main/resources/org/broadinstitute/gatk/utils/pairhmm</pairhmm.resources.directory>
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</properties>
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<build>
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<plugins>
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<!-- Print out the architecture - works only on GNU/Linux x86_64 systems -->
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<!-- Neither tested nor expected to work on any other platform. -->
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<!-- Requires icc (Intel C++ compiler) to be in your PATH. -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-enforcer-plugin</artifactId>
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<executions>
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<execution>
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<goals>
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<goal>display-info</goal>
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</goals>
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<phase>validate</phase>
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</execution>
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</executions>
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</plugin>
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<!-- Run make -->
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>exec-maven-plugin</artifactId>
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<executions>
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<execution>
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<goals>
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<goal>exec</goal>
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</goals>
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<phase>compile</phase>
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<configuration>
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<executable>make</executable>
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<workingDirectory>src/main/c++</workingDirectory>
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<environmentVariables>
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<JRE_HOME>${java.home}</JRE_HOME>
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<!--<USE_GCC>1</USE_GCC>-->
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<!--<C_COMPILER>/opt/gcc-4.8.2/bin/gcc</C_COMPILER>-->
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<!--<CPP_COMPILER>/opt/gcc-4.8.2/bin/g++</CPP_COMPILER>-->
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<OUTPUT_DIR>${project.build.directory}</OUTPUT_DIR>
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</environmentVariables>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<!-- Don't actually install this artifact into the user's repo -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-install-plugin</artifactId>
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<configuration>
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<skip>true</skip>
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</configuration>
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</plugin>
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<!-- Copy the built library into gatk-utils -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-resources-plugin</artifactId>
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<executions>
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<execution>
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<id>default-install</id>
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<goals>
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<goal>copy-resources</goal>
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</goals>
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<phase>install</phase>
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<configuration>
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<outputDirectory>${pairhmm.resources.directory}</outputDirectory>
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<resources>
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<resource>
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<directory>${project.build.directory}</directory>
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<includes>
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<include>**/*</include>
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</includes>
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</resource>
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</resources>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<!-- pom.xml cleanup, always sort according to the definitions in gatk-root -->
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<plugin>
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<groupId>com.google.code.sortpom</groupId>
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<artifactId>maven-sortpom-plugin</artifactId>
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<configuration>
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<createBackupFile>false</createBackupFile>
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<predefinedSortOrder>custom_1</predefinedSortOrder>
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<lineSeparator>\n</lineSeparator>
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<encoding>${sourceEncoding}</encoding>
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<keepBlankLines>true</keepBlankLines>
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<sortDependencies>scope</sortDependencies>
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<nrOfIndentSpace>4</nrOfIndentSpace>
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<expandEmptyElements>false</expandEmptyElements>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</project>
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