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)
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)
