build.gradle

group 'PL4'
version '2.0.0'

apply plugin: 'java'
apply plugin: 'jacoco'
apply plugin: 'checkstyle'
apply plugin: 'pmd'
apply plugin: 'findbugs'

jacoco {
    toolVersion = "0.8.0"
}

sourceCompatibility = 1.8

repositories {
    mavenCentral()
}

tasks.withType(FindBugs) {
    reports {
        xml.enabled = false
        html.enabled = true
    }
}

task fatJar(type: Jar, overwrite: true) {
    manifest {
        attributes 'Implementation-Title': 'Programming Life Consensus Jar',
                'Implementation-Version': version,
                'Main-Class': 'cli.Cli'
    }
    baseName = project.name
    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
    with jar
}

dependencies {
    testCompile group: 'junit', name: 'junit', version: '4.12',
            "org.mockito:mockito-core:2.+",
            "org.assertj:assertj-core:3.+"
    testCompile 'pl.pragmatists:JUnitParams:1.1.1'
    testCompileOnly 'com.google.code.findbugs:annotations:3.0.1'
    testCompileOnly 'com.google.code.findbugs:jsr305:3.0.1'
    compileOnly "org.projectlombok:lombok:1.16.16"
    compileOnly 'com.google.code.findbugs:annotations:3.0.1'
    compileOnly 'com.google.code.findbugs:jsr305:3.0.1'
    compile group: 'com.github.samtools', name: 'htsjdk', version: '2.1.1'
    compile group: 'commons-cli', name: 'commons-cli', version: '1.4'
    compile group: 'com.google.code.findbugs', name: 'annotations', version: '3.0.0'
}

sourceSets {
    test {
        java.srcDirs 'src/test/unit/java',
                'src/test/integration/java',
                'src/test/acceptance/java'
    }
}