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pom.xml
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<?xml version="1.0" encoding="ISO-8859-1"?>
<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>org.cruk.pipelines</groupId>
<artifactId>mga</artifactId>
<packaging>jar</packaging>
<version>1.8-SNAPSHOT</version>
<name>Multi-Genome Alignment Pipeline</name>
<inceptionYear></inceptionYear>
<organization>
<name>Cancer Research UK Cambridge Institute</name>
<url>https://www.cruk.cam.ac.uk/</url>
</organization>
<developers>
<developer>
<name>Matthew Eldridge</name>
<email>[email protected]</email>
<roles>
<role>Author</role>
<role>Lead Developer</role>
</roles>
</developer>
<developer>
<name>Richard Bowers</name>
<email>[email protected]</email>
<roles>
<role>Developer</role>
</roles>
</developer>
</developers>
<properties>
<application.name>mga-pipeline</application.name>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<dependency.locations.enabled>false</dependency.locations.enabled>
</properties>
<distributionManagement>
<repository>
<id>bioinformatics</id>
<url>scpexe://comp-httpdev001.cri.camres.org/var/www/html/bioinformatics/maven</url>
</repository>
<snapshotRepository>
<id>bioinformatics</id>
<url>scpexe://internal-bioinformatics.cruk.cam.ac.uk/var/www/html/maven</url>
</snapshotRepository>
</distributionManagement>
<pluginRepositories>
<pluginRepository>
<id>mulesoft</id>
<url>https://repository-master.mulesoft.org/nexus/content/groups/public</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</pluginRepository>
</pluginRepositories>
<repositories>
<repository>
<id>mulesoft</id>
<url>https://repository-master.mulesoft.org/nexus/content/groups/public</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>crukci-bioinformatics</id>
<url>http://content.cruk.cam.ac.uk/bioinformatics/maven</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>bioinformatics</id>
<url>http://internal-bioinformatics.cruk.cam.ac.uk/maven</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
<build>
<resources>
<resource>
<directory>${basedir}/src/main/resources</directory>
<targetPath>${project.build.outputDirectory}</targetPath>
</resource>
<resource>
<directory>${basedir}/src/test/resources</directory>
<targetPath>${project.build.testOutputDirectory}</targetPath>
</resource>
<resource>
<directory>${basedir}</directory>
<targetPath>META-INF</targetPath>
<includes>
<include>LICENSE</include>
</includes>
</resource>
</resources>
<extensions>
<extension>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-ssh</artifactId>
<version>2.12</version>
</extension>
<extension>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-ssh-external</artifactId>
<version>2.12</version>
</extension>
</extensions>
<pluginManagement>
<plugins>
<!-- Build plugins -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<encoding>UTF-8</encoding>
<compilerArgs>
<compilerArg>-Xlint:all</compilerArg>
</compilerArgs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>3.0.0-M1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>3.0.0-M1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<archive>
<index>true</index>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<encoding>UTF-8</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.9.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.0.0-M4</version>
</plugin>
<!-- Reporting plugins -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<encoding>UTF-8</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
<version>3.0.0-M4</version>
</plugin>
<!-- Third party plugins -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
<version>2.1.0</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.7</version>
<configuration>
<generateBackupPoms>false</generateBackupPoms>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.0.0-M3</version>
<executions>
<execution>
<id>enforce-maven</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>3.5.0</version>
</requireMavenVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>appassembler-maven-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>assemble</goal>
</goals>
</execution>
</executions>
<configuration>
<assembleDirectory>${project.build.directory}/${application.name}</assembleDirectory>
<copyConfigurationDirectory>true</copyConfigurationDirectory>
<repositoryLayout>flat</repositoryLayout>
<repositoryName>lib</repositoryName>
<platforms>
<platform>unix</platform>
</platforms>
<programs>
<program>
<mainClass>org.cruk.workflow.PipelineRunner</mainClass>
<name>run-pipeline</name>
</program>
<program>
<mainClass>org.cruk.mga.workflow.CreateMetadataFromSampleSheet</mainClass>
<name>prepare-pipeline</name>
</program>
<program>
<mainClass>org.cruk.seq.SampleFastq</mainClass>
<name>sample-fastq</name>
</program>
<program>
<mainClass>org.cruk.seq.TrimFastq</mainClass>
<name>trim-fastq</name>
</program>
<program>
<mainClass>org.cruk.seq.FastqToFasta</mainClass>
<name>fastq-to-fasta</name>
</program>
</programs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptors>
<descriptor>src/main/assembly/assembly.xml</descriptor>
</descriptors>
<tarLongFileMode>posix</tarLongFileMode>
<attach>false</attach>
</configuration>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<configuration>
<reportSets>
<reportSet>
<reports>
<report>dependencies</report>
<report>index</report>
<report>scm</report>
</reports>
</reportSet>
</reportSets>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<reportSets>
<reportSet>
<reports>
<report>javadoc</report>
</reports>
</reportSet>
</reportSets>
<configuration>
<!-- <overview>${project.build.sourceDirectory}/overview.html</overview> -->
<breakiterator>true</breakiterator>
<serialwarn>true</serialwarn>
<show>protected</show>
<links>
<link>https://docs.oracle.com/javase/8/docs/api</link>
<link>https://docs.oracle.com/javaee/7/api/</link>
<link>https://docs.groovy-lang.org/3.0.3/html/gapi</link>
<link>https://www.slf4j.org/apidocs/</link>
<link>http://commons.apache.org/proper/commons-beanutils/javadocs/v1.9.4/apidocs</link>
<link>http://commons.apache.org/proper/commons-collections/javadocs/api-4.4</link>
<link>http://commons.apache.org/proper/commons-io/javadocs/api-release</link>
<link>http://commons.apache.org/proper/commons-lang/javadocs/api-release</link>
<link>https://docs.spring.io/spring/docs/4.3.x/javadoc-api/</link>
<link>https://docs.spring.io/spring-integration/docs/4.3.x/api/</link>
<link>http://hc.apache.org/httpcomponents-client-4.5.x/httpclient/apidocs/</link>
<link>http://hc.apache.org/httpcomponents-core-ga/httpcore/apidocs/</link>
<link>https://eclipse.org/aspectj/doc/released/runtime-api/</link>
<link>https://eclipse.org/aspectj/doc/released/aspectj5rt-api/</link>
<link>http://ehcache.org/apidocs/2.6.9/</link>
<link>http://internal-bioinformatics.cruk.cam.ac.uk/docs/cruk-commons/apidocs</link>
<link>http://internal-bioinformatics.cruk.cam.ac.uk/docs/pipelinetools/apidocs</link>
<link>http://internal-bioinformatics.cruk.cam.ac.uk/docs/workflow-1.8/apidocs</link>
</links>
</configuration>
</plugin>
</plugins>
</reporting>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.cruk.workflow</groupId>
<artifactId>workflow-bom</artifactId>
<version>1.8.4</version>
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>org.cruk.workflow</groupId>
<artifactId>workflow-core</artifactId>
</dependency>
<dependency>
<groupId>org.cruk.workflow</groupId>
<artifactId>workflow-notifiers</artifactId>
</dependency>
<dependency>
<groupId>org.cruk.workflow</groupId>
<artifactId>workflow-cluster</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>com.io7m.xom</groupId>
<artifactId>xom</artifactId>
<version>1.2.10</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
<exclusion>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20171018</version>
</dependency>
</dependencies>
</project>