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)