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
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 test_create_volume_string_with_absolute_dir():
expected = "/tmp:/tmp:ro"
nose.assert_equal(ctn.volume_string("/tmp", "/tmp"), expected)
def test_create_volume_string_with_relative_dir():
expected = "{}/tmp:/tmp:ro".format(hlpr.project_root())
nose.assert_equal(ctn.volume_string("tmp", "/tmp"), expected)
def create_login_volume(dir_name, files):
src = util.mkdir_p(os.path.join(TEMPORARY_DIRECTORY, dir_name.strip("/")))
for f in files:
create_login_file(src, f)
return docker.volume_string(src, dir_name, False)
def test_create_volume_string_with_absolute_dir():
expected = "/tmp:/tmp:ro"
nose.assert_equal(ctn.volume_string("/tmp", "/tmp"), expected)
def test_create_volume_string_with_relative_dir():
expected = "{}/tmp:/tmp:ro".format(hlpr.project_root())
nose.assert_equal(ctn.volume_string("tmp", "/tmp"), expected)
