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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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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 file name 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)
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