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 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 run(argv): opts = util.parse_docopt(__doc__, argv, False) biobox = opts['<biobox_type>'] image = opts['<image>'] task = opts['--task'] from behave.__main__ import main as behave_main _, tmp_file = tempfile.mkstemp() cmd = "{file} --define IMAGE={image} --define TASK={task} --define TMPDIR={tmp_dir} --outfile {tmp_file} --no-summary --stop" args = {'file': verification_file(biobox), 'tmp_dir': tmp_feature_dir(), 'image': image, 'tmp_file': tmp_file, 'task': task} behave_main(cmd.format(**args)) with open(tmp_file, 'r') as f: output = f.read() if "Assertion Failed" in output: util.err_exit('failed_verification', {'image': image, 'biobox': biobox.replace('_', ' ')})
def run(argv): opts = util.parse_docopt(__doc__, argv, True) util.select_module("biobox_type", opts["<biobox_type>"]).run(argv)
def run(): args = input_args() opts = util.parse_docopt(__doc__, args, True) util.select_module("command", opts["<command>"]).run(args)