def things_to_do_if_initializing_flowcell_pipeline_with_input_directory(configs,storage_devices,mockdb,source_dir,pipeline_name=None,base_output_dir=None):
"""
Starts pipelines that read the entire flowcell data.
"""
if configs["system"].get("Logging","debug") is "True":
print " Starting post casava flowcell pipelines"
flowcell_dir_name = os.path.basename(source_dir)
automation_parameters_config = MyConfigParser()
automation_parameters_config.read(configs["system"].get("Filenames","automation_config"))
running_location = "Speed"
parsed = parse_sample_sheet(configs['system'],mockdb,source_dir)
description = parsed['description'].replace(parsed['SampleID']+'_','')
description_dict = parse_description_into_dictionary(description)
if configs["system"].get("Logging","debug") is "True":
print " Description = " + str(parsed['description'])
if 'Pipeline' in description_dict:
pipeline_key = description_dict['Pipeline']
else:
description_pieces = parsed['description'].split('_')
pipeline_key = description_pieces[-1]
if pipeline_key.startswith('CCGL'):
pipeline_key='CCGL'
pipeline_name_check = automation_parameters_config.safe_get("Flowcell pipeline",pipeline_key)
if pipeline_name_check != pipeline_name:
return 1
if pipeline_name is None:
return 1
if configs["system"].get("Logging","debug") is "True":
print "Starting " + pipeline_name
pipeline = mockdb[pipeline_name].__new__(configs['system'],input_dir=source_dir,pipeline_key=pipeline_key,seq_run_key=None,project=parsed['project_name'],flowcell_dir_name=flowcell_dir_name,running_location='Speed',pipeline_config=configs["pipeline"],**parsed)
return 1
def __is_complete__(self,configs,mockdb,*args,**kwargs):
"""
Checks to see if the pipeline is complete. If not, and it is ready to advance, then
the pipeline is advanced.
"""
if GenericProcess.__is_complete__(self,*args,**kwargs):
return True
if not hasattr(self,"generic_copy_key") or self.generic_copy_key is None:
if configs["system"].get("Logging","debug") is "True":
print "Copying bcls"
self.__launch_copy_bcls__(configs,mockdb)
return False
current_configs = {}
current_configs["system"] = configs["system"]
pipeline_config = MyConfigParser()
current_configs["pipeline"] = pipeline_config
pipeline_config.read(configs["system"].get('Pipeline','BclToFastqPipeline'))
if self.__handle_linear_steps__(current_configs,mockdb,skip_finish=True,*args,**kwargs):
casava = mockdb['Casava'].__get__(configs['system'],self.casava_key)
if configs["system"].get("Logging","debug") is "True":
print "Checking the pipeline first step results"
if casava.__do_all_relevant_pipelines_have_first_step_complete__(current_configs,mockdb):
self.__finish__(*args,**kwargs)
return True
return False
def __init__(self,config,key=int(-1),pipeline_config=None,prev_step=None,process_name='cp',pipeline=None,**kwargs):
if not prev_step is None:
if pipeline_config is None:
pipeline_config = MyConfigParser()
pipeline_config.read(config.get('Pipeline',pipeline.obj_type))
cp_input_dir_name = pipeline_config.safe_get('Common_directories','cp_subdir')
if cp_input_dir_name is None:
cp_input_dir_name = ""
if prev_step.obj_type == "CleanBcbio":
for root, dirs, files in os.walk(prev_step.output_dir,topdown=False):
for filename in files:
if filename.endswith(".vcf"):
full_path = os.path.join(root,filename)
cp_indput_dir = os.path.dirname(full_path)
cp_input_dir = os.path.join(pipeline.output_dir,cp_input_dir_name)
output_subdir_name = pipeline_config.safe_get('Common_directories','output_subdir','ngv3')
cp_dir = os.path.join(pipeline.input_dir,output_subdir_name)
if not os.path.exists(cp_dir):
os.makedirs(cp_dir)
self.cp_dir = cp_dir
SampleQsubProcess.__init__(self,config,key=key,input_dir=cp_input_dir,output_dir=pipeline.output_dir,process_name=process_name,**kwargs)
if self.sample_key is not None:
self.md5_file = os.path.join(cp_dir,self.sample_key + "_exome_md5checksums.txt")
else:
self.md5_file = "exome_md5checksums.txt"
def __init__(self,config,key=int(-1),sample=None,flowcell=None,description=None,recipe=None,input_dir=None,pipeline_config=None,pipeline_key=None,process_name='qcpipeline',running_location='Speed',storage_needed=500000000,project=None,flowcell_dir_name=None,seq_run_key=None,date=strftime("%Y%m%d",localtime()),*args,**kwargs):
if not pipeline_config is None or not pipeline_key is None:
if sample is None:
sample = Sample(config,key="dummy_sample_key")
if sample.__class__.__name__ != "Sample":
raise Exception("Trying to start a qcpipeline process on a non-sample.")
