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Updating poms with proper dependency versions and exclusions.

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heuermh authored and devin-petersohn committed Dec 12, 2017
1 parent 531d9c0 commit 6b961404f438d415100714daebc2affaa058b614
Showing with 705 additions and 878 deletions.
  1. +159 −203 lime-cli/pom.xml
  2. +80 −161 lime-core/pom.xml
  3. +466 −514 pom.xml
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@@ -1,214 +1,170 @@
<?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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-parent</artifactId>
<version>0.0.1-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>lime-cli</artifactId>
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-parent</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>lime-cli: Command line interface for distributed set theory on genomics</name>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>lime-cli</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>lime-cli: Command line interface for distributed set theory on genomics</name>
<properties>
<timestamp>${maven.build.timestamp}</timestamp>
<maven.build.timestamp.format>yyyy-MM-dd</maven.build.timestamp.format>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>templating-maven-plugin</artifactId>
<executions>
<execution>
<id>filter-src</id>
<goals>
<goal>filter-sources</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile-first</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>attach-scaladocs</id>
<phase>verify</phase>
<goals>
<goal>doc-jar</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
<useZincServer>true</useZincServer>
<args>
<arg>-unchecked</arg>
<arg>-optimise</arg>
<arg>-deprecation</arg>
</args>
<jvmArgs>
<jvmArg>-Xms64m</jvmArg>
<jvmArg>-Xms1024m</jvmArg>
<jvmArg>-Xmx1024m</jvmArg>
</jvmArgs>
<javacArgs>
<javacArg>-source</javacArg>
<javacArg>${java.version}</javacArg>
<javacArg>-target</javacArg>
<javacArg>${java.version}</javacArg>
</javacArgs>
</configuration>
</plugin>
<!-- disable surefire -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<!-- enable scalatest -->
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<configuration>
<reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>limeTestSuite.txt</filereports>
<argLine>-Xmx1024m</argLine>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>templating-maven-plugin</artifactId>
<executions>
<execution>
<id>filter-src</id>
<goals>
<goal>filter-sources</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- disable surefire -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<!-- enable scalatest -->
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<configuration>
<reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>limeTestSuite.txt</filereports>
<argLine>-Xmx1024m</argLine>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-cli-spark2_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-core</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
<exclusions>
<exclusion>
<groupId>javax.servlet</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-cli-spark2_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.version.prefix}</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-core</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-cli-spark2_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-core</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.utils</groupId>
<artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.lime</groupId>
<artifactId>lime-core</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-cli-spark2_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>args4j</groupId>
<artifactId>args4j</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.version.prefix}</artifactId>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.version.prefix}</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>
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