build.gradle

apply plugin: 'groovy'
apply plugin: 'application'

sourceCompatibility = 8
targetCompatibility = 8

group = 'com.antigenomics'
version = '1.2.1'

mainClassName = 'com.antigenomics.vdjtools.VdjTools'

repositories {
    mavenCentral()
    maven { url 'https://jitpack.io' }
    flatDir { dirs '/usr/share/java' }
}

jar {
    baseName = 'vdjtools'
    version = "$version"

    manifest {
        attributes("Main-Class": "$mainClassName", "Implementation-Version": version)
    }

    from {
        configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
    }
}

sourceSets {
    main {
        java { srcDirs = [] }    // no source dirs for the java compiler
        groovy { srcDirs = ["src/main/java", "src/main/groovy"] }  // compile   everything in src/ with groovy
    }
    test {
        java { srcDirs = [] }    // no source dirs for the java compiler
        groovy { srcDirs = ["src/test/java", "src/test/groovy"] }  // compile   everything in src/ with groovy
    }
}

dependencies {
    compile 'org.codehaus.groovy:groovy-all:2.5.2'
    compile 'org.codehaus.gpars:gpars:1.2.1'
    compile 'junit:junit:4.12'
    compile 'com.milaboratory:milib:1.8.3'
    compile 'commons-io:commons-io:1.2'
    compile 'org.apache.commons:commons-lang3:3.4'
}