gtf: path to GTF file (must have gene_id and transcript_id)
    multifasta: path to multifasta file
    build: name of organism build (e.g. hg19)

def prepare_rsem_reference(gtf, multifasta, build):
    """
    gtf: path to GTF file (must have gene_id and transcript_id)
    multifasta: path to multifasta file
    build: name of organism build (e.g. hg19)
    """
    if not utils.which("rsem-prepare-reference"):
        logger.info("Skipping prepping RSEM reference because "
                    "rsem-prepare-reference could not be found.")
        return None

    command = PREPARE_REFERENCE.format(gtf=gtf, multifasta=multifasta,
                                       build=build)
    with transaction.tx_tmpdir(remove=False) as rsem_genome_dir:
        with utils.chdir(rsem_genome_dir):
            message = "Preparing rsem reference from %s" % gtf
            do.run(command, message)
    return rsem_genome_dir