if flowcell is None:
sample = Flowcell(config,key="dummy_flowcell_key")
if flowcell.__class__.__name__ != "Flowcell":
raise Exception("Trying to start a qcpipeline process on a sample not from a flowcell.")
automation_parameters_config = MyConfigParser()
automation_parameters_config.read(config.get("Filenames","automation_config"))
#Specific information about this pipeline
self.description = description
self.recipe = recipe
self.storage_needed = storage_needed
self.input_dir = input_dir
self.running_location = running_location
self.seq_run_key = seq_run_key
capture_target_bed = automation_parameters_config.safe_get("Target",pipeline_key)
if not capture_target_bed is None:
self.capture_target_bed = capture_target_bed
if pipeline_config is None:
pipeline_name = automation_parameters_config.safe_get("Pipeline",pipeline_key)
pipeline_config = MyConfigParser()
pipeline_config.read(config.get('Pipeline',pipeline_name))
pipeline_steps = pipeline_config.get('Pipeline','steps').split(',')
for step in pipeline_steps:
setattr(self,step+"_key",None)
base_output_dir = pipeline_config.get('Common_directories','archive_directory')
if flowcell_dir_name is None:
self.client_dir = self.input_dir
else:
sample_dir_name = sample.key
if not str(sample_dir_name).startswith("Sample_"):
sample_dir_name = "Sample_" + sample_dir_name
self.client_dir = os.path.join(config.get('Common_directories','casava_output'),flowcell_dir_name+"/Project_"+str(project)+"/"+sample_dir_name)
self.flowcell_key = flowcell.key
base_client_dir = config.get('Common_directories','casava_output')
if project is None:
if base_output_dir is None:
base_output_dir = ""
self.output_dir = os.path.join(base_output_dir,sample.key + '_' + str(date))
else:
project_out = re.sub('_','-',project)
self.project = project_out
if re.search("[0-9]",project_out[0:1]):
project_out = "Project-" + project_out
if base_output_dir == None:
base_output_dir = ""
self.output_dir = os.path.join(base_output_dir,project_out + "_" + sample.key + '_' + str(date))
if not os.path.exists(self.output_dir) and not re.search('dummy',sample.key):
os.makedirs(self.output_dir)
GenericProcess.__init__(self,config,key=key,process_name=process_name,**kwargs)
self.date = date
self.sample_key = sample.key
self.altered_parameters = None
def __push_flowcells_into_relevant_pipelines__(self,configs,mockdb):
"""
Provides the interface from which all post casava flowcell pipelines are run.
"""
if configs["system"].get("Logging","debug") is "True":
print " Starting post casava flowcell pipelines for " + self.flowcell_key
flowcell_dir_name = os.path.basename(self.output_dir)
automation_parameters_config = MyConfigParser()
automation_parameters_config.read(configs["system"].get("Filenames","automation_config"))
running_location = "Speed"
parsed = parse_sample_sheet(configs['system'],mockdb,self.output_dir)
description = parsed['description'].replace(parsed['SampleID']+'_','')
description_dict = parse_description_into_dictionary(description)
if 'Pipeline' in description_dict:
pipeline_key = description_dict['Pipeline']
else:
description_pieces = parsed['description'].split('-')
pipeline_key = description_pieces[-1]
if pipeline_key.startswith('CCGL'):
pipeline_key='CCGL'
pipeline_name = automation_parameters_config.safe_get("Flowcell pipeline",pipeline_key)
if pipeline_name is None:
return 1
if configs["system"].get("Logging","debug") is "True":
print "Starting " + pipeline_name
pipeline_config = MyConfigParser()
pipeline_config.read(configs["system"].get('Pipeline',pipeline_name))
pipeline = mockdb[pipeline_name].__new__(configs['system'],input_dir=self.output_dir,pipeline_key=pipeline_key,seq_run_key=self.seq_run_key,project=parsed['project_name'],flowcell_dir_name=flowcell_dir_name,pipeline_config=pipeline_config,**parsed)
return 1
def __push_samples_into_relevant_pipelines__(self,configs,mockdb):
"""
Provides the interface from which all post casava sample pipelines are run.
