def __launch__(self,config,node_list=None):
"""
Checks to make sure there is enough storage. If
not, sends email. If so, sends the job to SGE and
records pertinent information.
"""
if node_list is None:
node_list = config.get('Zcat','nodes')
SampleQsubProcess.__launch__(self,config)
#SampleQsubProcess.__launch__(self,config,node_list=node_list,queue_name='single')
return True
def __launch__(self,config,command=None,**kwargs):
"""
Sends the job to SGE and records pertinent information.
"""
if command is None:
command = ['sleep 30;','qsub']
return SampleQsubProcess.__launch__(self,config,command=command,**kwargs)
def __launch__(self,configs,storage_device,node_list=None):
"""
Checks to make sure there is enough storage. If
not, sends email. If so, sends the job to SGE and
records pertinent information.
"""
#If storage device is full, send a notification and abort.
if storage_device.__is_full__(configs['pipeline'].get('Storage','required_fastq_size')):
send_email(self.__generate_full_error_text__(configs,storage_device))
return False
#This differs from the previous check by the fact that the previous does not
#account for jobs that are currently being copied. This error is not as
#restrictive due to the fact that the required_fastq_size should be larger than
#the actual fastq size thus leaving additional storage once complete.
if not storage_device.__is_available__(configs['pipeline'].get('Storage','required_fastq_size')) and self.fail_reported == False:
send_email(self.__generate_storage_error_text__(configs,storage_device))
self.fail_reported = True
return False
if node_list is None:
node_list = configs['pipeline'].get('Backup','nodes')
SampleQsubProcess.__launch__(self,configs['system'],node_list=node_list,queue_name='single')
return True
