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Full Discussion: How do I use grep output in an expect script?
Top Forums Shell Programming and Scripting How do I use grep output in an expect script? Post 302916058 by vagabond1964 on Saturday 6th of September 2014 12:16:00 PM
Old 09-06-2014
How do I use grep output in an expect script?
Hi,

I am using expect to ssh to a remote host and run a program on the remote machine which has a variable runtime. I need to wait until it finishes so I can grab the output file of this program. I am trying to use the output of grep to know when the process finishes. I am trying to capture the PID and use it in a loop to determine when it's finished, like this:

Code:
set program "nameOfProgram"
set psVar "ps -ef | grep $program | grep -v grep | {awk '{ print $2 }'}"

expect "$PROMPT" {   
    send "pidVar=`$psVar`\r"
}

while {1} {

    sleep $waitTime
    expect {
	"$pidVar*$PROMPT" {
	    send "$psVar\r"
	}
	"$PROMPT" {
	    sleep 1
	    break
	}
    }
}


The behavior of this code is that '$pidVar' is only visible in the remote shell, not in my expect script. If I replace the while loop with 'interact', I can echo $pidVar but I can't seem to use it in the while loop.

I seem to be missing something fundamental. Any suggestions??

vagabond1964
 

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LEARN ABOUT DEBIAN

cd-hit-para

CD-HIT-PARA.PL(1)						   User Commands						 CD-HIT-PARA.PL(1)

NAME

       cd-hit-para.pl - divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs

SYNOPSIS

       cd-hit-para.pl options

DESCRIPTION

	      This  script  divide a big clustering job into pieces and submit jobs to remote computers over a network to make it parallel.  After
	      all the jobs finished, the script merge the clustering results as if you just run a single cd-hit or cd-hit-est.

	      You can also use it to divide big jobs on a single computer if your computer does not have enough RAM (with -L option).

   Requirements:
	      1 When run this script over a network, the directory where you

	      run the scripts and the input files must be available on all the remote hosts with identical path.

	      2 If you choose "ssh" to submit jobs, you have to have

	      passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh.

	      3 I suggest to use queuing system instead of ssh,

	      I currently support PBS and SGE

	      4 cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d

	      cd-hit-div cd-hit-div.pl must be in same directory where this script is in.

       Options

       -i input filename in fasta format, required

       -o output filename, required

       --P program, "cd-hit" or "cd-hit-est", default "cd-hit"

       --B filename of list of hosts,

	      requred unless -Q or -L option is supplied

       --L number of cpus on local computer, default 0

	      when you are not running it over a cluster, you can use this option to divide a big clustering jobs into small pieces, I suggest you
	      just use "--L 1" unless you have enough RAM for each cpu

       --S Number of segments to split input DB into, default 64

       --Q number of jobs to submit to queue queuing system, default 0

	      by default, the program use ssh mode to submit remote jobs

       --T type of queuing system, "PBS", "SGE" are supported, default PBS

       --R restart file, used after a crash of run

       -h print this help

       More cd-hit/cd-hit-est options can be speicified in command line

	      Questions, bugs, contact Weizhong Li at liwz@sdsc.edu

cd-hit-para.pl 4.6-2012-04-25					    April 2012							 CD-HIT-PARA.PL(1)
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