"""
if configs["system"].get("Logging","debug") is "True":
print " Starting post casava sample pipelines for " + self.flowcell_key
print " Determining Sample dirs"
sample_dirs = list_project_sample_dirs(self.output_dir.split(":"))
if configs["system"].get("Logging","debug") is "True":
print " Samples: " + str(sample_dirs)
flowcell_dir_name = os.path.basename(self.output_dir)
automation_parameters_config = MyConfigParser()
automation_parameters_config.read(configs["system"].get("Filenames","automation_config"))
fastqc_pipeline_config = MyConfigParser()
fastqc_pipeline_config.read(configs["system"].get("Pipeline","FastQCPipeline"))
for project in sample_dirs:
for sample in sample_dirs[project]:
#running_location = identify_running_location_with_most_currently_available(configs,storage_devices)
running_location = "Speed"
parsed = parse_sample_sheet(configs['system'],mockdb,sample_dirs[project][sample][0])
if configs["system"].get("Logging","debug") is "True":
print " Pushing fastqc pipeline for " + sample
fastqc_pipeline = mockdb["FastQCPipeline"].__new__(configs['system'],input_dir=sample_dirs[project][sample][0],flowcell_dir_name=flowcell_dir_name,project=parsed['project_name'],pipeline_config=fastqc_pipeline_config,seq_run_key=self.seq_run_key,**parsed)
description_dict = parse_description_into_dictionary(parsed['description'])
if 'Pipeline' in description_dict:
pipeline_key = description_dict['Pipeline']
else:
description_pieces = parsed['description'].split('-')
pipeline_key = description_pieces[-1]
pipeline_name = automation_parameters_config.safe_get("Pipeline",pipeline_key)
if pipeline_name is None:
continue
if configs["system"].get("Logging","debug") is "True":
print "Starting " + pipeline_name + " for " + sample
pipeline = mockdb[pipeline_name].__new__(configs['system'],input_dir=sample_dirs[project][sample][0],pipeline_key=pipeline_key,seq_run_key=self.seq_run_key,project=parsed['project_name'],flowcell_dir_name=flowcell_dir_name,**parsed)
def __launch_copy_bcls__(self,configs,mockdb):
"""
This launches the process that will archive the fastq directories.
"""
input_dir = os.path.join(self.input_dir,"Data/Intensities")
output_dir = os.path.join(self.output_dir,"Data/Intensities")
if not os.path.exists(output_dir):
os.makedirs(output_dir)
copy_all_xml(self.input_dir,self.output_dir)
copy_all_xml(os.path.join(self.input_dir,"Data"),os.path.join(self.output_dir,"Data"))
current_configs = {}
current_configs["system"] = configs["system"]
pipeline_config = MyConfigParser()
current_configs["pipeline"] = pipeline_config
pipeline_config.read(configs["system"].get('Pipeline','BclToFastqPipeline'))
copy_bcls = mockdb['GenericCopy'].__new__(configs['system'],input_dir=input_dir,output_dir=output_dir)
self.generic_copy_key = copy_bcls.key
copy_bcls.__fill_qsub_file__(current_configs)
copy_bcls.__launch__(configs['system'])
def __do_all_relevant_pipelines_have_first_step_complete__(self,configs,mockdb):
"""
Since the first step of post casava pipelines is to copy the data,
moving the data after these pipelines are started must wait for
this step to complete. This is only a concern when everything is
automated. This checks that step and whether the FastQCPipeline is finished.
