<?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">
    <parent>
        <groupId>org.campagnelab.goby</groupId>
        <artifactId>goby-framework</artifactId>
        <version>3.3.1</version>
    </parent>
    <modelVersion>4.0.0</modelVersion>

    <artifactId>goby-distribution</artifactId>
    <name>Goby Full Distribution</name>
    <url>http://goby.campagnelab.org</url>
    <properties>
        <nd4j.version>0.8.0</nd4j.version>
        <dl4j.version>0.8.0</dl4j.version>
    </properties>
    <build>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <includes>
                    <include>**</include>
                </includes>
            </resource>
            <resource>
                <directory>src/main/java</directory>
                <includes>
                    <include>**/*.jsap</include>
                </includes>
            </resource>
        </resources>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.5.1</version>
                <configuration>
                    <source>${java.version}</source>
                    <target>${java.version}</target>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <version>3.0.1</version>
                <executions>
                    <execution>
                        <id>attach-sources</id>
                        <phase>package</phase>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <version>2.10.4</version>
                <executions>
                    <execution>
                        <id>attach-javadocs</id>
                        <phase>package</phase>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                        <configuration>
                            <additionalparam>-Xdoclint:none</additionalparam>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.6</version>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>org.campagnelab.goby.modes.GobyDriver</mainClass>
                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                        </manifest>
                    </archive>
                    <descriptors>
                        <descriptor>assembly/assembly.xml</descriptor>
                    </descriptors>
                    <finalName>goby</finalName>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id> <!-- this is used for inheritance merges -->
                        <phase>package</phase> <!-- bind to the packaging phase -->
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-antrun-plugin</artifactId>
                <executions>
                    <execution>
                        <phase>install</phase>
                        <configuration>
                            <tasks>
                                <copy file="${project.build.directory}/goby-bin.jar"
                                      tofile="${project.basedir}/../goby.jar"/>
                            </tasks>
                        </configuration>
                        <goals>
                            <goal>run</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

        </plugins>
    </build>

    <dependencies>
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
            <version>r08</version>
        </dependency>
        <dependency>
            <groupId>it.unimi.dsi</groupId>
            <artifactId>fastutil</artifactId>
            <version>7.0.12</version>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
            <version>2.4</version>
        </dependency>
        <dependency>
            <groupId>commons-lang</groupId>
            <artifactId>commons-lang</artifactId>
            <version>2.6</version>
        </dependency>
        <dependency>
            <groupId>commons-logging</groupId>
            <artifactId>commons-logging</artifactId>
            <version>1.1.1</version>
        </dependency>
        <dependency>
            <groupId>com.thoughtworks.xstream</groupId>
            <artifactId>xstream</artifactId>
            <version>1.4.8</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
            <version>1.7.21</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>log4j-over-slf4j</artifactId>
            <version>1.7.21</version>
        </dependency>
        <dependency>
            <groupId>it.unimi.dsi</groupId>
            <artifactId>dsiutils</artifactId>
            <version>2.3.3</version>
            <exclusions>
                <exclusion>
                    <groupId>com.google.guava</groupId>
                    <artifactId>*</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math</artifactId>
            <version>2.2</version>
        </dependency>
        <dependency>
            <groupId>commons-configuration</groupId>
            <artifactId>commons-configuration</artifactId>
            <version>1.6</version>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-exec</artifactId>
            <version>1.0.1</version>
        </dependency>
        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
            <version>2.2.4</version>
        </dependency>
        <dependency>
            <groupId>org.rosuda.REngine</groupId>
            <artifactId>REngine</artifactId>
            <version>2.1.0</version>
        </dependency>
        <dependency>
            <groupId>com.github.lucarosellini.rJava</groupId>
            <artifactId>JRI</artifactId>
            <version>0.9-7</version>
        </dependency>
        <dependency>
            <groupId>org.reflections</groupId>
            <artifactId>reflections</artifactId>
            <version>0.9.10</version>
            <exclusions>
                <exclusion>
                    <groupId>org.slf4j</groupId>
                    <artifactId>*</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-classic</artifactId>
            <version>1.1.7</version>
        </dependency>
        <dependency>
            <groupId>ch.qos.logback</groupId>
            <artifactId>logback-core</artifactId>
            <version>1.1.7</version>
        </dependency>
        <dependency>
            <groupId>org.campagnelab.icb</groupId>
            <artifactId>icb-utils</artifactId>
            <version>2.0.1</version>
        </dependency>
        <dependency>
            <groupId>com.google.protobuf</groupId>
            <artifactId>protobuf-java</artifactId>
            <version>${protobuf.version}</version>
        </dependency>
        <dependency>
            <groupId>org.campagnelab.ext</groupId>
            <artifactId>jsap</artifactId>
            <version>3.0.0</version>
            </dependency>
        <dependency>
            <groupId>edu.rit.pj</groupId>
            <artifactId>pj</artifactId>
            <version>1.0</version>
            <scope>system</scope>
            <systemPath>${basedir}/../lib/pj20091226.jar</systemPath>
        </dependency>
        <dependency>
            <groupId>edu.mssm.crover</groupId>
            <artifactId>cli</artifactId>
            <version>1.0</version>
            <scope>system</scope>
            <systemPath>${basedir}/../lib/edu.mssm.crover.cli.jar</systemPath>
        </dependency>

        <dependency>
            <groupId>edu.cornell.med.icb</groupId>
            <artifactId>tisim-api</artifactId>
            <version>1.0</version>
            <scope>system</scope>
            <systemPath>${basedir}/../lib/tisim-api.jar</systemPath>
        </dependency>
        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>deeplearning4j-core</artifactId>
            <version>${dl4j.version}</version>
        </dependency>
        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>nd4j-native</artifactId>
            <version>${nd4j.version}</version>
            <classifier>macosx-x86_64</classifier>
        </dependency>
        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>nd4j-native</artifactId>
            <version>${nd4j.version}</version>
            <classifier>windows-x86_64</classifier>
        </dependency>
        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>nd4j-native</artifactId>
            <version>${nd4j.version}</version>
            <classifier>linux-x86_64</classifier>
        </dependency>

        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>nd4j-native-platform</artifactId>
            <version>${dl4j.version}</version>
        </dependency>
        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>nd4j-api</artifactId>
            <version>${nd4j.version}</version>
        </dependency>

        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>deeplearning4j-core</artifactId>
            <version>${dl4j.version}</version>
        </dependency>

        <dependency>
            <groupId>org.deeplearning4j</groupId>
            <artifactId>deeplearning4j-nlp</artifactId>
            <version>${dl4j.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>org.slf4j</groupId>
                    <artifactId>log4j-over-slf4j</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.nd4j</groupId>
            <artifactId>canova-nd4j-image</artifactId>
            <version>0.0.0.17</version>
        </dependency>

        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.12</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>junit-addons</groupId>
            <artifactId>junit-addons</artifactId>
            <version>1.4</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.easymock</groupId>
            <artifactId>easymock</artifactId>
            <version>3.4</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>com.github.broadinstitute</groupId>
            <artifactId>picard</artifactId>
            <version>2.6.0</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>it.unimi.dsi</groupId>
            <artifactId>dsiutils</artifactId>
            <version>2.3.3</version>
        </dependency>
        <dependency>
            <groupId>org.campagnelab.goby</groupId>
            <artifactId>goby-io</artifactId>
            <version>${project.version}</version>
        </dependency>
    </dependencies>
</project>
