How to use the genomepy.utils.cmd_ok function in genomepy

def test_hisat2(genome, force):
    """Create hisat2 index."""
    assert os.path.exists(genome.filename)

    force = True if force == "overwrite" else False
    if cmd_ok("hisat2-build"):
        p = Hisat2Plugin()
        p.after_genome_download(genome)
        dirname = os.path.dirname(genome.filename)
        index_dir = os.path.join(dirname, "index", "hisat2")
        fname = os.path.join(index_dir, "{}.1.ht2".format(genome.name))
        assert os.path.exists(index_dir)
        assert os.path.exists(fname)

        force_test(p, fname, genome, force)

def test_gmap(genome, force):
    """Create gmap index."""
    assert os.path.exists(genome.filename)

    force = True if force == "overwrite" else False
    if cmd_ok("gmap"):
        p = GmapPlugin()
        p.after_genome_download(genome, force=force)
        dirname = os.path.dirname(genome.filename)
        index_dir = os.path.join(dirname, "index", "gmap")
        fname = os.path.join(index_dir, "{}.maps".format(genome.name))
        assert os.path.exists(index_dir)
        assert os.path.exists(fname)

        force_test(p, fname, genome, force)

def test_bowtie2(genome, force):
    """Create bbowtie2 index."""
    assert os.path.exists(genome.filename)

    force = True if force == "overwrite" else False
    if cmd_ok("bowtie2"):
        p = Bowtie2Plugin()
        p.after_genome_download(genome, force=force)
        dirname = os.path.dirname(genome.filename)
        index_dir = os.path.join(dirname, "index", "bowtie2")
        fname = os.path.join(index_dir, "{}.1.bt2".format(genome.name))
        assert os.path.exists(index_dir)
        assert os.path.exists(fname)

        force_test(p, fname, genome, force)

def test_bwa(genome, force):
    """Create bwa index."""
    assert os.path.exists(genome.filename)

    force = True if force == "overwrite" else False
    if cmd_ok("bwa"):
        p = BwaPlugin()
        p.after_genome_download(genome, force=force)
        dirname = os.path.dirname(genome.filename)
        index_dir = os.path.join(dirname, "index", "bwa")
        fname = os.path.join(index_dir, "{}.fa.sa".format(genome.name))
        assert os.path.exists(index_dir)
        assert os.path.exists(fname)

        force_test(p, fname, genome, force)

def test_minimap2(genome, force):
    """Create minimap2 index."""
    assert os.path.exists(genome.filename)

    force = True if force == "overwrite" else False
    if cmd_ok("minimap2"):
        p = Minimap2Plugin()
        p.after_genome_download(genome, force=force)
        dirname = os.path.dirname(genome.filename)
        index_dir = os.path.join(dirname, "index", "minimap2")
        fname = os.path.join(index_dir, "{}.mmi".format(genome.name))
        assert os.path.exists(index_dir)
        assert os.path.exists(fname)

        force_test(p, fname, genome, force)

def after_genome_download(self, genome, threads=1, force=False):
        if not cmd_ok("bowtie2-build"):
            return

        # Create index dir
        index_dir = genome.props["bowtie2"]["index_dir"]
        index_name = genome.props["bowtie2"]["index_name"]
        if force:
            # Start from scratch
            rmtree(index_dir, ignore_errors=True)
        mkdir_p(index_dir)

        if not any(fname.endswith(".bt2") for fname in os.listdir(index_dir)):
            # Create index
            cmd = "bowtie2-build --threads {} {} {}".format(
                threads, genome.filename, index_name
            )
            run_index_cmd("bowtie2", cmd)

def after_genome_download(self, genome, threads=1, force=False):
        if not cmd_ok("hisat2-build"):
            return

        # Create index dir
        index_dir = genome.props["hisat2"]["index_dir"]
        index_name = genome.props["hisat2"]["index_name"]
        if force:
            # Start from scratch
            rmtree(index_dir, ignore_errors=True)
        mkdir_p(index_dir)

        if not any(fname.endswith(".ht2") for fname in os.listdir(index_dir)):
            # unzip genome if zipped and return up-to-date genome name
            bgzip, fname = bgunzip_and_name(genome)

            # Create index
            cmd = "hisat2-build -p {} {} {}".format(threads, fname, index_name)

def after_genome_download(self, genome, threads=1, force=False):
        if not cmd_ok("bwa"):
            return

        # Create index dir
        index_dir = genome.props["bwa"]["index_dir"]
        index_name = genome.props["bwa"]["index_name"]
        if force:
            # Start from scratch
            rmtree(index_dir, ignore_errors=True)
        mkdir_p(index_dir)

        if not any(fname.endswith(".bwt") for fname in os.listdir(index_dir)):
            # Create index
            if not os.path.exists(index_name):
                os.symlink(genome.filename, index_name)

            cmd = "bwa index {}".format(index_name)

def after_genome_download(self, genome, threads=1, force=False):
        if not cmd_ok("STAR"):
            return

        # Create index dir
        index_dir = genome.props["star"]["index_dir"]
        index_name = genome.props["star"]["index_name"]
        if force:
            # Start from scratch
            rmtree(index_dir, ignore_errors=True)
        mkdir_p(index_dir)

        if not os.path.exists(index_name):
            # unzip genome if zipped and return up-to-date genome name
            bgzip, fname = bgunzip_and_name(genome)

            # Create index
            cmd = "STAR --runMode genomeGenerate --runThreadN {} --genomeFastaFiles {} --genomeDir {} --outFileNamePrefix {}".format(

def after_genome_download(self, genome, threads=1, force=False):
        if not cmd_ok("gmap_build"):
            return

        # Create index dir
        index_dir = genome.props["gmap"]["index_dir"]
        if force:
            # Start from scratch
            rmtree(index_dir, ignore_errors=True)

        if not os.path.exists(index_dir):
            # unzip genome if zipped and return up-to-date genome name
            bgzip, fname = bgunzip_and_name(genome)

            # gmap outputs a folder named genome.name
            # its content is moved to index dir, consistent with other plugins
            with TemporaryDirectory() as tmpdir:
                # Create index