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Top Forums Shell Programming and Scripting how to run non-standard commands in bash script? Post 302441898 by EinsteinMcfly on Monday 2nd of August 2010 11:55:44 PM
Old 08-03-2010
Quote:
Originally Posted by agama
When you say "it doesn't do anything" do you mean that you are getting an error message like "not found or no such file/directory," or literally nothing is happening?

There is a possibility that the command is being executed, but it is quietly aborting. Assuming that nwchem is either a bash or Kshell script, consider adding the command
Code:
set -x

at the start of nwchem -- if nwchem is being invoked, this might give you a clue as to why it is not executing as you intended.
I create all of the directories and then write the input file in that directory under the name $basis_name$func_name$spin_name".nw", then try to run the program by outputting
>> nwchem $basis_name$func_name$spin_name.nw
in the same manner that I would in the shell by hand but it tells me that this is not a command.

I included the set -x as you said in the following way:
path=$PATH:/opt/local/share/nwchem/nwchem
set -x nwchem $basis_name$func_name$spin_name".nw"
and it output a list of the failed if/then statements (but not the ones that passed), one (but not all) of the directory changes, the exit command etc. It didn't tell me "command not found" as before.
 

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WHICH(1)						      General Commands Manual							  WHICH(1)

NAME
which - shows the full path of (shell) commands. SYNOPSIS
which [options] [--] programname [...] DESCRIPTION
Which takes one or more arguments. For each of its arguments it prints to stdout the full path of the executables that would have been exe- cuted when this argument had been entered at the shell prompt. It does this by searching for an executable or script in the directories listed in the environment variable PATH using the same algorithm as bash(1). This man page is generated from the file which.texinfo. OPTIONS
--all, -a Print all matching executables in PATH, not just the first. --read-alias, -i Read aliases from stdin, reporting matching ones on stdout. This is useful in combination with using an alias for which itself. For example alias which='alias | which -i'. --skip-alias Ignore option `--read-alias', if any. This is useful to explicity search for normal binaries, while using the `--read-alias' option in an alias or function for which. --read-functions Read shell function definitions from stdin, reporting matching ones on stdout. This is useful in combination with using a shell func- tion for which itself. For example: which() { declare -f | which --read-functions $@ } export -f which --skip-functions Ignore option `--read-functions', if any. This is useful to explicity search for normal binaries, while using the `--read-functions' option in an alias or function for which. --skip-dot Skip directories in PATH that start with a dot. --skip-tilde Skip directories in PATH that start with a tilde and executables which reside in the HOME directory. --show-dot If a directory in PATH starts with a dot and a matching executable was found for that path, then print "./programname" rather than the full path. --show-tilde Output a tilde when a directory matches the HOME directory. This option is ignored when which is invoked as root. --tty-only Stop processing options on the right if not on tty. --version,-v,-V Print version information on standard output then exit successfully. --help Print usage information on standard output then exit successfully. RETURN VALUE
Which returns the number of failed arguments, or -1 when no `programname' was given. EXAMPLE
The recommended way to use this utility is by adding an alias (C shell) or shell function (Bourne shell) for which like the following: [ba]sh: which () { (alias; declare -f) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@ } export -f which [t]csh: alias which 'alias | /usr/bin/which --tty-only --read-alias --show-dot --show-tilde' This will print the readable ~/ and ./ when starting which from your prompt, while still printing the full path when used from a script: > which q2 ~/bin/q2 > echo `which q2` /home/carlo/bin/q2 BUGS
The HOME directory is determined by looking for the HOME environment variable, which aborts when this variable doesn't exist. Which will consider two equivalent directories to be different when one of them contains a path with a symbolic link. AUTHOR
Carlo Wood <carlo@gnu.org> SEE ALSO
bash(1) WHICH(1)
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