"""
pipeline_names = configs["system"].get('Pipeline','post_casava_automated').split(',')
for pipeline_name in pipeline_names:
try:
seq_run_key_dict = mockdb[pipeline_name].__attribute_value_to_object_dict__('seq_run_key')
pipeline_config = MyConfigParser()
pipeline_config.read(config.get('Pipeline',pipeline_name))
for pipeline in seq_run_key_dict[self.seq_run_key]:
if pipeline_name == "FastQCPipeline":
if not pipeline.__is_complete__():
return False
if not pipeline.__check_first_step__(pipeline_config):
return False
except:
continue
return True
def things_to_do_if_initializing_pipeline_with_input_directory(configs,storage_devices,mockdb,source_dir,pipeline_name=None,base_output_dir=None,combine_projects=True):
if combine_project:
sample_dirs["dummy_project"] = list_sample_dirs(source_dir)
else:
sample_dirs = list_project_sample_dirs(source_dir)
target_config = MyConfigParser()
target_config.read(configs["system"].get("Filenames","target_config"))
for project in sample_dirs:
for sample in sample_dirs[project]:
running_location = identify_running_location_with_most_currently_available(configs,storage_devices)
parsed = parse_sample_sheet(configs['system'],mockdb,sample_dirs[project][sample][0])
if base_output_dir is None:
base_output_dir = configs['pipeline'].get('Common_directories','archive_directory')
automation_parameters_config = MyConfigParser()
automation_parameters_config.read(configs["system"].get("Filenames","automation_config"))
description_dict = parse_description_into_dictionary(parsed['description'])
if 'Pipeline' in description_dict:
pipeline_key = description_dict['Pipeline']
else:
description_pieces = parsed['description'].split('_')
pipeline_key = description_pieces[-1]
pipeline_name_for_sample = automation_parameters_config.safe_get("Pipeline",pipeline_key)
if not pipeline_name_for_sample == pipeline_name:
continue
mockdb[pipeline_name].__new__(configs['system'],input_dir=sample_dirs[project][sample][0],pipeline_config=configs["pipeline"],project=parsed['project_name'],pipeline_key=pipeline_key,**parsed)
flowcell_dict = mockdb['SequencingRun'].__attribute_value_to_object_dict__('flowcell_key')
flowcell_dict = mockdb['SequencingRun'].__attribute_value_to_object_dict__('flowcell_key')
if parsed['flowcell'].key in flowcell_dict:
seq_run = flowcell_dict[parsed['flowcell'].key]
pass
else:
try:
base_dir = get_sequencing_run_base_dir(source_dir)
[date,machine_key,run_number,side,flowcell_key] = parse_sequencing_run_dir(base_dir)
machine = mockdb['HiSeqMachine'].__get__(configs['system'],machine_key)
run_type = determine_run_type(base_dir)
seq_run = mockdb['SequencingRun'].__new__(configs['system'],flowcell,machine,date,run_number,output_dir=base_dir,side=side,run_type=run_type)
fill_demultiplex_stats(configs['system'],mockdb,seq_run.output_dir,flowcell,machine)
except:
pass
return 1
parser = argparse.ArgumentParser(description='Manages data and submits new jobs.')
parser.add_argument('-i', dest='source_dir', nargs='+', help='fastq source', default=None)
parser.add_argument('-o', dest='dest_dir', help='vcf destination', default=None)
parser.add_argument('-p', '--pipeline', dest='pipeline', help='The version of the pipeline', default='QualityControlPipeline')
parser.add_argument('--analyze_sequencing_run', dest='seq_run', action='store_true', help='Reanalyze the give sequencing run.', default=False)
parser.add_argument('--system_config', dest='system_config_file', help='The system configuration file', default='/home/sequencing/src/pipeline_project/pipeline/config/ihg_system.cfg')
parser.add_argument('-d', '--debug', dest='debug', action='store_true', help='Turn debugging on', default=False)
parser.add_argument('--sample_sheet', dest='sample_sheet', type=str, help='For use for re-initializing a sequencing run. Specifies the samples sheet to be used for casava.', default=None)
options = parser.parse_args()
if options.debug is True:
print "Options are " + str(options)
#Load configs
configs = {}
system_config = MyConfigParser()
system_config.read(options.system_config_file)
system_config.add_section("Logging")
if options.debug is True:
system_config.set("Logging","debug","True")
else:
system_config.set("Logging","debug","False")
configs.update({'system':system_config})
config_instance = MyConfigParser()
configs.update({"seq_run":config_instance})
config_instance.read(system_config.get('Pipeline',"seq_run"))
pipelines = system_config.get('Pipeline','opts').split(',')
pipeline_config = {}
for pipeline_name in pipelines:
