def demux_run_with_docker(run_id, input_run_data_path, fastq_output_dir, samplesheet_csv_path, nb_mismatch, conf):
""" Demultiplexing the run with bcl2fastq on version parameter with image Docker.
Arguments:
run_id: The run id
input_run_data_path: input run data path to demultiplexing
fastq_output_dir: fastq directory to save result on demultiplexing
samplesheet_csv_path: samplesheet path in csv format, version used by bcl2fastq
conf: configuration dictionary
"""
# In docker mount with input_run_data_path
input_docker = '/data/input'
input_run_data_path_in_docker = input_docker
run_id_msg = " for run " + run_id + ' on ' + common.get_instrument_name(run_id, conf)
# In docker mount with fastq_output_dir
output_docker = '/data/output'
fastq_data_path_in_docker = output_docker + '/' + os.path.basename(fastq_output_dir)
tmp = conf[TMP_PATH_KEY]
tmp_docker = '/tmp'
bcl2fastq_log_file = tmp + "/bcl2fastq_output_" + run_id + ".err"
samplesheet_csv_docker = tmp_docker + '/' + os.path.basename(samplesheet_csv_path)
cmd = create_bcl2fastq_command_line(run_id, None, input_run_data_path_in_docker, fastq_data_path_in_docker,
samplesheet_csv_docker, tmp_docker, nb_mismatch, conf)
try:
# Set working in docker on parent demultiplexing run directory.
# Demultiplexing run directory will create by bcl2fastq
docker = DockerCommand(conf[Settings.DOCKER_URI_KEY], ['/bin/bash', '-c', cmd], 'bcl2fastq2', common.BCL2FASTQ2_VERSION)
common.log("CONFIG", "Demultiplexing using docker image from " + docker.getImageDockerName() +
" with command line " + cmd, conf)
common.log("CONFIG", "Bcl2fastq docker mount: " +
str(os.path.dirname(fastq_output_dir)) + ":" + str(output_docker) + "; " +
input_run_data_path + ":" + input_docker + "; " + tmp + ":" + tmp_docker, conf)
# Mount input directory
docker.addMountDirectory(input_run_data_path, input_docker)
docker.addMountDirectory(os.path.dirname(fastq_output_dir), output_docker)
docker.addMountDirectory(tmp, tmp_docker)
docker.run()
exit_code = docker.getExitValue()
if exit_code != 0:
error("Error while demultiplexing run " + run_id, 'Error while demultiplexing run (exit code: ' +
str(exit_code) + ').\nCommand line:\n' + cmd, conf)
msg = 'Error while executing bcl2fastq ' + run_id_msg + ' (exit code: ' + str(
exit_code) + ').\nCommand line:\n' + cmd
# Check if the log file has been generated
if not os.path.exists(bcl2fastq_log_file):
error("Error with bcl2fastq log for run " + run_id + ".", "No bcl2fastq log available " + bcl2fastq_log_file, conf)
common.send_msg('[Aozan] Failed demultiplexing ' + run_id_msg, msg, True, conf)
else:
msg += "\n\nPlease check the attached bcl2fastq output error file."
common.send_msg_with_attachment('[Aozan] Failed demultiplexing ' + run_id_msg, msg, bcl2fastq_log_file, True, conf)
return False
except Throwable, exp:
error("Error while running Docker image", common.exception_msg(exp, conf), conf)
return False
def qc(run_id, conf):
"""Proceed to quality control of a run.
