run_hmmsort_pbs.sh

#!/bin/bash

## make sure you have swap to session direcotry already
## input none for removing error and output, input 1 for running hmmsort_pbs.py also

cwd=$PWD
	
for i in `find . -name "channel???"`
do echo $i

cd $i
rm -rf decode* learn* hmmsort; 

case $1 in
1)
~/hmmsort/hmmsort_pbs_orig.py ~/hmmsort # run with short queue
;;

2)
~/hmmsort/hmmsort_pbs.py ~/hmmsort # submit with matlab queue
;;

*)
echo jobs output and hmmsort folders are removed...
;;

esac

cd $cwd

done