Ejemplo n.º 1
0
 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
Ejemplo n.º 2
0
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
Ejemplo n.º 3
0
 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)
Ejemplo n.º 4
0
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