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Top Forums Shell Programming and Scripting how to run non-standard commands in bash script? Post 302441867 by EinsteinMcfly on Monday 2nd of August 2010 07:16:29 PM
Old 08-02-2010
how to run non-standard commands in bash script?

Hello All. I suspect that this will be a clear noob question, but I haven't been able to figure it out using the usual methods, so I turn to you.

I've written a script to create input files for the quantum chemistry program NWCHEM. Generally you create an input file and then execute it by typing at the command line:
>> nwchem inputfile.nw
and hitting enter. I've written a script for a huge batch of jobs that will create the folders and sub-folders, write the correct input file to the sub-folders and then...

Well, then it has to execute the command "nwchem inputfile.nw", but "nwchem" isn't a standard command like "cd" or "mkdir" so it doesn't do anything. I've tried just echoing it to the line along with the inputfile.nw name, but then of course it doesn't actually RUN it. I'm guessing that this is a path issue, but I'm not sure who to a) find the folder that contains the nwchem command that I use when I just type it to the command line manually and b) how to specify that and run it from the .sh script.

Is there an easier way to do this? Something that just tells bash to treat a particular group of words as a command just like mkdir or cd?

Thanks for any help you can give me. The process of trying to get this done has almost taken longer than just doing it all by hand without a script.

cheers,
EMF
 

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SETUID(1)                                                     General Commands Manual                                                    SETUID(1)

NAME
setuid - run a command with a different uid. SYNOPSIS
setuid username|uid command [ args ] DESCRIPTION
Setuid changes user id, then executes the specified command. Unlike some versions of su(1), this program doesn't ever ask for a password when executed with effective uid=root. This program doesn't change the environment; it only changes the uid and then uses execvp() to find the command in the path, and execute it. (If the command is a script, execvp() passes the command name to /bin/sh for processing.) For example, setuid some_user $SHELL can be used to start a shell running as another user. Setuid is useful inside scripts that are being run by a setuid-root user -- such as a script invoked with super, so that the script can execute some commands using the uid of the original user, instead of root. This allows unsafe commands (such as editors and pagers) to be used in a non-root mode inside a super script. For example, an operator with permission to modify a certain protected_file could use a super command that simply does: cp protected_file temp_file setuid $ORIG_USER ${EDITOR:-/bin/vi} temp_file cp temp_file protected_file (Note: don't use this example directly. If the temp_file can somehow be replaced by another user, as might be the case if it's kept in a temporary directory, there will be a race condition in the time between editing the temporary file and copying it back to the protected file.) AUTHOR
Will Deich local SETUID(1)
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