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pom.xml
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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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.scripps.yates</groupId>
<version>1.3</version>
<name>PDB structures module</name>
<artifactId>pac-calculator</artifactId>
<description>Java module for managing PDB structures</description>
<distributionManagement>
<repository>
<id>internal</id>
<url>http://sealion.scripps.edu/archiva/repository/internal/</url>
</repository>
<snapshotRepository>
<id>snapshots</id>
<url>http://sealion.scripps.edu/archiva/repository/snapshots/</url>
</snapshotRepository>
</distributionManagement>
<properties>
<assembly.output.folder>PAC-calculator</assembly.output.folder>
<lib.dir>lib</lib.dir>
<project.build.sourceEncoding>ISO-8859-1</project.build.sourceEncoding>
<assembly.dir>PAC-calculator_v${project.version}</assembly.dir>
</properties>
<organization>
<name>TSRI</name>
</organization>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.1</version>
</dependency>
<dependency>
<groupId>net.sourceforge.jmol</groupId>
<artifactId>jmol</artifactId>
<version>13.0.14</version>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<version>4.3.21.RELEASE</version>
</dependency>
<dependency>
<groupId>com.compomics</groupId>
<artifactId>dbtoolkit</artifactId>
<version>4.2.6</version>
<exclusions>
<exclusion>
<artifactId>batik-all</artifactId>
<groupId>batik</groupId>
</exclusion>
<exclusion>
<artifactId>pdf-transcoder</artifactId>
<groupId>batik</groupId>
</exclusion>
<exclusion>
<artifactId>iText</artifactId>
<groupId>itext</groupId>
</exclusion>
<exclusion>
<artifactId>jcommon</artifactId>
<groupId>jfree</groupId>
</exclusion>
<exclusion>
<artifactId>lmjunit</artifactId>
<groupId>lennart</groupId>
</exclusion>
<exclusion>
<artifactId>cpdetector</artifactId>
<groupId>lennart</groupId>
</exclusion>
<exclusion>
<artifactId>statlib</artifactId>
<groupId>lennart</groupId>
</exclusion>
<exclusion>
<artifactId>xxindex</artifactId>
<groupId>lennart</groupId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
<exclusion>
<groupId>net.jimmc</groupId>
<artifactId>jshortcut</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>edu.scripps.yates</groupId>
<artifactId>pint.annotations</artifactId>
<version>1.0.2-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>edu.scripps.yates</groupId>
<artifactId>pint.model</artifactId>
<version>1.0.1-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.scripps.yates</groupId>
<artifactId>utilities</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>edu.scripps.yates</groupId>
<artifactId>pint.excel</artifactId>
<version>1.0.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>edu.scripps.yates</groupId>
<artifactId>dbindex</artifactId>
<version>1.2.1-SNAPSHOT</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.5.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${lib.dir}</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<!-- <overWriteIfNewer>true</overWriteIfNewer> -->
<!-- useBaseVersion=false makes the jar names match those -->
<!-- that maven-jar-plugin puts in the manifest classpath -->
<!-- Either append the artifact's baseVersion or uniqueVersion to the filename. Will only be used if isStripVersion() is false. -->
<useBaseVersion>true</useBaseVersion>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.0.0</version>
<executions>
<execution>
<phase>generate-resources</phase>
<goals>
<goal>write-project-properties</goal>
</goals>
<configuration>
<outputFile>
${project.build.outputDirectory}/app.properties
</outputFile>
<properties>
<property>
<name>revision</name>
<value>${revision}</value>
</property>
<property>
<name>buildnumber</name>
<value>${buildnumber}</value>
</property>
</properties>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<finalName>${assembly.dir}</finalName>
<descriptors>
<descriptor>${basedir}/src/main/resources/assembly.xml</descriptor>
</descriptors>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>edu.scripps.yates.pdb.Main</mainClass>
<classpathPrefix>lib/</classpathPrefix>
<useUniqueVersions>false</useUniqueVersions>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
<configuration>
<finalName>psa-calculator</finalName>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>edu.scripps.yates.pdb.Main</mainClass>
<classpathPrefix>lib/</classpathPrefix>
<useUniqueVersions>false</useUniqueVersions>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</project>