def run(self, trans, tmp_dir, kwd):
tmp_dir = os.path.abspath(tmp_dir)
lane = 1
fastq_dir, fastq_files, qual_format = self._prepare_fastq(
trans, lane, tmp_dir, kwd)
config_file, config = self._prepare_config(trans, lane, fastq_files,
qual_format, tmp_dir, kwd)
dirs = {
"work": tmp_dir,
"config": os.path.dirname(self._process_config_file)
}
send_data = {
"fc_dir": fastq_dir,
"run_yaml": config_file,
"directory": "%s_%s" % (config["fc_date"], config["fc_name"])
}
with open(self._process_config_file) as in_handle:
config = yaml.load(in_handle)
with utils.chdir(tmp_dir):
runner = messaging.runner("bcbio.distributed.tasks",
dirs,
config,
self._process_config_file,
wait=False)
runner("analyze_and_upload", [[send_data]])
def finished_message(fn_name, run_module, directory, files_to_copy,
config, config_file, pushed=False):
"""Wait for messages with the give tag, passing on to the supplied handler.
"""
logger2.debug("Calling remote function: %s" % fn_name)
user = getpass.getuser()
hostname = socket.gethostbyaddr(socket.gethostname())[0]
data = dict(
machine_type='illumina',
hostname=hostname,
user=user,
directory=directory,
to_copy=files_to_copy
)
dirs = {"work": os.getcwd(),
"config": os.path.dirname(config_file)}
runner = messaging.runner(run_module, dirs, config, config_file, wait=False)
if pushed:
config["directory"] = directory
runner(fn_name, [[config]])
else:
runner(fn_name, [[data]])
def queue_report(fc_date, fc_name, run_info_yaml, dirs, config, config_file):
if "gdocs_upload" not in config:
return False
runner = messaging.runner("bcbio.distributed.google_tasks", {"work": os.getcwd(),"config": os.path.dirname(config_file)}, config, config_file, wait=False)
runner("create_report_on_gdocs",[[fc_date,fc_name,run_info_yaml,dirs,config]])
return True
def _run_parallel(fn_name, items, dirs, config):
"""Process a supplied function: single, multi-processor or distributed.
"""
parallel = config["algorithm"]["num_cores"]
if str(parallel).lower() == "messaging":
runner = messaging.runner(dirs, config)
return runner(fn_name, items)
else:
out = []
fn = globals()[fn_name]
with utils.cpmap(int(parallel)) as cpmap:
for data in cpmap(fn, items):
if data:
out.extend(data)
return out
def queue_report(fc_date, fc_name, run_info_yaml, dirs, config, config_file):
if "gdocs_upload" not in config:
return False
runner = messaging.runner("bcbio.distributed.google_tasks", \
{"work": os.getcwd(), \
"config": os.path.dirname(config_file)}, \
config, \
config_file, \
wait=False)
runner("create_report_on_gdocs",
[[fc_date, fc_name, run_info_yaml, dirs, config]])
return True
