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'] # 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