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(self, argv):
doc = inspect.getdoc(inspect.getmodule(self))
opts = util.parse_docopt(doc, argv, False)
task = opts['--task']
image = opts['<image>']
output = opts['--output']
host_dst_dir = tmp.mkdtemp()
volumes = self.prepare_volumes(opts, host_dst_dir)
ctn.exit_if_no_image_available(image)
ctnr = ctn.create(image, task, volumes)
ctn.run(ctnr)
self.after_run(output, host_dst_dir)
return ctnr
def run(self, argv):
doc = inspect.getdoc(inspect.getmodule(self))
opts = util.parse_docopt(doc, argv, False)
task = opts['--task']
image = opts['<image>']
output = opts['--output']
host_dst_dir = tmp.mkdtemp()
volumes = self.prepare_volumes(opts, host_dst_dir)
ctn.exit_if_no_image_available(image)
ctnr = ctn.create(image, task, volumes)
ctn.run(ctnr)
self.after_run(output, host_dst_dir)
return ctnr
def run(self, argv):
doc = inspect.getdoc(inspect.getmodule(self))
opts = util.parse_docopt(doc, argv, False)
task = opts['--task']
image = opts['<image>']
output = opts['--output']
# Check the image exists
ctn.exit_if_no_image_available(image)
# Additional non-biobox args to pass to the docker daemon
docker_args = {'mem_limit': opts['--memory'],
'cpuset': opts['--cpuset'],
'cpu_shares': int_or_none(opts['--cpu-shares'])}
output_dir = tempfile.mkdtemp()
ctnr = biobox.create_container(image, self.prepare_config(opts), output_dir, task, docker_args)
ctn.run(ctnr)
self.after_run(output, output_dir)
return ctnr
