bioawk/flowr tutorial

bioawk.sh

# install this cool tools from Heng Li (https://github.com/lh3/bioawk)
brew install bioawk

# information regarding exit_code:
# - NA: not started yet

# show lines where job started and had errors
bioawk -tc hdr '{if($exit_code!=0 && $started=="TRUE") print $jobname, $cmd, $exit_code}' flow_details.txt

# show lines which did not start
bioawk -tc hdr '{if($started=="FALSE") print $jobname, $cmd, $exit_code}' flow_details.txt

# started, but have not finished yet (no exit status yet)
bioawk -tc hdr '{if($started=="TRUE" && $exit_code==-1) print $jobname, $cmd, $exit_code}' flow_details.txt

# get the 3rd column, cut -f3 and re-submit the jobs
jobs=$(bioawk -tc hdr '{if($exit_code!=0 && $started=="TRUE") print $jobname, $cmd, $exit_code}' flow_details.txt | cut -f2)
echo $jobs
# this will work, provided there were no pre requisite jobs
for j in $jobs; do bsub < $j; done











# END

# resubmission ex
 bsub -M 60384 -R rusage[mem=60384] < cnt_cmd_66.sh