Python biobox_file_volume_stringの例

コード例 #1

ファイル: short_read_assembler.py プロジェクト: apurvaraman/command-line-interface

    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

コード例 #2

    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

コード例 #3

ファイル: assembler_benchmark.py プロジェクト: pbelmann/command-line-interface

    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

コード例 #4

    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

コード例 #5

def test_create_output_volume_string():
    expected = "/tmp:/bbx/input:ro"
    nose.assert_equal(ctn.biobox_file_volume_string("/tmp"), expected)

コード例 #6

ファイル: test_container.py プロジェクト: apurvaraman/command-line-interface

def test_create_output_volume_string():
    expected = "/tmp:/bbx/input:ro"
    nose.assert_equal(ctn.biobox_file_volume_string("/tmp"), expected)