pom.xml

<?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>

    <groupId>no.uib</groupId>
    <artifactId>White-tailed</artifactId>
    <version>1.0.0</version>
    <packaging>jar</packaging>

    <name>White-tailed</name>

    <organization>
        <name>The European Bioinformatics Institute</name>
        <url>http://www.ebi.ac.uk/</url>
    </organization>

    <developers>
        <developer>
            <id>luis.sanchez</id>
            <name>Luis Francisco Hernández Sánchez</name>
            <email></email>
            <organization>http://www.uib.no/</organization>
        </developer>
    </developers>

    <properties>
        <jdk.version>1.8</jdk.version>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

        <reactome.graph.core>1.0.8</reactome.graph.core>
        <jasp.version>2.1</jasp.version>

        <maven.compiler.version>3.5.1</maven.compiler.version>
        <maven.jar.version>2.6</maven.jar.version>
        <jdk.version>1.8</jdk.version>
        <junit.version>4.12</junit.version>
    </properties>

    <dependencies>

        <!-- The neo4j driver -->
        <dependency>
            <groupId>org.neo4j.driver</groupId>
            <artifactId>neo4j-java-driver</artifactId>
            <version>1.2.3</version>
        </dependency>

        <!--JSAP console reader-->
        <dependency>
            <groupId>com.martiansoftware</groupId>
            <artifactId>jsap</artifactId>
            <version>${jasp.version}</version>
        </dependency>

        <!-- JUnit -->
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>${junit.version}</version>
            <scope>test</scope>
        </dependency>

        <!-- The CompOmics utilities package -->
        <dependency>
            <groupId>com.compomics</groupId>
            <artifactId>utilities</artifactId>
            <version>4.8.9</version>
            <exclusions>
                <exclusion>
                    <artifactId>commons-math</artifactId>
                    <groupId>commons-math</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>servlet-api</artifactId>
                    <groupId>javax.servlet</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>ssj</artifactId>
                    <groupId>umontreal.iro.lecuyer.gof</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>msv</artifactId>
                    <groupId>msv</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>relaxngDatatype</artifactId>
                    <groupId>msv</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>xsdlib</artifactId>
                    <groupId>msv</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>isorelax</artifactId>
                    <groupId>msv</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>xxindex</artifactId>
                    <groupId>psidev.psi.tools</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>ols-dialog</artifactId>
                    <groupId>no.uib</groupId>
                </exclusion>
            </exclusions>
        </dependency>


    </dependencies>

    <build>
        <finalName>White-tailed</finalName>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
            </resource>
        </resources>
        <testResources>
            <testResource>
                <directory>src/test/resources</directory>
                <filtering>true</filtering>
            </testResource>
        </testResources>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-resources-plugin</artifactId>
                <version>3.0.1</version>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>${maven.compiler.version}</version>
                <configuration>
                    <source>${jdk.version}</source>
                    <target>${jdk.version}</target>
                </configuration>
            </plugin>

            <!-- Generate the jar only -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>${maven.jar.version}</version>
                <configuration>
                    <excludes>
                        <exclude>**/logback.xml</exclude>
                    </excludes>
                </configuration>
            </plugin>

            <!-- Generate jar with dependencies -->
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.6</version>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>no.uib.PeptideToProteinMapper</mainClass>
                        </manifest>
                    </archive>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <repositories>

        <!-- Compomics Genesis Maven 2 repository -->
        <repository>
            <id>genesis-maven2-repository</id>
            <name>Genesis maven2 repository</name>
            <url>http://genesis.UGent.be/maven2</url>
            <layout>default</layout>
        </repository>

        <!-- old EBI repository -->
        <repository>
            <id>ebi-repo</id>
            <name>The EBI internal repository</name>
            <url>http://www.ebi.ac.uk/~maven/m2repo</url>
        </repository>

        <!-- EBI repository -->
        <repository>
            <id>pst-release</id>
            <name>EBI Nexus Repository</name>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
        </repository>
    </repositories>

    <!--Configures the distribution to nexus repository. mvn:deploy -->
    <distributionManagement>
        <!-- EBI repo -->
        <repository>
            <id>pst-release</id>
            <name>EBI Nexus Repository</name>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
        </repository>
        <!-- EBI SNAPSHOT repo -->
        <snapshotRepository>
            <uniqueVersion>false</uniqueVersion>
            <id>pst-snapshots</id>
            <name>EBI Nexus Snapshots Repository</name>
            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
        </snapshotRepository>
    </distributionManagement>

</project>