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>
  <groupId>gov.nih.ncats</groupId>
  <artifactId>lychi</artifactId>
  <packaging>jar</packaging>
  <version>0.7.1</version>
  <name>LyChI</name>

  <repositories>
    <repository>
      <id>jboss-repo</id>
      <url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
    </repository>
  </repositories>
  <properties>
    <java.version>1.8</java.version>
    <maven.compiler.plugin.version>2.3.2</maven.compiler.plugin.version>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <maven.compiler.source>1.8</maven.compiler.source>
    <maven.compiler.target>1.8</maven.compiler.target>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <commonsFileuploadVersion>1.2.1</commonsFileuploadVersion>
    <commonsIoVersion>2.3</commonsIoVersion>
    <junitVersion>3.8.2</junitVersion>
    <log4jVersion>1.2.16</log4jVersion>
    <commonsLang3Version>3.1</commonsLang3Version>
    <downloadLabel>Beta</downloadLabel>
    <gae.version>1.6.5</gae.version>
    <deploy.dir>binaries</deploy.dir>
    <sonatypeRepoId>sonatype-nexus-snapshots</sonatypeRepoId>
    <sonatypeUrl>http://oss.sonatype.org/content/repositories/snapshots</sonatypeUrl>
    <wikiSvnExec>true</wikiSvnExec>
  </properties>
  
  <dependencies>
    <dependency>
      <groupId>chemaxon</groupId>
      <artifactId>jchem</artifactId>
      <version>3.0.0</version>
    </dependency>

    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.13.1</version>
      <scope>provided</scope>
    </dependency>
  </dependencies>

  <build>
    
  	<finalName>${project.artifactId}-${project.version}</finalName>
    <outputDirectory>${deploy.dir}</outputDirectory>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>${maven.compiler.plugin.version}</version>
        <configuration>
          <source>${java.version}</source>
          <target>${java.version}</target>
          <compilerArgument>-proc:none</compilerArgument>
        </configuration>
      </plugin>
      <plugin>
        <artifactId>maven-assembly-plugin</artifactId>
        <executions>
          <execution>
            <phase>package</phase>
            <goals>
              <goal>single</goal>
            </goals>
          </execution>
        </executions>

        <configuration>
          <archive>
            <manifest>
              <mainClass>lychi.LyChIStandardizer</mainClass>
            </manifest>
          </archive>
          <descriptorRefs>
            <descriptorRef>jar-with-dependencies</descriptorRef>
          </descriptorRefs>
        </configuration>
      </plugin>
    </plugins>
    <resources>
      <resource>
        <directory>src/main/java</directory>
        <includes>
          <include>**/*.smi</include>
  	      <include>**/*.smirks</include>
        </includes>
      </resource>
      <resource>
        <directory>lib</directory>
        <includes>
          <include>**/*.md</include>
          <include>**/*.html</include>
        </includes>
      </resource>
    </resources>
  </build>
</project>