build.gradle

/* Copyright (c) 2017 Marius Wöste
 *
 * This file is part of VIPER.
 *
 * VIPER is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * VIPER is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with VIPER.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

apply plugin: 'java'
apply plugin: 'idea'
idea{
    module{
        downloadJavadoc=true
    }
}
sourceCompatibility = '1.8'
[compileJava, compileTestJava]*.options*.encoding = 'UTF-8'

// NetBeans will automatically add "run" and "debug" tasks relying on the
// "mainClass" property. You may however define the property prior executing
// tasks by passing a "-PmainClass=<QUALIFIED_CLASS_NAME>" argument.
//
// Note however, that you may define your own "run" and "debug" task if you
// prefer. In this case NetBeans will not add these tasks but you may rely on
// your own implementation.
if (!hasProperty('mainClass')) {
    ext.mainClass = 'de.imi.marw.viper.main.Main'
}

def getVersionName() {
    return "git describe --tags".execute(null, new File(""+projectDir)).text.trim()
}

//create a single Jar with all dependencies
task fatJar(type: Jar) {
    manifest {
        attributes 'Implementation-Title': 'Main',
            'Implementation-Version': getVersionName(),
            'Main-Class': 'de.imi.marw.viper.main.Main'
    }
    baseName = project.name + '-all'
    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
    with jar
}

repositories {
    mavenCentral()
    // You may define additional repositories, or even remove "mavenCentral()".
    // Read more about repositories here:
    //   http://www.gradle.org/docs/current/userguide/dependency_management.html#sec:repositories

}

dependencies {
    compile "com.sparkjava:spark-core:2.6.0"
    compile group: 'org.apache.commons', name: 'commons-csv', version: '1.4'
    compile group: 'org.apache.poi', name: 'poi', version: '3.16'
    compile group: 'org.apache.poi', name: 'poi-ooxml', version: '3.16'
    compile group: 'com.google.code.gson', name: 'gson', version: '2.8.1'
    compile group: 'org.slf4j', name: 'slf4j-simple', version: '1.7.25'
    compile group: 'org.slf4j', name: 'slf4j-api', version: '1.7.25'
    compile group: 'com.github.samtools', name: 'htsjdk', version: '2.11.0'
    testCompile group: 'junit', name: 'junit', version: '4.12'
    testCompile group: 'com.mashape.unirest', name: 'unirest-java', version: '1.4.9'
}