job_list[block] = {"basecaller": jobid}
for block, jobid in alignment_job_dict.items():
f.write(jobid + "\n")
if job_list.has_key(block):
job_list[block]["alignment"] = jobid
else:
job_list[block] = {"alignment": jobid}
for jobname, jobid in merge_job_dict.items():
f.write(jobid + "\n")
f.close()
# write more descriptive json list of jobs
with open("job_list.json", "w") as f:
f.write(json.dumps(job_list, indent=2))
# multilevel plugins preprocessing level
blockprocessing.runplugins(plugins, env, pluginbasefolder, url_root, "pre")
# Watch status of jobs. As they finish remove the job from the list.
pl_started = False
alignment_job_list = alignment_job_dict.values()
while len(alignment_job_list) > 0:
for job in alignment_job_list:
block = [block for block in blocks if block["jobid"] == job][0]
# check status of jobid
try:
block["status"] = jobserver.jobstatus(block["jobid"])
except:
traceback.print_exc()
continue
job_list[block] = {'basecaller': jobid}
for block, jobid in alignment_job_dict.items():
f.write(jobid+'\n')
if job_list.has_key(block):
job_list[block]['alignment'] = jobid
else:
job_list[block] = {'alignment': jobid}
for jobname, jobid in merge_job_dict.items():
f.write(jobid+'\n')
f.close()
# write more descriptive json list of jobs
with open('job_list.json','w') as f:
f.write(json.dumps(job_list,indent=2))
# multilevel plugins preprocessing level
blockprocessing.runplugins(plugins, env, pluginbasefolder, url_root, 'pre')
# Watch status of jobs. As they finish remove the job from the list.
pl_started = False
alignment_job_list = alignment_job_dict.values()
while len(alignment_job_list) > 0:
for job in alignment_job_list:
block = [block for block in blocks if block['jobid'] == job][0]
#check status of jobid
try:
block['status'] = jobserver.jobstatus(block['jobid'])
except:
traceback.print_exc()
continue
os.system(cmd)
except:
printtime("RSM createExperimentMetrics.py failed")
########################################################
# Write checksum_status.txt to raw data directory #
########################################################
if is_wholechip:
try:
if os.path.isfile("analysis_return_code.txt"):
shutil.copyfile("analysis_return_code.txt", os.path.join(env["pathToRaw"], "checksum_status.txt"))
except:
traceback.print_exc()
if is_thumbnail or is_wholechip:
blockprocessing.runplugins(env, basefolder, url_root)
else:
plugin_set = set()
plugin_set.add("torrentscout")
plugin_set.add("rawPlots")
blockprocessing.run_selective_plugins(plugin_set, env, basefolder, url_root)
if env["isReverseRun"] and env["pe_forward"] != "None":
try:
crawler = xmlrpclib.ServerProxy(
"http://%s:%d" % (CRAWLER_HOST, CRAWLER_PORT), verbose=False, allow_none=True
)
except (socket.error, xmlrpclib.Fault):
traceback.print_exc()
printtime("crawler hostname: " + crawler.hostname())
printtime("Submitted zipping job with job ID (%s)" % (str(merge_job_dict['merge'])))
else:
# Proton Full Chip
merge_job_dict['merge'] = spawn_cluster_job('.','MergeTLScript.py',['--do-alignment','--do-zipping'],block_job_dict.values())
printtime("Submitted merge alignment job with job ID (%s)" % (str(merge_job_dict['merge'])))
# write job id's to file
job_list = {}
job_list['merge'] = merge_job_dict
for block, jobid in block_job_dict.items():
job_list[block] = {'block_processing': jobid}
with open('job_list.json','w') as f:
f.write(json.dumps(job_list,indent=2))
# multilevel plugins preprocessing level
plugins = blockprocessing.runplugins(plugins, env, RunLevel.PRE, plugins_params)
# Watch status of jobs. As they finish remove the job from the list.
pl_started = False
block_job_list = block_job_dict.values()
while len(block_job_list) > 0:
for job in block_job_list:
block = [block for block in blocks if block['jobid'] == job][0]
#check status of jobid
try:
block['status'] = jobserver.jobstatus(block['jobid'])
except:
traceback.print_exc()
continue
job_list[block] = {'basecaller': jobid}
for block, jobid in alignment_job_dict.items():
f.write(jobid + '\n')
if job_list.has_key(block):
job_list[block]['alignment'] = jobid
else:
job_list[block] = {'alignment': jobid}
for jobname, jobid in merge_job_dict.items():
f.write(jobid + '\n')
f.close()
# write more descriptive json list of jobs
with open('job_list.json', 'w') as f:
f.write(json.dumps(job_list, indent=2))
# multilevel plugins preprocessing level
blockprocessing.runplugins(plugins, env, pluginbasefolder, url_root,
'pre')
# Watch status of jobs. As they finish remove the job from the list.
pl_started = False
alignment_job_list = alignment_job_dict.values()
while len(alignment_job_list) > 0:
for job in alignment_job_list:
block = [block for block in blocks if block['jobid'] == job][0]
#check status of jobid
try:
block['status'] = jobserver.jobstatus(block['jobid'])
except:
traceback.print_exc()
continue
