qsub in a bash script?


 
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Old 07-12-2010
qsub in a bash script?

I was just wondering if it is permissible to qsub from a bash script as follows:

Code:
#! /bin/sh

echo "altering .txt in dir $DIR with retokenize.py"
for f in $DIR/txt/*.txt; do
  echo $f;
  /l2/nlp/i2b2/retokenize.py < $f > ${f//.txt/.tok};
done


echo "altering .tok in dir $DIR with awk <s> </s>"
for f in $DIR/txt/*.tok; do
  echo $f;
  cat $f | awk '{printf("<s> %s </s>\n",$0)}' > ${f//.tok/.ecIN};
done


echo "altering .tok in dir $DIR with tagger.stayTOK.py "
for f in $DIR/txt/*.tok; do
  echo $f;
  cat $f | /l2/nlp/i2b2/tagger.stayTOK.py < $f > ${f//.tok/.ecIN-POS};
done


export MODEL=/data/nlp/src/charniak/DATA/DATA_DEV24/;
echo "qsubbing for $DIR";
qsub -o $DIR/ecOUT.log -q kiwi.q /l2/nlp/i2b2/runEC.unconstrained.sh;
qsub -o $DIR/ecOUT-POS.log -q kiwi.q l2/nlp/i2b2/runEC.POS.sh;

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RBASH(1)						      General Commands Manual							  RBASH(1)

NAME
rbash - restricted bash, see bash(1) RESTRICTED SHELL
If bash is started with the name rbash, or the -r option is supplied at invocation, the shell becomes restricted. A restricted shell is used to set up an environment more controlled than the standard shell. It behaves identically to bash with the exception that the follow- ing are disallowed or not performed: o changing directories with cd o setting or unsetting the values of SHELL, PATH, ENV, or BASH_ENV o specifying command names containing / o specifying a filename containing a / as an argument to the . builtin command o specifying a filename containing a slash as an argument to the -p option to the hash builtin command o importing function definitions from the shell environment at startup o parsing the value of SHELLOPTS from the shell environment at startup o redirecting output using the >, >|, <>, >&, &>, and >> redirection operators o using the exec builtin command to replace the shell with another command o adding or deleting builtin commands with the -f and -d options to the enable builtin command o using the enable builtin command to enable disabled shell builtins o specifying the -p option to the command builtin command o turning off restricted mode with set +r or set +o restricted. These restrictions are enforced after any startup files are read. When a command that is found to be a shell script is executed, rbash turns off any restrictions in the shell spawned to execute the script. SEE ALSO
bash(1) GNU Bash-4.0 2004 Apr 20 RBASH(1)