pom.xml 13.2 KB
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<?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/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

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    <!--TODO: replace groupId -->
    <groupId>org.example.group</groupId>

    <!--TODO: replace artifactId -->
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    <artifactId>ExternalExample</artifactId>
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    <!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
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    <version>0.6.0-SNAPSHOT</version>
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    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <scoverage.plugin.version>1.0.4</scoverage.plugin.version>
        <sting.shade.phase>package</sting.shade.phase>
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        <!--
        TODO: replace app.main.class, this is the class that get executed when running the jar file
        This can be any executable that have a main method. In Biopet any pipeline can be used as direct executable.
        Value for direct pipeline: 'org.example.group.pipelines.SimplePipeline'
        In the given example is an extension of the biopet executable. In this example there are multiple pipelines in 1 executable.

        It's also possible to make your own main function and call the main function with it's argument of the pipeline from there.
        -->
        <app.main.class>org.example.group.ExecutableExample</app.main.class>
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    </properties>

    <dependencies>
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        <!--
        In here maven dependencies can be placed, when importing a biopet pipeline 'Biopet-Framework' is not required.
        When only using the framework without pipeline you need to import BiopetFramework.
        It's advised to not use different versions of the pipeline and the framework.
         -->
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
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            <artifactId>BiopetCore</artifactId>
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            <!--TODO: replace version of pipeline to a fixed version -->
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            <version>0.6.0-SNAPSHOT</version>
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        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>BiopetExtensions</artifactId>
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            <version>0.6.0-SNAPSHOT</version>
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        </dependency>
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        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Shiva</artifactId>
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            <!--TODO: replace version of pipeline to a fixed version -->
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            <version>0.6.0-SNAPSHOT</version>
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        </dependency>
    </dependencies>

    <build>
        <sourceDirectory>${basedir}/src/main/scala</sourceDirectory>
        <testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory>
        <testResources>
            <testResource>
                <directory>${basedir}/src/test/resources</directory>
                <includes>
                    <include>**/*</include>
                </includes>
            </testResource>
        </testResources>
        <resources>
            <resource>
                <directory>${basedir}/src/main/resources</directory>
                <includes>
                    <include>**/*</include>
                </includes>
            </resource>
        </resources>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>2.4.1</version>
                <configuration>
                    <!--suppress MavenModelInspection -->
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                    <finalName>${project.artifactId}-${project.version}-${git.commit.id.abbrev}</finalName>
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                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                            <manifestEntries>
                                <Main-Class>${app.main.class}</Main-Class>
                                <!--suppress MavenModelInspection -->
                                <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
                                <!--suppress MavenModelInspection -->
                                <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
                            </manifestEntries>
                        </transformer>
                    </transformers>
                    <filters>
                    </filters>
                </configuration>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.18.1</version>
                <configuration>
                    <forkCount>1C</forkCount>
                    <workingDirectory>${project.build.directory}</workingDirectory>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>2.10</version>
                <executions>
                    <execution>
                        <id>copy-installed</id>
                        <phase>prepare-package</phase>
                        <goals>
                            <goal>list</goal>
                        </goals>
                        <configuration>
                            <outputFile>${project.build.outputDirectory}/dependency_list.txt</outputFile>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>net.alchim31.maven</groupId>
                <artifactId>scala-maven-plugin</artifactId>
                <version>3.2.0</version>
                <executions>
                    <execution>
                        <id>scala-compile</id>
                        <goals>
                            <goal>compile</goal>
                            <goal>testCompile</goal>
                        </goals>
                        <configuration>
                            <args>
                                <arg>-dependencyfile</arg>
                                <arg>${project.build.directory}/.scala_dependencies</arg>
                                <arg>-deprecation</arg>
                                <arg>-feature</arg>
                            </args>
                        </configuration>
                    </execution>
                </executions>
                <!-- ... (see other usage or goals for details) ... -->
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>2.5</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>test-jar</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <archive>
                        <manifest>
                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
                        </manifest>
                    </archive>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.3.2</version>
                <configuration>
                    <showDeprecation>true</showDeprecation>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.scalariform</groupId>
                <artifactId>scalariform-maven-plugin</artifactId>
                <version>0.1.4</version>
                <executions>
                    <execution>
                        <phase>process-sources</phase>
                        <goals>
                            <goal>format</goal>
                        </goals>
                        <configuration>
                            <rewriteArrowSymbols>false</rewriteArrowSymbols>
                            <alignParameters>true</alignParameters>
                            <alignSingleLineCaseStatements_maxArrowIndent>40
                            </alignSingleLineCaseStatements_maxArrowIndent>
                            <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
                            <compactStringConcatenation>false</compactStringConcatenation>
                            <compactControlReadability>false</compactControlReadability>
                            <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
                            <formatXml>true</formatXml>
                            <indentLocalDefs>false</indentLocalDefs>
                            <indentPackageBlocks>true</indentPackageBlocks>
                            <indentSpaces>2</indentSpaces>
                            <placeScaladocAsterisksBeneathSecondAsterisk>false
                            </placeScaladocAsterisksBeneathSecondAsterisk>
                            <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
                            <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
                            <rewriteArrowSymbols>false</rewriteArrowSymbols>
                            <spaceBeforeColon>false</spaceBeforeColon>
                            <spaceInsideBrackets>false</spaceInsideBrackets>
                            <spaceInsideParentheses>false</spaceInsideParentheses>
                            <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>pl.project13.maven</groupId>
                <artifactId>git-commit-id-plugin</artifactId>
                <version>2.1.10</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>revision</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <prefix>git</prefix>
                    <dateFormat>dd.MM.yyyy '@' HH:mm:ss z</dateFormat>
                    <verbose>false</verbose>
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                    <!-- TODO: This directory need to be changed depening where your .git folder is relative from this pom.xml -->
                    <dotGitDirectory>${basedir}/../.git</dotGitDirectory>
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                    <useNativeGit>true</useNativeGit>
                    <skipPoms>false</skipPoms>
                    <generateGitPropertiesFile>true</generateGitPropertiesFile>
                    <generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
                    <failOnNoGitDirectory>false</failOnNoGitDirectory>
                    <abbrevLength>8</abbrevLength>
                    <skip>false</skip>
                    <gitDescribe>
                        <skip>false</skip>
                        <always>false</always>
                        <abbrev>8</abbrev>
                        <dirty>-dirty</dirty>
                        <forceLongFormat>false</forceLongFormat>
                    </gitDescribe>
                </configuration>
            </plugin>
            <plugin>
                <groupId>com.mycila</groupId>
                <artifactId>license-maven-plugin</artifactId>
                <version>2.6</version>
                <configuration>
                    <excludes>
                        <exclude>**/*git*</exclude>
                        <exclude>**/License*</exclude>
                        <exclude>**/*.bam</exclude>
                        <exclude>**/*.bai</exclude>
                        <exclude>**/*.gtf</exclude>
                        <exclude>**/*.fq</exclude>
                        <exclude>**/*.sam</exclude>
                        <exclude>**/*.bed</exclude>
                        <exclude>**/*.refFlat</exclude>
                        <exclude>**/*.R</exclude>
                        <exclude>**/*.rscript</exclude>
                    </excludes>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.scoverage</groupId>
                <artifactId>scoverage-maven-plugin</artifactId>
                <version>${scoverage.plugin.version}</version>
                <configuration>
                    <scalaVersion>2.10.2</scalaVersion>
                    <!-- other parameters -->
                </configuration>
            </plugin>
        </plugins>
    </build>
    <reporting>
        <plugins>
            <plugin>
                <groupId>org.scoverage</groupId>
                <artifactId>scoverage-maven-plugin</artifactId>
                <version>${scoverage.plugin.version}</version>
            </plugin>
        </plugins>
    </reporting>
</project>