Description

<dependency>
    <groupId>org.opencb.cellbase</groupId>
    <artifactId>cellbase-build</artifactId>
    <version>3.0.0</version>
</dependency>

<?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>
    <parent>
        <groupId>org.opencb.cellbase</groupId>
        <artifactId>cellbase</artifactId>
        <version>3.0.0</version>
        <relativePath>..</relativePath>
    </parent>

    <artifactId>cellbase-build</artifactId>
    <version>${cellbase.version}</version>

    <properties>
        <installation.dir>installation-dir</installation.dir>
        <dest.installation.dir>/opt/cellbase</dest.installation.dir>
    </properties>

    <dependencies>
        <dependency>
            <groupId>org.opencb.cellbase</groupId>
            <artifactId>cellbase-core</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.cellbase</groupId>
            <artifactId>cellbase-mongodb</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.biodata</groupId>
            <artifactId>biodata-models</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.biodata</groupId>
            <artifactId>biodata-formats</artifactId>
        </dependency>
        <dependency>
            <groupId>org.opencb.datastore</groupId>
            <artifactId>datastore-mongodb</artifactId>
        </dependency>
        <dependency>
            <groupId>psidev.psi.mi</groupId>
            <artifactId>psimitab</artifactId>
            <version>1.8.4</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-simple</artifactId>
        </dependency>
        <!--<dependency>-->
        <!--<groupId>org.slf4j</groupId>-->
        <!--<artifactId>slf4j-log4j12</artifactId>-->
        <!--</dependency>-->
        <!--<dependency>-->
        <!--<groupId>log4j</groupId>-->
        <!--<artifactId>log4j</artifactId>-->
        <!--</dependency>-->
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-databind</artifactId>
        </dependency>
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
        </dependency>
        <dependency>
            <groupId>org.xerial</groupId>
            <artifactId>sqlite-jdbc</artifactId>
        </dependency>
        <dependency>
            <groupId>org.mongodb</groupId>
            <artifactId>mongo-java-driver</artifactId>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <sourceDirectory>src/main/java</sourceDirectory>
        <testSourceDirectory>src/test/java</testSourceDirectory>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.1</version>
                <configuration>
                    <source>${compileSource}</source>
                    <target>${compileSource}</target>
                    <showDeprecation>true</showDeprecation>
                    <showWarnings>true</showWarnings>
                    <encoding>UTF-8</encoding>
                    <excludes>
                        <exclude>**/DrugParser.java</exclude>
                    </excludes>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-resources-plugin</artifactId>
                <version>2.6</version>
                <configuration>
                    <encoding>UTF-8</encoding>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>org.opencb.cellbase.build.CellBaseMain</mainClass>
                            <addClasspath>true</addClasspath>
                        </manifest>
                    </archive>
                    <outputDirectory>${installation.dir}/libs</outputDirectory>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>2.8</version>
                <executions>
                    <execution>
                        <id>copy-dependencies</id>
                        <phase>install</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${installation.dir}/libs</outputDirectory>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-antrun-plugin</artifactId>
                <version>1.7</version>
                <executions>
                    <execution>
                        <phase>install</phase>
                        <configuration>
                            <target>
                                <echo>Copying to ${dest.installation.dir}</echo><!-- <copy todir="${installation.dir}">
									<fileset dir="installation" includes="**" /> </copy> -->
                                <exec executable="cp">
                                    <arg value="-r" />
                                    <arg value="${installation.dir}/example" />
                                    <arg value="${installation.dir}/libs" />
                                    <arg value="${installation.dir}/bin" />
                                    <arg value="${installation.dir}/mongodb-scripts" />
                                    <arg value="${installation.dir}/cellbase-build.sh" />
                                    <arg value="${installation.dir}/cellbase-installer.py" />
                                    <arg value="${dest.installation.dir}" />
                                </exec>
                            </target>
                        </configuration>
                        <goals>
                            <goal>run</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>appassembler-maven-plugin</artifactId>
                <version>1.5</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>assemble</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <repositoryName>libs</repositoryName>
                    <repositoryLayout>flat</repositoryLayout>
                    <useWildcardClassPath>true</useWildcardClassPath>
                    <programs>
                        <program>
                            <mainClass>org.opencb.cellbase.build.CellBaseMain</mainClass>
                            <name>cellbase-build.sh</name>
                        </program>
                    </programs>
                </configuration>
            </plugin>
        </plugins>
    </build>

    <repositories>
        <repository>
            <id>intact.nexus</id>
            <name>IntAct Nexus</name>
            <url>http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public</url>
        </repository>
    </repositories>

</project>