Arguments:
run_id: The run id
conf: configuration dictionary
"""
start_time = time.time()
input_run_data_path = common.get_input_run_data_path(run_id, conf)
if input_run_data_path is None:
return False
fastq_input_dir = conf[FASTQ_DATA_PATH_KEY] + '/' + run_id
reports_data_base_path = conf[REPORTS_DATA_PATH_KEY]
reports_data_path = reports_data_base_path + '/' + run_id
qc_output_dir = reports_data_path + '/qc_' + run_id
tmp_extension = '.tmp'
common.log('INFO', 'QC step: Starting', conf)
# Check if input run data data exists
if input_run_data_path is None:
error("Basecalling data directory does not exist", "Basecalling data directory does not exist.", conf)
return False
# Check if input root fastq root data exists
if not common.is_dir_exists(FASTQ_DATA_PATH_KEY, conf):
error("FASTQ data directory does not exist",
"FASTQ data directory does not exist: " + conf[FASTQ_DATA_PATH_KEY], conf)
return False
# Create if not exist report directory for the run
if not os.path.exists(reports_data_path):
os.mkdir(reports_data_path)
# Check if temporary directory exists
if not common.is_dir_exists(TMP_PATH_KEY, conf):
error("Temporary directory does not exist", "Temporary directory does not exist: " + conf[TMP_PATH_KEY], conf)
return False
# Check if the output directory already exists
if os.path.exists(qc_output_dir):
error("The quality control report directory already exists for run " + run_id,
'The quality control report directory already exists for run ' + run_id + ': ' + qc_output_dir, conf)
return False
# Check if the output directory already exists
if os.path.exists(reports_data_path + '/qc_' + run_id + '.tar.bz2'):
error("The quality control report archive already exists for run " + run_id,
'The quality control report archive already exists for run ' + run_id + ': ' +
reports_data_path + '/qc_' + run_id + '.tar.bz2', conf)
return False
# Check if enough free space is available
if common.df(conf[REPORTS_DATA_PATH_KEY]) < 1 * 1024 * 1024 * 1024:
error("Not enough disk space to store aozan quality control for run " + run_id,
"Not enough disk space to store aozan reports for run " + run_id +
'.\nNeed more than 10 Gb on ' + conf[REPORTS_DATA_PATH_KEY] + '.', conf)
return False
# Create temporary temporary directory
qc_output_dir += tmp_extension
if not os.path.exists(qc_output_dir):
os.mkdir(qc_output_dir)
try:
# Initialize the QC object
qc = QC(Settings(conf), input_run_data_path, fastq_input_dir, qc_output_dir, conf[TMP_PATH_KEY], run_id)
# Compute the report
report = qc.computeReport()
except AozanException, exp:
error("Error while computing QC report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
def aozan_main():
"""Aozan main method.
"""
# Define command line parser
parser = OptionParser(usage='usage: ' + Globals.APP_NAME_LOWER_CASE + '.sh [options] conf_file')
parser.add_option('-q', '--quiet', action='store_true', dest='quiet',
default=False, help='quiet')
parser.add_option('-v', '--version', action='store_true', dest='version', help='Aozan version')
parser.add_option('-e', '--exit-code', action='store_true', dest='exit_code',
help='Returns non zero exit code if a step fails')
parser.add_option('-c', '--conf', action='store_true', dest='conf',
help='Default Aozan configuration, loads before configuration file.')
# Parse command line arguments
(options, args) = parser.parse_args()
# Print Aozan current version
if options.version:
print Globals.WELCOME_MSG
sys.exit(0)
# Print default configuration option
if options.conf:
print common.print_default_configuration()
sys.exit(0)
# If no argument print usage
if len(args) < 1:
parser.print_help()
sys.exit(1)
# Create configuration object
conf = LinkedHashMap()
# Set the default value in the configuration object
common.set_default_conf(conf)
# Use default (US) locale
Locale.setDefault(Globals.DEFAULT_LOCALE)
# Check if OS is Linux
if not SystemUtils.isLinux():
sys.stderr.write('ERROR: Aozan can not be executed. Operating system is not Linux\n')
sys.exit(1)
# Check if configuration file exists
conf_file = args[0]
if not os.path.isfile(conf_file):
sys.stderr.write('ERROR: Aozan can not be executed. Configuration file is missing: ' + \
conf_file + '\n')
sys.exit(1)
# Load Aozan conf file
common.load_conf(conf, conf_file)
# End of Aozan if aozan is not enable
if common.is_conf_value_defined(AOZAN_ENABLE_KEY, 'false', conf):
sys.exit(0)
# Init logger
try:
Common.initLogger(conf[AOZAN_LOG_PATH_KEY], conf[AOZAN_LOG_LEVEL_KEY])
except AozanException, exp:
common.exception_msg(exp, conf)
qc_output_dir += tmp_extension
if not os.path.exists(qc_output_dir):
os.mkdir(qc_output_dir)
try:
# Initialize the QC object
qc = QC(Settings(conf), input_run_data_path, fastq_input_dir, qc_output_dir, conf[TMP_PATH_KEY], run_id)
# Compute the report
report = qc.computeReport()
except AozanException, exp:
error("Error while computing QC report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
except Throwable, exp:
error("Error while computing QC report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
# Remove QC data if not demand
if common.is_conf_value_defined(QC_REPORT_SAVE_RAW_DATA_KEY, 'false', conf):
try:
os.remove(qc_output_dir + '/data-' + run_id + '.txt')
# qc.writeRawData(report, qc_output_dir + '/data-' + run_id + '.txt')
except AozanException, exp:
error("Error while removing QC raw data for run " + run_id + ".", exp.getMessage(), conf)
return False
# Write the XML report
if common.is_conf_value_equals_true(QC_REPORT_SAVE_REPORT_DATA_KEY, conf):
try:
qc.writeXMLReport(report, qc_output_dir + '/' + run_id + '.xml')
