build.gradle

plugins {
    id 'java'
    id 'application'
}

repositories {
    mavenCentral()
    maven {
        // url for javaml:0.1.7
        url "https://bio.informatik.uni-jena.de/repository/libs-release-oss/"
    }
}

dependencies {
    implementation 'org.apache.commons:commons-math3:3.6.1'
    implementation 'net.sourceforge:javaml:0.1.7'
    implementation 'com.github.samtools:htsjdk:3.0.0'
    implementation 'colt:colt:1.2.0'
}

group = 'HMMRATAC'
version = '2.0.0'
description = """Hidden Markov Model for ATAC-seq"""

application {
    mainClass.set('HMMR_ATAC.Main_HMMR_Driver')
}

jar {
    manifest {
        attributes 'Main-Class': 'HMMR_ATAC.Main_HMMR_Driver'
    }
    doFirst {
        from { configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) } }
    }
    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA','META-INF/*.txt'
}