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* Add pom.xml for java build * Add maven build to Dockerfile * Create package with dependencies from maven
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,162 @@ | ||
| <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>4.10</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> |