# TODO
doblocks = 1
if doblocks:
sigproc_job_dict = {}
basecaller_job_dict = {}
alignment_job_dict = {}
merge_job_dict = {}
result_dirs = {}
for block in blocks:
result_dirs[block["id_str"]] = blockprocessing.initBlockReport(
block,
env["SIGPROC_RESULTS"],
env["BASECALLER_RESULTS"],
env["ALIGNMENT_RESULTS"],
pluginbasefolder,
env["oninstranalysis"],
)
# create a list of blocks
blocks_to_process = []
blocks_to_process.extend(blocks)
timeout = 3 * 60 * 60
if env["oninstranalysis"] and is_blockprocessing:
timeout = 20 * 60 * 60
env["block_dirs"] = [
os.path.join(env["report_root_dir"], result_dirs[block["id_str"]]) for block in blocks_to_process
]
# dirs = ['%s/block_%s' % (SIGPROC_RESULTS, block['id_str']) for block in blocks]
#####################################################
# Create block reports #
#####################################################
#TODO
doblocks = 1
if doblocks:
block_job_dict = {}
merge_job_dict = {}
result_dirs = {}
for block in blocks:
result_dirs[block['id_str']] = blockprocessing.initBlockReport(block, env['SIGPROC_RESULTS'], env['BASECALLER_RESULTS'], env['ALIGNMENT_RESULTS'], pluginbasefolder, from_sigproc_analysis=(env['blockArgs'] == "fromRaw"))
# create a list of blocks
blocks_to_process = []
blocks_to_process.extend(blocks)
timeout = 3*60*60
if is_composite:
if doSigproc:
timeout = 1* 1*60 # sec , skip OIA, process diagnosis blocks
else:
timeout = 20*60*60 # sec
plugins_params['block_dirs'] = [os.path.join(env['report_root_dir'],result_dirs[block['id_str']]) for block in blocks_to_process]
while len(blocks_to_process) > 0 and timeout > 0:
#####################################################
# Create block reports #
#####################################################
#TODO
doblocks = 1
if doblocks:
sigproc_job_dict = {}
basecaller_job_dict = {}
alignment_job_dict = {}
merge_job_dict = {}
result_dirs = {}
for block in blocks:
result_dirs[block['id_str']] = blockprocessing.initBlockReport(block, env['SIGPROC_RESULTS'], env['BASECALLER_RESULTS'], env['ALIGNMENT_RESULTS'], pluginbasefolder, env['oninstranalysis'])
# create a list of blocks
blocks_to_process = []
blocks_to_process.extend(blocks)
timeout = 3*60*60
if env['oninstranalysis'] and is_blockprocessing:
timeout = 20*60*60
env['block_dirs'] = [os.path.join(env['report_root_dir'],result_dirs[block['id_str']]) for block in blocks_to_process]
while len(blocks_to_process) > 0 and timeout > 0:
printtime('waiting for %s block(s) to schedule' % str(len(blocks_to_process)))
sys.stdout.flush()
sys.stderr.flush()
# Create block reports #
#####################################################
#TODO
doblocks = 1
if doblocks:
sigproc_job_dict = {}
basecaller_job_dict = {}
alignment_job_dict = {}
merge_job_dict = {}
result_dirs = {}
for block in blocks:
result_dirs[block['id_str']] = blockprocessing.initBlockReport(
block, env['SIGPROC_RESULTS'], env['BASECALLER_RESULTS'],
env['ALIGNMENT_RESULTS'], pluginbasefolder,
env['oninstranalysis'])
# create a list of blocks
blocks_to_process = []
blocks_to_process.extend(blocks)
timeout = 3 * 60 * 60
if env['oninstranalysis'] and is_blockprocessing:
timeout = 36 * 60 * 60
env['block_dirs'] = [
os.path.join(env['report_root_dir'], result_dirs[block['id_str']])
for block in blocks_to_process
]
while len(blocks_to_process) > 0 and timeout > 0: