# get default align_pipeline.py args
pipeline_args = ' '.join(['%s="%s"'%(k,v) for k,v in pipeline_args])
print 'align_pipeline.py %s --run-name=%s %s %s --print-args'%(aln,run_name,annoj_args,pipeline_args)
def_args = Popen("align_pipeline.py %s --run-name=%s %s %s --print-args"%(aln,run_name,annoj_args,pipeline_args),shell=True,stdout=PIPE,stderr=PIPE).communicate()[0]
print def_args
wb('Creating script...\n')
script_fn = '%s_aln_pipeline.sh'%run_name
if (all_tool_settings['tools']['use_modules']):
load_modules = """\
%(run_init)s
module load %(modules_list)s
"""%({'run_init':all_tool_settings['modules']['run_init'],'modules_list':' '.join(modules_list)})
else:
load_modules = ""
with open(script_fn,'w') as script_f :
script_f.write(script_template%{'species':species,'aligner':aln,
'load_modules':load_modules,'def_args':def_args})
os.chmod(script_f.name,stat.S_IRWXU|stat.S_IRWXG|stat.S_IROTH)
print end_text%{'script_fn':script_fn}
wb('Creating parameter file...\n')
json_fn = '%s_aln_params.json'%run_name
with open(json_fn,'w') as json_f :
json.dump(json_dict,json_f,indent=4)
except KeyboardInterrupt :
sys.stderr.write('\n')
error('Script creation interrupted, aborting')
cntrl_fn = 'cntrl_'+cntrl_fn
os.symlink(cntrl_path,cntrl_fn)
else :
cntrl_fn = ''
# get default chipseq_pipeline.py args
pipeline_args = ' '.join(['%s="%s"'%(k,v) for k,v in pipeline_args.items()])
print 'chipseq_pipeline.py --exp-name=%s %s %s --print-args'%(exp_name,ucsc_args,pipeline_args)
def_args = Popen('chipseq_pipeline.py --exp-name=%s %s %s %s --print-args'%(exp_name,ucsc_args,parallel,pipeline_args),shell=True,stdout=PIPE,stderr=PIPE).communicate()[0]
print 'def_args=',def_args
wb('Creating script...\n')
script_fn = '%s_pipeline.sh'%exp_name
with open(script_fn,'w') as script_f :
script_f.write(script_template%{'exp_path':exp_fn,'cnt_path':cntrl_fn,'organism':org,'exp_name':exp_name,'def_args':def_args})
os.chmod(script_f.name,stat.S_IRWXU|stat.S_IRWXG|stat.S_IROTH)
print end_text%{'script_fn':script_fn}
wb('Creating parameter file...\n')
json_fn = '%s_params.json'%exp_name
with open(json_fn,'w') as json_f :
json.dump(json_dict,json_f,indent=4)
except ValueError as e:
sys.stderr.write(e.msg)
error('Error encountered in creating script, aborting')
except KeyboardInterrupt :
sys.stderr.write('\n')
error('Script creation interrupted, aborting')
