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dependency-reduced-pom.xml
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dependency-reduced-pom.xml
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<?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">
<parent>
<artifactId>gatk-aggregator</artifactId>
<groupId>org.broadinstitute.gatk</groupId>
<version>3.8</version>
<relativePath>../pom.xml/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>org.scut.ccnl</groupId>
<artifactId>sparkhc</artifactId>
<version>1.0-SNAPSHOT</version>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<relocations>
<relocation>
<pattern>com.google.protobuf</pattern>
<shadedPattern>whatever.asynchbase.shaded.com.google.protobuf</shadedPattern>
</relocation>
</relocations>
<transformers>
<transformer>
<mainClass>org.scut.ccnl.genomics.SparkHC</mainClass>
</transformer>
<transformer />
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
<filter>
<artifact>org.seqdoop:hadoop-bam</artifact>
<excludes>
<exlude>org/seqdoop/hadoop_bam/BAMRecordReader.class</exlude>
</excludes>
</filter>
<filter>
<artifact>com.github.samtools:htsjdk</artifact>
<excludes>
<exlude>htsjdk/tribble/util/ParsingUtils.class</exlude>
<exlude>htsjdk/samtools/reference/AbstractFastaSequenceFile.class</exlude>
<exlude>htsjdk/samtools/reference/FastaSequenceIndex.class</exlude>
<exlude>htsjdk/samtools/reference/FastaSequenceIndexEntry.class</exlude>
<exlude>htsjdk/samtools/reference/IndexedFastaSequenceFile.class</exlude>
</excludes>
</filter>
<filter>
<artifact>org.broadinstitute.gatk:gatk-utils</artifact>
<excludes>
<exlude>org/broadinstitute/gatk/utils/GenomeLocParser.class</exlude>
<exlude>org/broadinstitute/gatk/utils/ActiveRegion.class</exlude>
<exlude>org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.class</exlude>
<exlude>org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.class</exlude>
<exlude>org/broadinstitute/gatk/utils/MathUtils.class</exlude>
<exlude>org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.class</exlude>
</excludes>
</filter>
<filter>
<artifact>org.broadinstitute.gatk:gatk-engine</artifact>
<excludes>
<exlude>org/broadinstitute/gatk/engine/datasources/providers/ShardDataProvider.class</exlude>
<exlude>org/broadinstitute/gatk/engine/datasources/providers/LocusShardDataProvider.class</exlude>
<exlude>org/broadinstitute/gatk/engine/datasources/providers/LocusReferenceView.class</exlude>
<exlude>org/broadinstitute/gatk/engine/datasources/providers/ReferenceView.class</exlude>
<exlude>org/broadinstitute/gatk/engine/datasources/providers/AllLocusView.class</exlude>
<exlude>org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.class</exlude>
<exlude>org/broadinstitute/gatk/engine/GATKVCFUtils.class</exlude>
<exlude>org/broadinstitute/gatk/engine/io/stubs/VariantContextWriterStub.class</exlude>
<exlude>org/broadinstitute/gatk/engine/iterators/ReadTransformingIterator.class</exlude>
<exlude>org/broadinstitute/gatk/engine/iterators/MisencodedBaseQualityReadTransformer.class</exlude>
</excludes>
</filter>
<filter>
<artifact>org.broadinstitute.gatk:gatk-tools-protected</artifact>
<excludes>
<exlude>org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.class</exlude>
<exlude>org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.class</exlude>
<exlude>org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.class</exlude>
<exlude>org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.class</exlude>
<exlude>org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.class</exlude>
<exlude>org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProvider.class</exlude>
<exlude>org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.class</exlude>
<exlude>org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.class</exlude>
</excludes>
</filter>
<filter>
<artifact>org.broadinstitute.gatk:gatk-tools-public</artifact>
<excludes>
<exlude>org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.class</exlude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>java.net</id>
<url>http://repo.maven.apache.org/maven2</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.apache.hbase</groupId>
<artifactId>hbase-client</artifactId>
