Run a variant comparison using the bcbio.variation toolkit, given an input configuration.

def _bcbio_variation_ensemble(vrn_files, out_file, ref_file, config_file, base_dir, data):
    """Run a variant comparison using the bcbio.variation toolkit, given an input configuration.
    """
    vrn_files = [_handle_somatic_ensemble(v, data) for v in vrn_files]
    tmp_dir = utils.safe_makedir(os.path.join(base_dir, "tmp"))
    resources = config_utils.get_resources("bcbio_variation", data["config"])
    jvm_opts = resources.get("jvm_opts", ["-Xms750m", "-Xmx2g"])
    java_args = ["-Djava.io.tmpdir=%s" % tmp_dir]
    cmd = ["bcbio-variation"] + jvm_opts + java_args + \
          ["variant-ensemble", config_file, ref_file, out_file] + vrn_files
    with utils.chdir(base_dir):
        cmd = "%s %s" % (utils.local_path_export(), " ".join(str(x) for x in cmd))
        do.run(cmd, "Ensemble calling: %s" % os.path.basename(base_dir))