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Full Discussion: how to run non-standard commands in bash script?
Top Forums Shell Programming and Scripting how to run non-standard commands in bash script? Post 302442491 by bluejayek on Wednesday 4th of August 2010 12:24:26 PM
Old 08-04-2010
Have you tried simply putting the full path in your bash script rather than changing the $PATH variable?
What I mean is, inside your script that creates the folders and such write

Code:
... make folders ...
/opt/local/share/nwchem/nwchem
... other stuff ...

This works fine for me. Below is a script named script that makes a directory and a file, and then runs nwchem. nwchem for me simply prints out "This is nwchem". Note that nwchem is called by its full path (~ is just a shortform for /Users/****/).

Code:
  1 #!/bin/bash
  2 mkdir newdir
  3 touch newdir/file1
  4 ~/Documents/nwchem/nwchem

output as follows

Code:
dhcp23:nwchem ******n$ ./script
This is nwchem
dhcp23:nwchem *****$ ls -l
total 40
drwxr-xr-x  3 ****  staff   102  4 Aug 12:20 newdir
-rwxr-xr-x  1 *****  staff  9560  4 Aug 12:17 nwchem
-rw-r--r--  1 ***** staff    81  4 Aug 12:17 nwchem.cxx
-rwxrwxrwx  1 *****  staff    71  4 Aug 12:18 script

nwchem is run and the directory and file inside it is created.
You may also want to check that you have execute permissions for nwchem.
If not, change it with chmod, chmod 744 nwchem will give you read write and execute permissions and others only read.
This User Gave Thanks to bluejayek For This Post:
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LEARN ABOUT DEBIAN

service

service(8)						      System Manager's Manual							service(8)

NAME

       service - run a System V init script

SYNOPSIS

       service SCRIPT COMMAND [OPTIONS]

       service --status-all

       service --help | -h | --version

DESCRIPTION

       service	runs a System V init script in as predictable an environment as possible, removing most environment variables and with the current
       working directory set to /.

       The SCRIPT parameter specifies a System V init script, located in /etc/init.d/SCRIPT.  The  supported  values  of  COMMAND  depend  on  the
       invoked	script.  service passes COMMAND and OPTIONS to the init script unmodified.  All scripts should support at least the start and stop
       commands.  As a special case, if COMMAND is --full-restart, the script is run twice, first with the stop command, then with the start  com-
       mand.

       service --status-all runs all init scripts, in alphabetical order, with the status command.

EXIT CODES

       service calls the init script and returns the status returned by it.

FILES

       /etc/init.d
	      The directory containing System V init scripts.

ENVIRONMENT

       LANG, TERM
	      The only environment variables passed to the init scripts.

SEE ALSO

       /etc/init.d/skeleton,
       update-rc.d(8),
       init(8),
       invoke-rc.d(8).

								     Jan 2006								service(8)
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