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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>
<!-- TODO: replace SUBPACKAGE with the rest of the package name. Often this
will be the same as the svn module name. The full groupId should be the
name of the java package that contains the main code for the module. -->
<groupId>org.stjude.compbio.rnapeg</groupId>
<!-- TODO: replace MODULE with the module name used in svn. This may not
always match the svn name for some of the earliest projects added to svn -->
<artifactId>rnapeg</artifactId>
<version>2.6.0</version>
<!-- TODO: Use the same module as was used in the artifactId -->
<name>RNApeg: RNA junction extraction and mapping correction</name>
<!-- TODO: Provide a brief description, e.g. 'Sample name parsing and building
library'. It can go onto multiple lines -->
<description>RNApeg extracts RNA junctions from BAM files, corrects and standardizes mapping ambiguities, and performs gene annotations.</description>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>fully.qualified.MainClass</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- This plugin is required, do not remove it -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.8.1</version>
<configuration>
<show>public</show>
<sourcepath>src/main/java</sourcepath>
</configuration>
</plugin>
<!-- This plugin is required if you have any scripts or any other non-java
files in your module. Usually you should leave it in -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.5</version>
<executions>
<!-- This execution will copy scripts to target; delete or comment out
if you don't have any shell scripts -->
<execution>
<id>copy-scripts</id>
<phase>compile</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/scripts</outputDirectory>
<resources>
<resource>
<directory>src/main/scripts</directory>
</resource>
</resources>
</configuration>
</execution>
<!-- This execution will copy perl modules to target; delete or comment
out if you don't have any perl modules in perllib -->
<execution>
<id>copy-perllib</id>
<phase>compile</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/perllib</outputDirectory>
<resources>
<resource>
<directory>src/main/perllib</directory>
</resource>
</resources>
</configuration>
</execution>
<!-- This execution will copy javascript to target; uncomment-out if
you have any javascript source (most projects don't) -->
<!--
<execution>
<id>copy-js</id>
<phase>compile</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${basedir}/target/js</outputDirectory>
<resources>
<resource>
<directory>src/main/js</directory>
</resource>
</resources>
</configuration>
</execution>
-->
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<!-- You should leave this in. If you don't have unit tests, then you
should write some someday! -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.1</version>
<scope>test</scope>
</dependency>
<!-- An example dependency to another CompBio module. The groupId,
artifactId, and version are taken from the pom.xml of that module. The
scope value will always be "provided": -->
<!-- https://mvnrepository.com/artifact/com.github.broadinstitute/picard -->
<dependency>
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
<version>2.6.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.github.samtools/htsjdk -->
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>1.129</version>
</dependency>
<!--
<dependency>
<groupId>org.stjude.compbio.common.sam</groupId>
<artifactId>common-java-sam</artifactId>
<version>1.0</version>
<scope>provided</scope>
</dependency>
-->
<!-- An example dependency to a "library" (stored in subversion under
"lib/java") -->
<!--
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.2</version>
<scope>provided</scope>
</dependency>
-->
</dependencies>
<properties>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</properties>
</project>