def run(argv):
    opts = util.parse_docopt(__doc__, argv, False)
    image       = opts['<image>']
    fastq_file  = opts['--input']
    contig_file = opts['--output']
    task        = opts['--task']

    if not ctn.image_available(image):
        util.err_exit('unknown_image', {'image': image})

    cntr_src_dir = "/fastq"
    biobox_yaml = fle.generate([
        fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])])

    host_src_dir = os.path.abspath(os.path.dirname(fastq_file))
    host_dst_dir = tmp.mkdtemp()

    mount_strings = [
        ctn.mount_string(host_src_dir, cntr_src_dir),
        ctn.biobox_file_mount_string(fle.create_biobox_directory(biobox_yaml)),
        ctn.output_directory_mount_string(host_dst_dir)]

    ctn.run(ctn.create(image, task, mount_strings))
    biobox_output = fle.parse(host_dst_dir)
    copy_contigs_file(host_dst_dir, biobox_output, contig_file)
Exemple #2
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def run(argv):
    opts = util.parse_docopt(__doc__, argv, False)
    image = opts['<image>']
    fastq_file = opts['--input']
    contig_file = opts['--output']
    task = opts['--task']

    if not ctn.image_available(image):
        util.err_exit('unknown_image', {'image': image})

    cntr_src_dir = "/fastq"
    biobox_yaml = fle.generate(
        [fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])])

    host_src_dir = os.path.abspath(os.path.dirname(fastq_file))
    host_dst_dir = tmp.mkdtemp()

    mount_strings = [
        ctn.mount_string(host_src_dir, cntr_src_dir),
        ctn.biobox_file_mount_string(fle.create_biobox_directory(biobox_yaml)),
        ctn.output_directory_mount_string(host_dst_dir)
    ]

    ctn.run(ctn.create(image, task, mount_strings))
    biobox_output = fle.parse(host_dst_dir)
    copy_contigs_file(host_dst_dir, biobox_output, contig_file)
def test_fastq_arguments_with_single_arg():
    fastq_values = [("/fastq/input.fq", "paired")]
    expected = {
        "fastq": [{
            "id": "fastq_0",
            "type": "paired",
            "value": "/fastq/input.fq"
        }]
    }
    nt.assert_equal(bbf.fastq_arguments(fastq_values), expected)
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def test_fastq_arguments_with_single_arg():
    args = ["file_path", "paired"]
    expected = {
        "fastq": [{
            "id": "fastq_0",
            "type": "paired",
            "value": "/mount/file_path"
        }]
    }
    nt.assert_equal(bbf.fastq_arguments("/mount", args), expected)
    def prepare_volumes(self, opts, host_dst_dir):
        fastq_file  = opts['--input']

        cntr_fastq_file = "/fastq/input.fq.gz"
        fastq_values = [(cntr_fastq_file, "paired")]
        yaml_data = [fle.fastq_arguments(fastq_values)]
        biobox_yaml = fle.generate(yaml_data)

        host_src_dir = os.path.abspath(fastq_file)

        volumes = [
            ctn.volume_string(host_src_dir, cntr_fastq_file),
            ctn.biobox_file_volume_string(fle.create_biobox_directory(biobox_yaml)),
            ctn.output_directory_volume_string(host_dst_dir)]
        return volumes
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    def prepare_volumes(self, opts, host_dst_dir):
        fastq_file = opts['--input']

        cntr_fastq_file = "/fastq/input.fq.gz"
        fastq_values = [(cntr_fastq_file, "paired")]
        yaml_data = [fle.fastq_arguments(fastq_values)]
        biobox_yaml = fle.generate(yaml_data)

        host_src_dir = os.path.abspath(fastq_file)

        volumes = [
            ctn.volume_string(host_src_dir, cntr_fastq_file),
            ctn.biobox_file_volume_string(
                fle.create_biobox_directory(biobox_yaml)),
            ctn.output_directory_volume_string(host_dst_dir)
        ]
        return volumes
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def test_fastq_arguments_with_single_arg():
    args = ["file_path", "paired"]
    expected = {"fastq" :
      [{"id" : "fastq_0", "type": "paired", "value" : "/mount/file_path"}]}
    nt.assert_equal(bbf.fastq_arguments("/mount", args), expected)
def test_fastq_arguments_with_single_arg():
    fastq_values = [("/fastq/input.fq", "paired")]
    expected = {"fastq" :
      [{"id" : "fastq_0", "type": "paired", "value" : "/fastq/input.fq"}]}
    nt.assert_equal(bbf.fastq_arguments(fastq_values), expected)