def main(demux_fcid_dir, restrict_to_projects=None, restrict_to_samples=None):
demux_fcid_dir = "/proj/a2014205/INBOX/140528_D00415_0049_BC423WACXX" # G.Grigelioniene_14_01
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140702_D00415_0052_AC41A2ANXX" # M.Kaller_14_06 sample P1171_102, P1171_104, P1171_106, P1171_108
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140905_D00415_0057_BC45KVANXX" # M.Kaller_14_06 sample P1171_102, P1171_104, P1171_106 ---- rerun
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140815_SN1025_0222_AC4HA6ACXX" # M.Kaller_14_05 sample P1170_101, P1170_103, P1170_105
process_demultiplexed_flowcell(demux_fcid_dir, None, None) # M.Kaller_14_08 sample P1272_101, P1272_104
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140815_SN1025_0223_BC4HAPACXX" # M.Kaller_14_05 sample P1170_101, P1170_103, P1170_105
process_demultiplexed_flowcell(demux_fcid_dir, None, None) # M.Kaller_14_08 sample P1272_101, P1272_104
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140919_SN1018_0203_BHA3THADXX" # M.Kaller_14_05 P1170_103, P1170_105 --- rerun
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
###UPPSALA
demux_fcid_dir = "/proj/a2014205/INBOX/140821_D00458_0029_AC45JGANXX" # uppsala run
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140917_D00458_0034_AC4FF3ANXX" # -- rerun
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
#and now a loop to update the DB
time.sleep(3800)
charon_session = CharonSession()
####charon_session.project_delete("ND-0522")
while True:
update_charon_with_local_jobs_status() ## this updated local_db and charon accordingly
# grab all projects from Charon
projects_dict = charon_session.projects_get_all()['projects']
for project_charon in projects_dict:
project_name = project_charon["name"]
project_dir = os.path.join("/proj/a2014205/nobackup/NGI/analysis_ready/DATA", project_name)
if os.path.isdir(project_dir):
projectObj = recreate_project_from_filesystem(project_dir, None)
launch_analysis_for_samples([projectObj])
time.sleep(3800)
def main(demux_fcid_dir, restrict_to_projects=None, restrict_to_samples=None):
demux_fcid_dir = "/proj/a2014205/INBOX/140528_D00415_0049_BC423WACXX" # G.Grigelioniene_14_01
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140702_D00415_0052_AC41A2ANXX" # M.Kaller_14_06 sample P1171_102, P1171_104, P1171_106, P1171_108
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140905_D00415_0057_BC45KVANXX" # M.Kaller_14_06 sample P1171_102, P1171_104, P1171_106 ---- rerun
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140815_SN1025_0222_AC4HA6ACXX" # M.Kaller_14_05 sample P1170_101, P1170_103, P1170_105
process_demultiplexed_flowcell(
demux_fcid_dir, None,
None) # M.Kaller_14_08 sample P1272_101, P1272_104
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140815_SN1025_0223_BC4HAPACXX" # M.Kaller_14_05 sample P1170_101, P1170_103, P1170_105
process_demultiplexed_flowcell(
demux_fcid_dir, None,
None) # M.Kaller_14_08 sample P1272_101, P1272_104
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140919_SN1018_0203_BHA3THADXX" # M.Kaller_14_05 P1170_103, P1170_105 --- rerun
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
###UPPSALA
demux_fcid_dir = "/proj/a2014205/INBOX/140821_D00458_0029_AC45JGANXX" # uppsala run
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
demux_fcid_dir = "/proj/a2014205/INBOX/140917_D00458_0034_AC4FF3ANXX" # -- rerun
process_demultiplexed_flowcell(demux_fcid_dir, None, None)
time.sleep(60) #wait for 1 minutes
#and now a loop to update the DB
time.sleep(3800)
charon_session = CharonSession()
####charon_session.project_delete("ND-0522")
while True:
update_charon_with_local_jobs_status(
) ## this updated local_db and charon accordingly
# grab all projects from Charon
projects_dict = charon_session.projects_get_all()['projects']
for project_charon in projects_dict:
project_name = project_charon["name"]
project_dir = os.path.join(
"/proj/a2014205/nobackup/NGI/analysis_ready/DATA",
project_name)
if os.path.isdir(project_dir):
projectObj = recreate_project_from_filesystem(
project_dir, None)
launch_analysis_for_samples([projectObj])
time.sleep(3800)
import argparse
import os
from ngi_pipeline.conductor.flowcell import process_demultiplexed_flowcell
if __name__ == '__main__':
parser = argparse.ArgumentParser("Launch seqrun-level analysis.")
parser.add_argument("-p", "--project", dest="restrict_to_projects", action="append",
help=("Restrict processing to these projects. "
"Use flag multiple times for multiple projects."))
parser.add_argument("-s", "--sample", dest= "restrict_to_samples", action="append",
help=("Restrict processing to these samples. "
"Use flag multiple times for multiple samples."))
parser.add_argument("-f", "--restart-failed", dest="restart_failed_jobs", action="store_true",
help=("Restart jobs marked as 'FAILED' in Charon"))
parser.add_argument("demux_fcid_dir", nargs="?", action="store",
help=("The path to the Illumina demultiplexed fc directories "
"to process."))
args_ns = parser.parse_args()
process_demultiplexed_flowcell(args_ns.demux_fcid_dir,
args_ns.restrict_to_projects,
args_ns.restrict_to_samples,
args_ns.restart_failed_jobs)
args = parser.parse_args()
# The following option will be available only if the script has been called with the 'analyze' option
if args.__dict__.get('restart_all_jobs'):
args.restart_failed_jobs = True
args.restart_finished_jobs = True
args.restart_running_jobs = True
# Finally execute corresponding functions
### TODO change to work with multiple flowcells
if 'analyze_fc_dir' in args:
LOG.info("Starting flowcell analysis in directory {}".format(args.analyze_fc_dir))
flowcell.process_demultiplexed_flowcell(args.analyze_fc_dir,
args.restrict_to_projects,
args.restrict_to_samples,
args.restart_failed_jobs,
args.restart_finished_jobs,
args.restart_running_jobs,
quiet=args.quiet,
manual=True)
### TODO change to work with multiple projects
elif 'analyze_project_dir' in args:
project = recreate_project_from_filesystem(project_dir=args.analyze_project_dir,
restrict_to_samples=args.restrict_to_samples)
if project and os.path.split(project.base_path)[1] == "DATA":
project.base_path = os.path.split(project.base_path)[0]
launchers.launch_analysis([project],
restart_failed_jobs=args.restart_failed_jobs,
restart_finished_jobs=args.restart_finished_jobs,
restart_running_jobs=args.restart_running_jobs,
quiet=args.quiet,