pom.xml 11.7 KB
Newer Older
1
<?xml version="1.0" encoding="UTF-8"?>
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
<!--

    Biopet is built on top of GATK Queue for building bioinformatic
    pipelines. It is mainly intended to support LUMC SHARK cluster which is running
    SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
    should also be able to execute Biopet tools and pipelines.

    Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center

    Contact us at: sasc@lumc.nl

    A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
    license; For commercial users or users who do not want to follow the AGPL
    license, please contact us to obtain a separate license.

-->
18 19 20 21 22
<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>

23 24 25 26
    <!--TODO: replace groupId -->
    <groupId>org.example.group</groupId>

    <!--TODO: replace artifactId -->
Peter van 't Hof's avatar
Peter van 't Hof committed
27
    <artifactId>ExternalExample</artifactId>
28 29

    <!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
Peter van 't Hof's avatar
Peter van 't Hof committed
30
    <version>0.9.0</version>
31 32 33 34 35

    <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>
36

Peter van 't Hof's avatar
Peter van 't Hof committed
37 38 39 40 41 42 43 44 45
        <!--
        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>
46 47 48
    </properties>

    <dependencies>
49 50 51 52 53 54 55
        <!--
        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>
56
            <artifactId>BiopetCore</artifactId>
57 58

            <!--TODO: replace version of pipeline to a fixed version -->
59
            <version>0.10.0-SNAPSHOT</version>
60
        </dependency>
Peter van 't Hof's avatar
Peter van 't Hof committed
61 62 63
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>BiopetExtensions</artifactId>
64
            <version>0.10.0-SNAPSHOT</version>
Peter van 't Hof's avatar
Peter van 't Hof committed
65
        </dependency>
66 67 68
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Shiva</artifactId>
69 70

            <!--TODO: replace version of pipeline to a fixed version -->
71
            <version>0.10.0-SNAPSHOT</version>
72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
        </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 -->
Peter van 't Hof's avatar
Peter van 't Hof committed
101
                    <finalName>${project.artifactId}-${project.version}-${git.commit.id.abbrev}</finalName>
102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                            <manifestEntries>
                                <Main-Class>${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>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>
Peter van 't Hof's avatar
Peter van 't Hof committed
216 217
                    <!-- TODO: This directory need to be changed depening where your .git folder is relative from this pom.xml -->
                    <dotGitDirectory>${basedir}/../.git</dotGitDirectory>
218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274
                    <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>