libs="/home/sark/ximmer/eval/pipeline/tools/groovy-ngs-utils/1.0.9/groovy-ngs-utils.jar"
R {
    executable="Rscript"
}

groovy {
    executable="./tools/groovy/2.4.6/bin/groovy"
}



install {
    title = "Ximmer"
    tools {
        bwa = "0.9.7"
        xhmm = "1.0"
        ExomeDepth = "0.2.2"
        conifer = "0.2.2"
        'cn.mops' {
            version="0.3.4"
        }
        CODEX = "0.0"
        pandas = '0.18.0'
        pysam = '0.14.1'
        VariantAnnotation = '*'
        matplotlib='*'
        seaborn='*'
    }
}

commands {
    plot_cnv_coverage {
        // Enable to use multiple procs for plotting CNVs
        procs=1
    }

    exome_depth {
        // walltime="24:00:00"
        // queue="long"
    }


    cnmops {
    }
}