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 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
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
def prepare_volumes(self, opts, host_dst_dir):
fasta_file = opts["--input-fasta"]
ref_dir = opts["--input-ref"]
host_src_fasta_file = os.path.abspath(fasta_file)
host_src_ref_dir = os.path.abspath(ref_dir)
cntr_src_fasta = "/fasta/input.fa"
fasta_values = [(cntr_src_fasta, "contig")]
fasta_yaml_values = fle.fasta_arguments(fasta_values)
cntr_src_ref_dir = "/ref"
ref_dir_yaml_values = fle.reference_argument(ref_dir)
biobox_yaml = fle.generate([fasta_yaml_values, ref_dir_yaml_values])
volume_strings = [
ctn.volume_string(host_src_fasta_file, cntr_src_fasta),
ctn.volume_string(host_src_ref_dir, cntr_src_ref_dir),
ctn.biobox_file_volume_string(fle.create_biobox_directory(biobox_yaml)),
ctn.output_directory_volume_string(host_dst_dir),
]
return volume_strings
def prepare_volumes(self, opts, host_dst_dir):
fasta_file = opts['--input-fasta']
ref_dir = opts['--input-ref']
host_src_fasta_file = os.path.abspath(fasta_file)
host_src_ref_dir = os.path.abspath(ref_dir)
cntr_src_fasta = "/fasta/input.fa"
fasta_values = [(cntr_src_fasta, "contig")]
fasta_yaml_values = fle.fasta_arguments(fasta_values)
cntr_src_ref_dir = "/ref"
ref_dir_yaml_values = fle.reference_argument(ref_dir)
biobox_yaml = fle.generate([fasta_yaml_values, ref_dir_yaml_values])
volume_strings = [
ctn.volume_string(host_src_fasta_file, cntr_src_fasta),
ctn.volume_string(host_src_ref_dir, cntr_src_ref_dir),
ctn.biobox_file_volume_string(
fle.create_biobox_directory(biobox_yaml)),
ctn.output_directory_volume_string(host_dst_dir)
]
return volume_strings
