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Converting project over to maven. #7

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Dec 16, 2013
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Converting project over to maven. #7

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7 changes: 2 additions & 5 deletions README.md
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Expand Up @@ -19,10 +19,7 @@ Avocado is currently in its infancy, but we hope to have something interesting t

## Building avocado

avocado uses [sbt](http://www.scala-sbt.org/) to build. To build avocado, cd into the repository and run "sbt compile".
avocado uses [Maven](http://maven.apache.org/) to build. To build avocado, cd into the repository and run "mvn package".

Known issues with building:
* There is a current issue where the first time that the project is built, it fails on the first build before succeeding on the second build. This is because of an issue with a local dependency, that should hopefully be fixed soon.
* And... that local dependency is Adam. To install Adam locally, check out Adam and do "mvn package install" (for build instructions, see [the Adam readme](https://github.com/bigdatagenomics/adam)). We are picky though: currently, avocado depends on an Adam pull request that hasn't merged in yet. This pull request is available as the "avocado-patch" branch at [fnothaft/adam](https://github.com/fnothaft/adam).

Standalone JARs are built using [sbt assembly](https://github.com/sbt/sbt-assembly). Once you have compiled, you can build the JAR by running "sbt assembly". Currently, the initial JAR takes about 10 minutes to build, but YMMV.
* This project requires Adam as a local dependency. To install Adam locally, check out Adam and do "mvn package install" (for build instructions, see [the Adam readme](https://github.com/bigdatagenomics/adam)). We build off of the Adam trunk.
53 changes: 0 additions & 53 deletions build.sbt
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129 changes: 129 additions & 0 deletions 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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.berkeley.cs.amplab.avocado</groupId>
<artifactId>avocado</artifactId>
<version>0.0.1</version>
<packaging>jar</packaging>
<name>avocado: A Variant Caller, Distributed</name>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.1</version>
<configuration>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>edu.berkeley.cs.amplab.avocado.Avocado</mainClass>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>reference.conf</resource>
</transformer>
</transformers>
<finalName>avocado-${project.version}</finalName>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
<exclude>META-INF/LICENSE</exclude>
<exclude>META-INF/license</exclude>
</excludes>
</filter>
</filters>
<artifactSet>
<excludes>
<exclude>org.eclipse.jdt:*</exclude>
<exclude>org.scalatest:*</exclude>
<exclude>org.apache.maven:lib:tests</exclude>
</excludes>
</artifactSet>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.1.5</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile-first</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>attach-scaladocs</id>
<phase>verify</phase>
<goals>
<goal>doc-jar</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
<recompileMode>incremental</recompileMode>
<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>
<version>2.7</version>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
</plugins>
</build>

<dependencies>
<dependency>
<groupId>edu.berkeley.cs.amplab.adam</groupId>
<artifactId>adam-format</artifactId>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.berkeley.cs.amplab.adam</groupId>
<artifactId>adam-commands</artifactId>
<version>0.5.0-SNAPSHOT</version>
</dependency>
</dependencies>
</project>
1 change: 0 additions & 1 deletion project/build.properties
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4 changes: 0 additions & 4 deletions project/plugins.sbt
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