<version>1.2.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>hbase-annotations</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>hbase-protocol</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>htrace-core</artifactId>
<groupId>org.apache.htrace</groupId>
</exclusion>
<exclusion>
<artifactId>jcodings</artifactId>
<groupId>org.jruby.jcodings</groupId>
</exclusion>
<exclusion>
<artifactId>joni</artifactId>
<groupId>org.jruby.joni</groupId>
</exclusion>
<exclusion>
<artifactId>metrics-core</artifactId>
<groupId>com.yammer.metrics</groupId>
</exclusion>
<exclusion>
<artifactId>findbugs-annotations</artifactId>
<groupId>com.github.stephenc.findbugs</groupId>
</exclusion>
<exclusion>
<artifactId>junit</artifactId>
<groupId>junit</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.hbase</groupId>
<artifactId>hbase-common</artifactId>
<version>1.2.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>hbase-protocol</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>hbase-annotations</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>htrace-core</artifactId>
<groupId>org.apache.htrace</groupId>
</exclusion>
<exclusion>
<artifactId>findbugs-annotations</artifactId>
<groupId>com.github.stephenc.findbugs</groupId>
</exclusion>
<exclusion>
<artifactId>junit</artifactId>
<groupId>junit</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.hbase</groupId>
<artifactId>hbase-server</artifactId>
<version>1.2.0</version>
<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>hbase-procedure</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>hbase-prefix-tree</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>hbase-hadoop-compat</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>hbase-hadoop2-compat</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>jetty-sslengine</artifactId>
<groupId>org.mortbay.jetty</groupId>
</exclusion>
<exclusion>
<artifactId>jsp-2.1</artifactId>
<groupId>org.mortbay.jetty</groupId>
</exclusion>
<exclusion>
<artifactId>jsp-api-2.1</artifactId>
<groupId>org.mortbay.jetty</groupId>
</exclusion>
<exclusion>
<artifactId>servlet-api-2.5</artifactId>
<groupId>org.mortbay.jetty</groupId>
</exclusion>
<exclusion>
<artifactId>jasper-compiler</artifactId>
<groupId>tomcat</groupId>
</exclusion>
<exclusion>
<artifactId>jamon-runtime</artifactId>
<groupId>org.jamon</groupId>
</exclusion>
<exclusion>
<artifactId>disruptor</artifactId>
<groupId>com.lmax</groupId>
</exclusion>
<exclusion>
<artifactId>esapi</artifactId>
<groupId>org.owasp.esapi</groupId>
</exclusion>
<exclusion>
<artifactId>metrics-core</artifactId>
<groupId>com.yammer.metrics</groupId>
</exclusion>
<exclusion>
<artifactId>hbase-protocol</artifactId>
<groupId>org.apache.hbase</groupId>
</exclusion>
<exclusion>
<artifactId>htrace-core</artifactId>
<groupId>org.apache.htrace</groupId>
</exclusion>
<exclusion>
<artifactId>findbugs-annotations</artifactId>
<groupId>com.github.stephenc.findbugs</groupId>
</exclusion>
<exclusion>
<artifactId>junit</artifactId>
<groupId>junit</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.sun</groupId>
<artifactId>tools</artifactId>
<version>1.4.2</version>
<scope>system</scope>
<systemPath>C:\Program Files\Java\jdk1.8.0_65\jre/../lib/tools.jar</systemPath>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>bsh</artifactId>
<groupId>org.beanshell</groupId>
</exclusion>
<exclusion>
<artifactId>jcommander</artifactId>
<groupId>com.beust</groupId>
</exclusion>
<exclusion>
<artifactId>snakeyaml</artifactId>
<groupId>org.yaml</groupId>
</exclusion>
<exclusion>
<artifactId>junit</artifactId>
<groupId>junit</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.uncommons</groupId>
<artifactId>reportng</artifactId>
<version>1.1.2</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>testng</artifactId>
<groupId>org.testng</groupId>
</exclusion>
<exclusion>
<artifactId>velocity</artifactId>
<groupId>velocity</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.inject</groupId>
<artifactId>guice</artifactId>
<version>3.0</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>aopalliance</artifactId>
<groupId>aopalliance</groupId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
</project>